Daily Papers

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

Molecule generation with desired properties has grown immensely in popularity by disruptively changing the way scientists design molecular structures and providing support for chemical and materials design. However, despite the promising outcome, previous machine learning-based deep generative models suffer from a reliance on complex, task-specific fine-tuning, limited dimensional latent spaces, or the quality of expert rules. In this work, we propose MolGen, a pre-trained molecular language model that effectively learns and shares knowledge across multiple generation tasks and domains. Specifically, we pre-train MolGen with the chemical language SELFIES on more than 100 million unlabelled molecules. We further propose multi-task molecular prefix tuning across several molecular generation tasks and different molecular domains (synthetic & natural products) with a self-feedback mechanism. Extensive experiments show that MolGen can obtain superior performances on well-known molecular generation benchmark datasets. The further analysis illustrates that MolGen can accurately capture the distribution of molecules, implicitly learn their structural characteristics, and efficiently explore the chemical space with the guidance of multi-task molecular prefix tuning. Codes, datasets, and the pre-trained model will be available in https://github.com/zjunlp/MolGen.

Advancements in DNA sequencing technologies have significantly improved our ability to decode genomic sequences. However, the prediction and interpretation of these sequences remain challenging due to the intricate nature of genetic material. Large language models (LLMs) have introduced new opportunities for biological sequence analysis. Recent developments in genomic language models have underscored the potential of LLMs in deciphering DNA sequences. Nonetheless, existing models often face limitations in robustness and application scope, primarily due to constraints in model structure and training data scale. To address these limitations, we present GENERator, a generative genomic foundation model featuring a context length of 98k base pairs (bp) and 1.2B parameters. Trained on an expansive dataset comprising 386B bp of eukaryotic DNA, the GENERator demonstrates state-of-the-art performance across both established and newly proposed benchmarks. The model adheres to the central dogma of molecular biology, accurately generating protein-coding sequences that translate into proteins structurally analogous to known families. It also shows significant promise in sequence optimization, particularly through the prompt-responsive generation of promoter sequences with specific activity profiles. These capabilities position the GENERator as a pivotal tool for genomic research and biotechnological advancement, enhancing our ability to interpret and predict complex biological systems and enabling precise genomic interventions.

We consider the task of text generation in language models with constraints specified in natural language. To this end, we first create a challenging benchmark Cognac that provides as input to the model a topic with example text, along with a constraint on text to be avoided. Unlike prior work, our benchmark contains knowledge-intensive constraints sourced from databases like Wordnet and Wikidata, which allows for straightforward evaluation while striking a balance between broad attribute-level and narrow lexical-level controls. We find that even state-of-the-art language models like GPT-3 fail often on this task, and propose a solution to leverage a language model's own internal knowledge to guide generation. Our method, called CognacGen, first queries the language model to generate guidance terms for a specified topic or constraint, and uses the guidance to modify the model's token generation probabilities. We propose three forms of guidance (binary verifier, top-k tokens, textual example), and employ prefix-tuning approaches to distill the guidance to tackle diverse natural language constraints. Through extensive empirical evaluations, we demonstrate that CognacGen can successfully generalize to unseen instructions and outperform competitive baselines in generating constraint conforming text.

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model, nach0, capable of solving various chemical and biological tasks: biomedical question answering, named entity recognition, molecular generation, molecular synthesis, attributes prediction, and others. nach0 is a multi-domain and multi-task encoder-decoder LLM pre-trained on unlabeled text from scientific literature, patents, and molecule strings to incorporate a range of chemical and linguistic knowledge. We employed instruction tuning, where specific task-related instructions are utilized to fine-tune nach0 for the final set of tasks. To train nach0 effectively, we leverage the NeMo framework, enabling efficient parallel optimization of both base and large model versions. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on single-domain and cross-domain tasks. Furthermore, it can generate high-quality outputs in molecular and textual formats, showcasing its effectiveness in multi-domain setups.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

We propose a constraint learning schema for fine-tuning Large Language Models (LLMs) with attribute control. Given a training corpus and control criteria formulated as a sequence-level constraint on model outputs, our method fine-tunes the LLM on the training corpus while enhancing constraint satisfaction with minimal impact on its utility and generation quality. Specifically, our approach regularizes the LLM training by penalizing the KL divergence between the desired output distribution, which satisfies the constraints, and the LLM's posterior. This regularization term can be approximated by an auxiliary model trained to decompose the sequence-level constraints into token-level guidance, allowing the term to be measured by a closed-form formulation. To further improve efficiency, we design a parallel scheme for concurrently updating both the LLM and the auxiliary model. We evaluate the empirical performance of our approach by controlling the toxicity when training an LLM. We show that our approach leads to an LLM that produces fewer inappropriate responses while achieving competitive performance on benchmarks and a toxicity detection task.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

Text generation under constraints have seen increasing interests in natural language processing, especially with the rapidly improving capabilities of large language models. However, existing benchmarks for constrained generation usually focus on fixed constraint types (e.g.,generate a sentence containing certain words) that have proved to be easy for state-of-the-art models like GPT-4. We present COLLIE, a grammar-based framework that allows the specification of rich, compositional constraints with diverse generation levels (word, sentence, paragraph, passage) and modeling challenges (e.g.,language understanding, logical reasoning, counting, semantic planning). We also develop tools for automatic extraction of task instances given a constraint structure and a raw text corpus. Using COLLIE, we compile the COLLIE-v1 dataset with 2080 instances comprising 13 constraint structures. We perform systematic experiments across five state-of-the-art instruction-tuned language models and analyze their performances to reveal shortcomings. COLLIE is designed to be extensible and lightweight, and we hope the community finds it useful to develop more complex constraints and evaluations in the future.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as chemical molecules and amino acid sequences. To bridge these gaps, we introduce SciDFM, a mixture-of-experts LLM, which is trained from scratch and is able to conduct college-level scientific reasoning and understand molecules and amino acid sequences. We collect a large-scale training corpus containing numerous scientific papers and books from different disciplines as well as data from domain-specific databases. We further fine-tune the pre-trained model on lots of instruction data to improve performances on downstream benchmarks. From experiment results, we show that SciDFM achieves strong performance on general scientific benchmarks such as SciEval and SciQ, and it reaches a SOTA performance on domain-specific benchmarks among models of similar size. We further analyze the expert layers and show that the results of expert selection vary with data from different disciplines. To benefit the broader research community, we open-source SciDFM at https://huggingface.co/OpenDFM/SciDFM-MoE-A5.6B-v1.0.

Large Language Models (LLMs) have demonstrated a powerful ability for text generation. However, achieving optimal results with a given prompt or instruction can be challenging, especially for billion-sized models. Additionally, undesired behaviors such as toxicity or hallucinations can manifest. While much larger models (e.g., ChatGPT) may demonstrate strength in mitigating these issues, there is still no guarantee of complete prevention. In this work, we propose formalizing text generation as a future-constrained generation problem to minimize undesirable behaviors and enforce faithfulness to instructions. The estimation of future constraint satisfaction, accomplished using LLMs, guides the text generation process. Our extensive experiments demonstrate the effectiveness of the proposed approach across three distinct text generation tasks: keyword-constrained generation (Lin et al., 2020), toxicity reduction (Gehman et al., 2020), and factual correctness in question-answering (Gao et al., 2023).

Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery.

Despite the success of autoregressive large language models in text generation, it remains a major challenge to generate text that satisfies complex constraints: sampling from the conditional distribution {Pr}(text | alpha) is intractable for even the simplest lexical constraints alpha. To overcome this challenge, we propose to use tractable probabilistic models (TPMs) to impose lexical constraints in autoregressive text generation models, which we refer to as GeLaTo (Generating Language with Tractable Constraints). To demonstrate the effectiveness of this framework, we use distilled hidden Markov models, where we can efficiently compute {Pr}(text | alpha), to guide autoregressive generation from GPT2. GeLaTo achieves state-of-the-art performance on challenging benchmarks for constrained text generation (e.g., CommonGen), beating various strong baselines by a large margin. Our work not only opens up new avenues for controlling large language models but also motivates the development of more expressive TPMs.

Large Language Models (LLMs) struggle with reliably generating highly structured outputs, such as program code, mathematical formulas, or well-formed markup. Constrained decoding approaches mitigate this problem by greedily restricting what tokens an LLM can output at each step to guarantee that the output matches a given constraint. Specifically, in grammar-constrained decoding (GCD), the LLM's output must follow a given grammar. In this paper, we demonstrate that GCD techniques (and in general constrained decoding techniques) can distort the LLM's distribution, leading to outputs that are grammatical but appear with likelihoods that are not proportional to the ones given by the LLM, and so ultimately are low-quality. We call the problem of aligning sampling with a grammar constraint, grammar-aligned decoding (GAD), and propose adaptive sampling with approximate expected futures (ASAp), a decoding algorithm that guarantees the output to be grammatical while provably producing outputs that match the conditional probability of the LLM's distribution conditioned on the given grammar constraint. Our algorithm uses prior sample outputs to soundly overapproximate the future grammaticality of different output prefixes. Our evaluation on code generation and structured NLP tasks shows how ASAp often produces outputs with higher likelihood (according to the LLM's distribution) than existing GCD techniques, while still enforcing the desired grammatical constraints.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

This paper investigates controllable generation for large language models (LLMs) with prompt-based control, focusing on Lexically Constrained Generation (LCG). We systematically evaluate the performance of LLMs on satisfying lexical constraints with prompt-based control, as well as their efficacy in downstream applications. We conclude that LLMs face significant challenges in consistently satisfying lexical constraints with prompt-based control. We identified three key limitations of LLMs for LCG, including (1) position bias, where LLMs tend to satisfy constraints that appear in specific positions within the input; (2) low responsiveness to decoding parameters, which render minimal impact on control of LLMs; and (3) struggle with handling the inherent complexity of certain constraints (e.g., compound words). To address these issues, we introduce a Divide and Conquer Generation strategy, effective for both white-box and black-box LLMs, to enhance LLMs performance in LCG tasks, which demonstrates over 90% improvement on success rate in the most challenging LCG task. Our analysis provides valuable insights into the performance of LLMs in LCG with prompt-based control, and our proposed strategy offers a pathway to more sophisticated and customized text generation applications.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

Despite recent advancements, most computational methods for molecule optimization are constrained to single- or double-property optimization tasks and suffer from poor scalability and generalizability to novel optimization tasks. Meanwhile, Large Language Models (LLMs) demonstrate remarkable out-of-domain generalizability to novel tasks. To demonstrate LLMs' potential for molecule optimization, we introduce MoMUInstruct, the first high-quality instruction-tuning dataset specifically focused on complex multi-property molecule optimization tasks. Leveraging MoMUInstruct, we develop GeLLM^3Os, a series of instruction-tuned LLMs for molecule optimization. Extensive evaluations across 5 in-domain and 5 out-of-domain tasks demonstrate that GeLLM^3Os consistently outperform state-of-the-art baselines. GeLLM^3Os also exhibit outstanding zero-shot generalization to unseen tasks, significantly outperforming powerful closed-source LLMs. Such strong generalizability demonstrates the tremendous potential of GeLLM^3Os as foundational models for molecule optimization, thereby tackling novel optimization tasks without resource-intensive retraining. MoMUInstruct, models, and code are accessible through https://github.com/ninglab/GeLLMO.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

The success of Large Language Models (LLMs) is inherently linked to the availability of vast, diverse, and high-quality data for training and evaluation. However, the growth rate of high-quality data is significantly outpaced by the expansion of training datasets, leading to a looming data exhaustion crisis. This underscores the urgent need to enhance data efficiency and explore new data sources. In this context, synthetic data has emerged as a promising solution. Currently, data generation primarily consists of two major approaches: data augmentation and synthesis. This paper comprehensively reviews and summarizes data generation techniques throughout the lifecycle of LLMs, including data preparation, pre-training, fine-tuning, instruction-tuning, preference alignment, and applications. Furthermore, We discuss the current constraints faced by these methods and investigate potential pathways for future development and research. Our aspiration is to equip researchers with a clear understanding of these methodologies, enabling them to swiftly identify appropriate data generation strategies in the construction of LLMs, while providing valuable insights for future exploration.

Here we show that a Large Language Model (LLM) can serve as a foundation model for a Chemical Language Model (CLM) which performs at or above the level of CLMs trained solely on chemical SMILES string data. Using supervised fine-tuning (SFT) and direct preference optimization (DPO) on the open-source Llama LLM, we demonstrate that we can train an LLM to respond to prompts such as generating molecules with properties of interest to drug development. This overall framework allows an LLM to not just be a chatbot client for chemistry and materials tasks, but can be adapted to speak more directly as a CLM which can generate molecules with user-specified properties.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

In real-world applications of natural language generation, there are often constraints on the target sentences in addition to fluency and naturalness requirements. Existing language generation techniques are usually based on recurrent neural networks (RNNs). However, it is non-trivial to impose constraints on RNNs while maintaining generation quality, since RNNs generate sentences sequentially (or with beam search) from the first word to the last. In this paper, we propose CGMH, a novel approach using Metropolis-Hastings sampling for constrained sentence generation. CGMH allows complicated constraints such as the occurrence of multiple keywords in the target sentences, which cannot be handled in traditional RNN-based approaches. Moreover, CGMH works in the inference stage, and does not require parallel corpora for training. We evaluate our method on a variety of tasks, including keywords-to-sentence generation, unsupervised sentence paraphrasing, and unsupervised sentence error correction. CGMH achieves high performance compared with previous supervised methods for sentence generation. Our code is released at https://github.com/NingMiao/CGMH

The dominant paradigm for neural text generation is left-to-right decoding from autoregressive language models. Constrained or controllable generation under complex lexical constraints, however, requires foresight to plan ahead feasible future paths. Drawing inspiration from the A* search algorithm, we propose NeuroLogic A*esque, a decoding algorithm that incorporates heuristic estimates of future cost. We develop efficient lookahead heuristics that are efficient for large-scale language models, making our method a drop-in replacement for common techniques such as beam search and top-k sampling. To enable constrained generation, we build on NeuroLogic decoding (Lu et al., 2021), combining its flexibility in incorporating logical constraints with A*esque estimates of future constraint satisfaction. Our approach outperforms competitive baselines on five generation tasks, and achieves new state-of-the-art performance on table-to-text generation, constrained machine translation, and keyword-constrained generation. The improvements are particularly notable on tasks that require complex constraint satisfaction or in few-shot or zero-shot settings. NeuroLogic A*esque illustrates the power of decoding for improving and enabling new capabilities of large-scale language models.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

Despite rapid advancement in the field of Constrained Natural Language Generation, little time has been spent on exploring the potential of language models which have had their vocabularies lexically, semantically, and/or phonetically constrained. We find that most language models generate compelling text even under significant constraints. We present a simple and universally applicable technique for modifying the output of a language model by compositionally applying filter functions to the language models vocabulary before a unit of text is generated. This approach is plug-and-play and requires no modification to the model. To showcase the value of this technique, we present an easy to use AI writing assistant called Constrained Text Generation Studio (CTGS). CTGS allows users to generate or choose from text with any combination of a wide variety of constraints, such as banning a particular letter, forcing the generated words to have a certain number of syllables, and/or forcing the words to be partial anagrams of another word. We introduce a novel dataset of prose that omits the letter e. We show that our method results in strictly superior performance compared to fine-tuning alone on this dataset. We also present a Huggingface space web-app presenting this technique called Gadsby. The code is available to the public here: https://github.com/Hellisotherpeople/Constrained-Text-Generation-Studio

Existing large language models have to run K times to generate a sequence of K tokens. In this paper, we present RecycleGPT, a generative language model with fast decoding speed by recycling pre-generated model states without running the whole model in multiple steps. Our approach relies on the observation that adjacent tokens in a sequence usually have strong correlations and the next token in a sequence can be reasonably guessed or inferred based on the preceding ones. Through theoretical evaluations and practical tests on downstream text generation tasks, we demonstrate the effectiveness of our approach in lowering inference latency, achieving up to 1.4x speedup while preserving high performance.

Pretrained language models (PLMs) have shown remarkable generalization toward multiple tasks and languages. Nonetheless, the generalization of PLMs towards unseen languages is poor, resulting in significantly worse language performance, or even generating nonsensical responses that are comparable to a random baseline. This limitation has been a longstanding problem of PLMs raising the problem of diversity and equal access to language modeling technology. In this work, we solve this limitation by introducing LinguAlchemy, a regularization technique that incorporates various aspects of languages covering typological, geographical, and phylogenetic constraining the resulting representation of PLMs to better characterize the corresponding linguistics constraints. LinguAlchemy significantly improves the accuracy performance of mBERT and XLM-R on unseen languages by ~18% and ~2%, respectively compared to fully finetuned models and displaying a high degree of unseen language generalization. We further introduce AlchemyScale and AlchemyTune, extension of LinguAlchemy which adjusts the linguistic regularization weights automatically, alleviating the need for hyperparameter search. LinguAlchemy enables better cross-lingual generalization to unseen languages which is vital for better inclusivity and accessibility of PLMs.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

In recent years, groundbreaking advancements in natural language processing have culminated in the emergence of powerful large language models (LLMs), which have showcased remarkable capabilities across a vast array of domains, including the understanding, generation, and translation of natural language, and even tasks that extend beyond language processing. In this report, we delve into the performance of LLMs within the context of scientific discovery, focusing on GPT-4, the state-of-the-art language model. Our investigation spans a diverse range of scientific areas encompassing drug discovery, biology, computational chemistry (density functional theory (DFT) and molecular dynamics (MD)), materials design, and partial differential equations (PDE). Evaluating GPT-4 on scientific tasks is crucial for uncovering its potential across various research domains, validating its domain-specific expertise, accelerating scientific progress, optimizing resource allocation, guiding future model development, and fostering interdisciplinary research. Our exploration methodology primarily consists of expert-driven case assessments, which offer qualitative insights into the model's comprehension of intricate scientific concepts and relationships, and occasionally benchmark testing, which quantitatively evaluates the model's capacity to solve well-defined domain-specific problems. Our preliminary exploration indicates that GPT-4 exhibits promising potential for a variety of scientific applications, demonstrating its aptitude for handling complex problem-solving and knowledge integration tasks. Broadly speaking, we evaluate GPT-4's knowledge base, scientific understanding, scientific numerical calculation abilities, and various scientific prediction capabilities.

We present MolT5 - a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. MolT5 allows for new, useful, and challenging analogs of traditional vision-language tasks, such as molecule captioning and text-based de novo molecule generation (altogether: translation between molecules and language), which we explore for the first time. Since MolT5 pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Furthermore, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. Our results show that MolT5-based models are able to generate outputs, both molecules and captions, which in many cases are high quality.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

Large Language Models (LLMs) exhibit remarkably powerful capabilities. One of the crucial factors to achieve success is aligning the LLM's output with human preferences. This alignment process often requires only a small amount of data to efficiently enhance the LLM's performance. While effective, research in this area spans multiple domains, and the methods involved are relatively complex to understand. The relationships between different methods have been under-explored, limiting the development of the preference alignment. In light of this, we break down the existing popular alignment strategies into different components and provide a unified framework to study the current alignment strategies, thereby establishing connections among them. In this survey, we decompose all the strategies in preference learning into four components: model, data, feedback, and algorithm. This unified view offers an in-depth understanding of existing alignment algorithms and also opens up possibilities to synergize the strengths of different strategies. Furthermore, we present detailed working examples of prevalent existing algorithms to facilitate a comprehensive understanding for the readers. Finally, based on our unified perspective, we explore the challenges and future research directions for aligning large language models with human preferences.

This paper introduces a neural model for concept-to-text generation that scales to large, rich domains. We experiment with a new dataset of biographies from Wikipedia that is an order of magnitude larger than existing resources with over 700k samples. The dataset is also vastly more diverse with a 400k vocabulary, compared to a few hundred words for Weathergov or Robocup. Our model builds upon recent work on conditional neural language model for text generation. To deal with the large vocabulary, we extend these models to mix a fixed vocabulary with copy actions that transfer sample-specific words from the input database to the generated output sentence. Our neural model significantly out-performs a classical Kneser-Ney language model adapted to this task by nearly 15 BLEU.

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Sequence generation applications require satisfying semantic constraints, such as ensuring that programs are correct, using certain keywords, or avoiding undesirable content. Language models, whether fine-tuned or prompted with few-shot demonstrations, frequently violate these constraints, and lack a mechanism to iteratively revise their outputs. Moreover, some powerful language models are of extreme scale or inaccessible, making it inefficient, if not infeasible, to update their parameters for task-specific adaptation. We present Self-Correction, an approach that decouples an imperfect base generator (an off-the-shelf language model or supervised sequence-to-sequence model) from a separate corrector that learns to iteratively correct imperfect generations. To train the corrector, we propose an online training procedure that can use either scalar or natural language feedback on intermediate imperfect generations. We show that Self-Correction improves upon the base generator in three diverse generation tasks - mathematical program synthesis, lexically-constrained generation, and toxicity control - even when the corrector is much smaller than the base generator.

High-throughput reaction condition (RC) screening is fundamental to chemical synthesis. However, current RC screening suffers from laborious and costly trial-and-error workflows. Traditional computer-aided synthesis planning (CASP) tools fail to find suitable RCs due to data sparsity and inadequate reaction representations. Nowadays, large language models (LLMs) are capable of tackling chemistry-related problems, such as molecule design, and chemical logic Q\&A tasks. However, LLMs have not yet achieved accurate predictions of chemical reaction conditions. Here, we present MM-RCR, a text-augmented multimodal LLM that learns a unified reaction representation from SMILES, reaction graphs, and textual corpus for chemical reaction recommendation (RCR). To train MM-RCR, we construct 1.2 million pair-wised Q\&A instruction datasets. Our experimental results demonstrate that MM-RCR achieves state-of-the-art performance on two open benchmark datasets and exhibits strong generalization capabilities on out-of-domain (OOD) and High-Throughput Experimentation (HTE) datasets. MM-RCR has the potential to accelerate high-throughput condition screening in chemical synthesis.

Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations. Our code is available at http://github.com/zoom-wang112358/MOLLEO

Despite their impressive performance, large language models (LMs) still struggle with reliably generating complex output structures when not finetuned to follow the required output format exactly. To address this issue, grammar-constrained decoding (GCD) can be used to control the generation of LMs, guaranteeing that the output follows a given structure. Most existing GCD methods are, however, limited to specific tasks, such as parsing or code generation. In this work, we demonstrate that formal grammars can describe the output space for a much wider range of tasks and argue that GCD can serve as a unified framework for structured NLP tasks in general. For increased flexibility, we introduce input-dependent grammars, which allow the grammar to depend on the input and thus enable the generation of different output structures for different inputs. We then empirically demonstrate the power and flexibility of GCD-enhanced LMs on (1) information extraction, (2) entity disambiguation, and (3) constituency parsing. Our results indicate that grammar-constrained LMs substantially outperform unconstrained LMs or even beat task-specific finetuned models. Grammar constraints thus hold great promise for harnessing off-the-shelf LMs for a wide range of structured NLP tasks, especially where training data is scarce or finetuning is expensive. Code and data: https://github.com/epfl-dlab/GCD.

Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences between LLMs used for NLP, which effectively handle multiple tasks and are available in small sizes, and protein language models that are often specialized for specific tasks and only exist in larger sizes. In this work, we introduce two small protein language models, based on Llama-3-8B and Phi-3-mini, that are capable of both uncontrollable and controllable protein generation. For the uncontrollable generation task, our best model achieves an average pLDDT score of 69.75, demonstrating robust performance in generating viable protein structures. For the controllable generation task, in which the model generates proteins according to properties specified in the prompt, we achieve a remarkable average TM-Score of 0.84, indicating high structural similarity to target proteins. We chose 10 properties, including six classes of enzymes, to extend the capabilities of prior protein language models. Our approach utilizes the Low-Rank Adaptor (LoRA) technique, reducing trainable parameters to just 4% of the original model size, lowering computational requirements. By using a subset of the UniRef50 dataset and small models, we reduced the overall training time by 70% without compromising performance. Notably, Phi-3-mini reduced trainable parameters by 60%, decreasing training cost by 30% compared to Llama 3. Consequently, Phi-3 achieved a comparable TM-Score of 0.81, demonstrating that smaller models can match the performance of larger ones, like Llama 3. We also demonstrate the deployment of our models on the energy efficient ET-SoC-1 chip, significantly improving the TPS/W by a factor of 3.

Recent advances in large language models (LLMs) have stepped forward the development of multilingual speech and machine translation by its reduced representation errors and incorporated external knowledge. However, both translation tasks typically utilize beam search decoding and top-1 hypothesis selection for inference. These techniques struggle to fully exploit the rich information in the diverse N-best hypotheses, making them less optimal for translation tasks that require a single, high-quality output sequence. In this paper, we propose a new generative paradigm for translation tasks, namely "GenTranslate", which builds upon LLMs to generate better results from the diverse translation versions in N-best list. Leveraging the rich linguistic knowledge and strong reasoning abilities of LLMs, our new paradigm can integrate the rich information in N-best candidates to generate a higher-quality translation result. Furthermore, to support LLM finetuning, we build and release a HypoTranslate dataset that contains over 592K hypotheses-translation pairs in 11 languages. Experiments on various speech and machine translation benchmarks (e.g., FLEURS, CoVoST-2, WMT) demonstrate that our GenTranslate significantly outperforms the state-of-the-art model.

Generative AI models have impressive performance on many Natural Language Processing tasks such as language understanding, reasoning and language generation. One of the most important questions that is being asked by the AI community today is about the capabilities and limits of these models, and it is clear that evaluating generative AI is very challenging. Most studies on generative Large Language Models (LLMs) are restricted to English and it is unclear how capable these models are at understanding and generating other languages. We present the first comprehensive benchmarking of generative LLMs - MEGA, which evaluates models on standard NLP benchmarks, covering 8 diverse tasks and 33 typologically diverse languages. We also compare the performance of generative LLMs to State of the Art (SOTA) non-autoregressive models on these tasks to determine how well generative models perform compared to the previous generation of LLMs. We present a thorough analysis of the performance of models across languages and discuss some of the reasons why generative LLMs are currently not optimal for all languages. We create a framework for evaluating generative LLMs in the multilingual setting and provide directions for future progress in the field.

In an era of model and data proliferation in machine learning/AI especially marked by the rapid advancement of open-sourced technologies, there arises a critical need for standardized consistent documentation. Our work addresses the information incompleteness in current human-generated model and data cards. We propose an automated generation approach using Large Language Models (LLMs). Our key contributions include the establishment of CardBench, a comprehensive dataset aggregated from over 4.8k model cards and 1.4k data cards, coupled with the development of the CardGen pipeline comprising a two-step retrieval process. Our approach exhibits enhanced completeness, objectivity, and faithfulness in generated model and data cards, a significant step in responsible AI documentation practices ensuring better accountability and traceability.

Large Language Models (LLMs) are frequently used for multi-faceted language generation and evaluation tasks that involve satisfying intricate user constraints or taking into account multiple aspects and criteria. However, their performance can fall short, due to the model's lack of coherence and inability to plan and decompose the problem. We propose Branch-Solve-Merge (BSM), a Large Language Model program (Schlag et al., 2023) for tackling such challenging natural language tasks. It consists of branch, solve, and merge modules that are parameterized with specific prompts to the base LLM. These three modules plan a decomposition of the task into multiple parallel sub-tasks, independently solve them, and fuse the solutions to the sub-tasks. We apply our method to the tasks of LLM response evaluation and constrained text generation and evaluate its effectiveness with multiple LLMs, including Vicuna, LLaMA-2-chat, and GPT-4. BSM improves the evaluation correctness and consistency for each LLM by enhancing human-LLM agreement by up to 26%, reducing length and pairwise position biases by up to 50%, and allowing LLaMA-2-chat to match or outperform GPT-4 on most domains. On the constraint story generation task, BSM improves the coherence of the stories while also improving constraint satisfaction by 12%.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Within the evolving landscape of deep learning, the dilemma of data quantity and quality has been a long-standing problem. The recent advent of Large Language Models (LLMs) offers a data-centric solution to alleviate the limitations of real-world data with synthetic data generation. However, current investigations into this field lack a unified framework and mostly stay on the surface. Therefore, this paper provides an organization of relevant studies based on a generic workflow of synthetic data generation. By doing so, we highlight the gaps within existing research and outline prospective avenues for future study. This work aims to shepherd the academic and industrial communities towards deeper, more methodical inquiries into the capabilities and applications of LLMs-driven synthetic data generation.

We study the ability of state-of-the art models to answer constraint satisfaction queries for information retrieval (e.g., 'a list of ice cream shops in San Diego'). In the past, such queries were considered to be tasks that could only be solved via web-search or knowledge bases. More recently, large language models (LLMs) have demonstrated initial emergent abilities in this task. However, many current retrieval benchmarks are either saturated or do not measure constraint satisfaction. Motivated by rising concerns around factual incorrectness and hallucinations of LLMs, we present KITAB, a new dataset for measuring constraint satisfaction abilities of language models. KITAB consists of book-related data across more than 600 authors and 13,000 queries, and also offers an associated dynamic data collection and constraint verification approach for acquiring similar test data for other authors. Our extended experiments on GPT4 and GPT3.5 characterize and decouple common failure modes across dimensions such as information popularity, constraint types, and context availability. Results show that in the absence of context, models exhibit severe limitations as measured by irrelevant information, factual errors, and incompleteness, many of which exacerbate as information popularity decreases. While context availability mitigates irrelevant information, it is not helpful for satisfying constraints, identifying fundamental barriers to constraint satisfaction. We open source our contributions to foster further research on improving constraint satisfaction abilities of future models.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Large language models (LLMs) show great potential for synthetic data generation. This work shows that useful data can be synthetically generated even for tasks that cannot be solved directly by the LLM: we show that, for problems with structured outputs, it is possible to prompt an LLM to perform the task in the opposite direction, to generate plausible text for the target structure. Leveraging the asymmetry in task difficulty makes it possible to produce large-scale, high-quality data for complex tasks. We demonstrate the effectiveness of this approach on closed information extraction, where collecting ground-truth data is challenging, and no satisfactory dataset exists to date. We synthetically generate a dataset of 1.8M data points, demonstrate its superior quality compared to existing datasets in a human evaluation and use it to finetune small models (220M and 770M parameters). The models we introduce, SynthIE, outperform existing baselines of comparable size with a substantial gap of 57 and 79 absolute points in micro and macro F1, respectively. Code, data, and models are available at https://github.com/epfl-dlab/SynthIE.

While recent studies have looked into the abilities of large language models in various benchmark tasks, including question generation, reading comprehension, multilingual and etc, there have been few studies looking into the controllability of large language models on generation tasks. We present an extensive analysis of various benchmarks including a sentence planning benchmark with different granularities. After comparing large language models against state-of-the-start finetuned smaller models, we present a spectrum showing large language models falling behind, are comparable, or exceed the ability of smaller models. We conclude that **large language models struggle at meeting fine-grained hard constraints**.

The development of generative language models that can create long and coherent textual outputs via autoregression has lead to a proliferation of uses and a corresponding sweep of analyses as researches work to determine the limitations of this new paradigm. Unlike humans, these 'Large Language Models' (LLMs) are highly sensitive to small changes in their inputs, leading to unwanted inconsistency in their behavior. One problematic inconsistency when LLMs are used to answer multiple-choice questions or analyze multiple inputs is order dependency: the output of an LLM can (and often does) change significantly when sub-sequences are swapped, despite both orderings being semantically identical. In this paper we present , a technique that guarantees the output of an LLM will not have order dependence on a specified set of sub-sequences. We show that this method provably eliminates order dependency, and that it can be applied to any transformer-based LLM to enable text generation that is unaffected by re-orderings. Delving into the implications of our method, we show that, despite our inputs being out of distribution, the impact on expected accuracy is small, where the expectation is over the order of uniformly chosen shuffling of the candidate responses, and usually significantly less in practice. Thus, can be used as a 'dropped-in' method on fully trained models. Finally, we discuss how our method's success suggests that other strong guarantees can be obtained on LLM performance via modifying the input representations.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Despite the success of Large Language Models (LLMs) on various tasks following human instructions, controlling model generation at inference time poses a persistent challenge. In this paper, we introduce Ctrl-G, an adaptable framework that facilitates tractable and flexible control of LLM generation to reliably follow logical constraints. Ctrl-G combines any production-ready LLM with a Hidden Markov Model, enabling LLM outputs to adhere to logical constraints represented as deterministic finite automata. We show that Ctrl-G, when applied to a TULU2-7B model, outperforms GPT3.5 and GPT4 on the task of interactive text editing: specifically, for the task of generating text insertions/continuations following logical constraints, Ctrl-G achieves over 30% higher satisfaction rate in human evaluation compared to GPT4. When applied to medium-size language models (e.g., GPT2-large), Ctrl-G also beats its counterparts for constrained generation by large margins on standard benchmarks. Additionally, as a proof-of-concept study, we experiment Ctrl-G on the Grade School Math benchmark to assist LLM reasoning, foreshadowing the application of Ctrl-G, as well as other constrained generation approaches, beyond traditional language generation tasks.

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Large language models (LLMs) struggle to follow instructions with complex constraints in format, length, etc. Following the conventional instruction-tuning practice, previous works conduct post-training on complex instruction-response pairs generated by feeding complex instructions to advanced LLMs. However, even advanced LLMs cannot follow complex instructions well, thus limiting the quality of generated data. In this work, we find that existing datasets inherently contain implicit complex constraints and propose a novel data generation technique, constraint back-translation. Specifically, we take the high-quality instruction-response pairs in existing datasets and only adopt advanced LLMs to add complex constraints already met by the responses to the instructions, which naturally reduces costs and data noise. In the experiments, we adopt Llama3-70B-Instruct to back-translate constraints and create a high-quality complex instruction-response dataset, named CRAB. We present that post-training on CRAB improves multiple backbone LLMs' complex instruction-following ability, evaluated on extensive instruction-following benchmarks. We further find that constraint back-translation also serves as a useful auxiliary training objective in post-training. Our code, data, and models will be released to facilitate future research.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

Large Language Models (LLMs) have become ubiquitous across various domains, transforming the way we interact with information and conduct research. However, most high-performing LLMs remain confined behind proprietary walls, hindering scientific progress. Most open-source LLMs, on the other hand, are limited in their ability to support longer sequence lengths, which is a key requirement for many tasks that require inference over an input context. To address this, we have trained XGen, a series of 7B parameter models on up to 8K sequence length for up to 1.5T tokens. We have also finetuned the XGen models on public-domain instructional data, creating their instruction-tuned counterparts (XGen-Inst). We open-source our models for both research advancements and commercial applications. Our evaluation on standard benchmarks shows that XGen models achieve comparable or better results when compared with state-of-the-art open-source LLMs. Our targeted evaluation on long sequence modeling tasks shows the benefits of our 8K-sequence models over 2K-sequence open-source LLMs.

Large pre-trained language models are capable of generating realistic text. However, controlling these models so that the generated text satisfies lexical constraints, i.e., contains specific words, is a challenging problem. Given that state-of-the-art language models are too large to be trained from scratch in a manageable time, it is desirable to control these models without re-training them. Methods capable of doing this are called plug-and-play. Recent plug-and-play methods have been successful in constraining small bidirectional language models as well as forward models in tasks with a restricted search space, e.g., machine translation. However, controlling large transformer-based models to meet lexical constraints without re-training them remains a challenge. In this work, we propose Directed Beam Search (DBS), a plug-and-play method for lexically constrained language generation. Our method can be applied to any language model, is easy to implement and can be used for general language generation. In our experiments we use DBS to control GPT-2. We demonstrate its performance on keyword-to-phrase generation and we obtain comparable results as a state-of-the-art non-plug-and-play model for lexically constrained story generation.

Despite the recent advancements in Large Language Models (LLMs), which have significantly enhanced the generative capabilities for various NLP tasks, LLMs still face limitations in directly handling retrieval tasks. However, many practical applications demand the seamless integration of both retrieval and generation. This paper introduces a novel and efficient One-pass Generation and retrieval framework (OneGen), designed to improve LLMs' performance on tasks that require both generation and retrieval. The proposed framework bridges the traditionally separate training approaches for generation and retrieval by incorporating retrieval tokens generated autoregressively. This enables a single LLM to handle both tasks simultaneously in a unified forward pass. We conduct experiments on two distinct types of composite tasks, RAG and Entity Linking, to validate the pluggability, effectiveness, and efficiency of OneGen in training and inference. Furthermore, our results show that integrating generation and retrieval within the same context preserves the generative capabilities of LLMs while improving retrieval performance. To the best of our knowledge, OneGen is the first to enable LLMs to conduct vector retrieval during the generation.

The evolving sophistication and intricacies of Large Language Models (LLMs) yield unprecedented advancements, yet they simultaneously demand considerable computational resources and incur significant costs. To alleviate these challenges, this paper introduces a novel, simple, and effective method named ``\growlength'' to accelerate the pretraining process of LLMs. Our method progressively increases the training length throughout the pretraining phase, thereby mitigating computational costs and enhancing efficiency. For instance, it begins with a sequence length of 128 and progressively extends to 4096. This approach enables models to process a larger number of tokens within limited time frames, potentially boosting their performance. In other words, the efficiency gain is derived from training with shorter sequences optimizing the utilization of resources. Our extensive experiments with various state-of-the-art LLMs have revealed that models trained using our method not only converge more swiftly but also exhibit superior performance metrics compared to those trained with existing methods. Furthermore, our method for LLMs pretraining acceleration does not require any additional engineering efforts, making it a practical solution in the realm of LLMs.

Intelligently extracting and linking complex scientific information from unstructured text is a challenging endeavor particularly for those inexperienced with natural language processing. Here, we present a simple sequence-to-sequence approach to joint named entity recognition and relation extraction for complex hierarchical information in scientific text. The approach leverages a pre-trained large language model (LLM), GPT-3, that is fine-tuned on approximately 500 pairs of prompts (inputs) and completions (outputs). Information is extracted either from single sentences or across sentences in abstracts/passages, and the output can be returned as simple English sentences or a more structured format, such as a list of JSON objects. We demonstrate that LLMs trained in this way are capable of accurately extracting useful records of complex scientific knowledge for three representative tasks in materials chemistry: linking dopants with their host materials, cataloging metal-organic frameworks, and general chemistry/phase/morphology/application information extraction. This approach represents a simple, accessible, and highly-flexible route to obtaining large databases of structured knowledge extracted from unstructured text. An online demo is available at http://www.matscholar.com/info-extraction.

Most research about natural language generation (NLG) relies on evaluation benchmarks with limited references for a sample, which may result in poor correlations with human judgements. The underlying reason is that one semantic meaning can actually be expressed in different forms, and the evaluation with a single or few references may not accurately reflect the quality of the model's hypotheses. To address this issue, this paper presents a simple and effective method, named Div-Ref, to enhance existing evaluation benchmarks by enriching the number of references. We leverage large language models (LLMs) to diversify the expression of a single reference into multiple high-quality ones to cover the semantic space of the reference sentence as much as possible. We conduct comprehensive experiments to empirically demonstrate that diversifying the expression of reference can significantly enhance the correlation between automatic evaluation and human evaluation. This idea is compatible with recent LLM-based evaluation which can similarly derive advantages from incorporating multiple references. We strongly encourage future generation benchmarks to include more references, even if they are generated by LLMs, which is once for all. We release all the code and data at https://github.com/RUCAIBox/Div-Ref to facilitate research.

We propose that small pretrained foundational generative language models with millions of parameters can be utilized as a general learning framework for sequence-based tasks. Our proposal overcomes the computational resource, skill set, and timeline challenges associated with training neural networks and language models from scratch. Further, our approach focuses on creating small and highly specialized models that can accurately execute a challenging task of which the base model is incapable of performing. We demonstrate that 125M, 350M, and 1.3B parameter pretrained foundational language models can be instruction fine-tuned with 10,000-to-1,000,000 instruction examples to achieve near state-of-the-art results on challenging cheminformatics tasks. We also demonstrate the role of successive language model fine-tuning epochs on improved outcomes, as well as the importance of both data formatting and pretrained foundational language model selection for instruction fine-tuning success.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Despite the rapid development of large language models (LLMs), a fundamental challenge persists: the lack of high-quality optimization modeling datasets hampers LLMs' robust modeling of practical optimization problems from natural language descriptions (NL). This data scarcity also contributes to the generalization difficulties experienced by learning-based methods. To address these challenges, we propose a scalable framework for synthesizing a high-quality dataset, named OptMATH. Starting from curated seed data with mathematical formulations (MF), this framework automatically generates problem data (PD) with controllable complexity. Then, a back-translation step is employed to obtain NL. To verify the correspondence between the NL and the PD, a forward modeling step followed by rejection sampling is used. The accepted pairs constitute the training part of OptMATH. Then a collection of rejected pairs is identified and further filtered. This collection serves as a new benchmark for optimization modeling, containing difficult instances whose lengths are much longer than these of NL4OPT and MAMO. Through extensive experiments, we demonstrate that models of various sizes (0.5B-32B parameters) trained on OptMATH achieve superior results on multiple modeling benchmarks, thereby validating the effectiveness and scalability of our approach. Our dataset is publicly available at https://github.com/AuroraLHL/OptMATH.

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Large language models (LLMs) exhibit remarkable generative capabilities but often suffer from hallucinations. Retrieval-augmented generation (RAG) offers an effective solution by incorporating external knowledge, but existing methods still face several limitations: additional deployment costs of separate retrievers, redundant input tokens from retrieved text chunks, and the lack of joint optimization of retrieval and generation. To address these issues, we propose RetroLLM, a unified framework that integrates retrieval and generation into a single, cohesive process, enabling LLMs to directly generate fine-grained evidence from the corpus with constrained decoding. Moreover, to mitigate false pruning in the process of constrained evidence generation, we introduce (1) hierarchical FM-Index constraints, which generate corpus-constrained clues to identify a subset of relevant documents before evidence generation, reducing irrelevant decoding space; and (2) a forward-looking constrained decoding strategy, which considers the relevance of future sequences to improve evidence accuracy. Extensive experiments on five open-domain QA datasets demonstrate RetroLLM's superior performance across both in-domain and out-of-domain tasks. The code is available at https://github.com/sunnynexus/RetroLLM.

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated through rule-based algorithms that map molecules to a sparse discrete space. However, these algorithms perform poorly for shallow prediction models or small datasets. To address this issue, we present SMILES Transformer. Inspired by Transformer and pre-trained language models from natural language processing, SMILES Transformer learns molecular fingerprints through unsupervised pre-training of the sequence-to-sequence language model using a huge corpus of SMILES, a text representation system for molecules. We performed benchmarks on 10 datasets against existing fingerprints and graph-based methods and demonstrated the superiority of the proposed algorithms in small-data settings where pre-training facilitated good generalization. Moreover, we define a novel metric to concurrently measure model accuracy and data efficiency.

We propose a Distributional Approach for addressing Controlled Text Generation from pre-trained Language Models (LMs). This approach permits to specify, in a single formal framework, both "pointwise" and "distributional" constraints over the target LM -- to our knowledge, the first model with such generality -- while minimizing KL divergence from the initial LM distribution. The optimal target distribution is then uniquely determined as an explicit EBM (Energy-Based Model) representation. From that optimal representation we then train a target controlled Autoregressive LM through an adaptive distributional variant of Policy Gradient. We conduct a first set of experiments over pointwise constraints showing the advantages of our approach over a set of baselines, in terms of obtaining a controlled LM balancing constraint satisfaction with divergence from the initial LM. We then perform experiments over distributional constraints, a unique feature of our approach, demonstrating its potential as a remedy to the problem of Bias in Language Models. Through an ablation study, we show the effectiveness of our adaptive technique for obtaining faster convergence. (Code available at https://github.com/naver/gdc)

Despite the crucial importance of accelerating text generation in large language models (LLMs) for efficiently producing content, the sequential nature of this process often leads to high inference latency, posing challenges for real-time applications. Various techniques have been proposed and developed to address these challenges and improve efficiency. This paper presents a comprehensive survey of accelerated generation techniques in autoregressive language models, aiming to understand the state-of-the-art methods and their applications. We categorize these techniques into several key areas: speculative decoding, early exiting mechanisms, and non-autoregressive methods. We discuss each category's underlying principles, advantages, limitations, and recent advancements. Through this survey, we aim to offer insights into the current landscape of techniques in LLMs and provide guidance for future research directions in this critical area of natural language processing.

Multilingual Large Language Models are capable of using powerful Large Language Models to handle and respond to queries in multiple languages, which achieves remarkable success in multilingual natural language processing tasks. Despite these breakthroughs, there still remains a lack of a comprehensive survey to summarize existing approaches and recent developments in this field. To this end, in this paper, we present a thorough review and provide a unified perspective to summarize the recent progress as well as emerging trends in multilingual large language models (MLLMs) literature. The contributions of this paper can be summarized: (1) First survey: to our knowledge, we take the first step and present a thorough review in MLLMs research field according to multi-lingual alignment; (2) New taxonomy: we offer a new and unified perspective to summarize the current progress of MLLMs; (3) New frontiers: we highlight several emerging frontiers and discuss the corresponding challenges; (4) Abundant resources: we collect abundant open-source resources, including relevant papers, data corpora, and leaderboards. We hope our work can provide the community with quick access and spur breakthrough research in MLLMs.

This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

Chemistry plays a crucial role in many domains, such as drug discovery and material science. While large language models (LLMs) such as GPT-4 exhibit remarkable capabilities on natural language processing tasks, existing work shows their performance on chemistry tasks is discouragingly low. In this paper, however, we demonstrate that our developed LLMs can achieve very strong results on a comprehensive set of chemistry tasks, outperforming the most advanced GPT-4 across all the tasks by a substantial margin and approaching the SoTA task-specific models. The key to our success is a large-scale, comprehensive, high-quality dataset for instruction tuning named SMolInstruct. It contains 14 meticulously selected chemistry tasks and over three million high-quality samples, laying a solid foundation for training and evaluating LLMs for chemistry. Based on SMolInstruct, we fine-tune a set of open-source LLMs, among which, we find that Mistral serves as the best base model for chemistry tasks. We further conduct analysis on the impact of trainable parameters, providing insights for future research.

The evolution of Neural Machine Translation (NMT) has been significantly influenced by six core challenges (Koehn and Knowles, 2017), which have acted as benchmarks for progress in this field. This study revisits these challenges, offering insights into their ongoing relevance in the context of advanced Large Language Models (LLMs): domain mismatch, amount of parallel data, rare word prediction, translation of long sentences, attention model as word alignment, and sub-optimal beam search. Our empirical findings indicate that LLMs effectively lessen the reliance on parallel data for major languages in the pretraining phase. Additionally, the LLM-based translation system significantly enhances the translation of long sentences that contain approximately 80 words and shows the capability to translate documents of up to 512 words. However, despite these significant improvements, the challenges of domain mismatch and prediction of rare words persist. While the challenges of word alignment and beam search, specifically associated with NMT, may not apply to LLMs, we identify three new challenges for LLMs in translation tasks: inference efficiency, translation of low-resource languages in the pretraining phase, and human-aligned evaluation. The datasets and models are released at https://github.com/pangjh3/LLM4MT.

Pretrained general-purpose language models can achieve state-of-the-art accuracies in various natural language processing domains by adapting to downstream tasks via zero-shot, few-shot and fine-tuning techniques. Because of their success, the size of these models has increased rapidly, requiring high-performance hardware, software, and algorithmic techniques to enable training such large models. As the result of a joint effort between Microsoft and NVIDIA, we present details on the training of the largest monolithic transformer based language model, Megatron-Turing NLG 530B (MT-NLG), with 530 billion parameters. In this paper, we first focus on the infrastructure as well as the 3D parallelism methodology used to train this model using DeepSpeed and Megatron. Next, we detail the training process, the design of our training corpus, and our data curation techniques, which we believe is a key ingredient to the success of the model. Finally, we discuss various evaluation results, as well as other interesting observations and new properties exhibited by MT-NLG. We demonstrate that MT-NLG achieves superior zero-, one-, and few-shot learning accuracies on several NLP benchmarks and establishes new state-of-the-art results. We believe that our contributions will help further the development of large-scale training infrastructures, large-scale language models, and natural language generations.

Large language models (LLMs) effectively generate fluent text when the target output follows natural language patterns. However, structured prediction tasks confine the output format to a limited ontology, causing even very large models to struggle since they were never trained with such restrictions in mind. The difficulty of using LLMs for direct prediction is exacerbated in few-shot learning scenarios, which commonly arise due to domain shift and resource limitations. We flip the problem on its head by leveraging the LLM as a tool for data augmentation rather than direct prediction. Our proposed Mixture of Soft Prompts (MSP) serves as a parameter-efficient procedure for generating data in a controlled manner. Denoising mechanisms are further applied to improve the quality of synthesized data. Automatic metrics show our method is capable of producing diverse and natural text, while preserving label semantics. Moreover, MSP achieves state-of-the-art results on three benchmarks when compared against strong baselines. Our method offers an alternate data-centric approach for applying LLMs to complex prediction tasks.

Large Language Models (LLMs) have demonstrated a remarkable ability to generalize zero-shot to various language-related tasks. This paper focuses on the study of exploring generative LLMs such as ChatGPT and GPT-4 for relevance ranking in Information Retrieval (IR). Surprisingly, our experiments reveal that properly instructed ChatGPT and GPT-4 can deliver competitive, even superior results than supervised methods on popular IR benchmarks. Notably, GPT-4 outperforms the fully fine-tuned monoT5-3B on MS MARCO by an average of 2.7 nDCG on TREC datasets, an average of 2.3 nDCG on eight BEIR datasets, and an average of 2.7 nDCG on ten low-resource languages Mr.TyDi. Subsequently, we delve into the potential for distilling the ranking capabilities of ChatGPT into a specialized model. Our small specialized model that trained on 10K ChatGPT generated data outperforms monoT5 trained on 400K annotated MS MARCO data on BEIR. The code to reproduce our results is available at www.github.com/sunnweiwei/RankGPT

This tutorial explores the advancements and challenges in the development of Large Language Models (LLMs) such as ChatGPT and Gemini. It addresses inherent limitations like temporal knowledge cutoffs, mathematical inaccuracies, and the generation of incorrect information, proposing solutions like Retrieval Augmented Generation (RAG), Program-Aided Language Models (PAL), and frameworks such as ReAct and LangChain. The integration of these techniques enhances LLM performance and reliability, especially in multi-step reasoning and complex task execution. The paper also covers fine-tuning strategies, including instruction fine-tuning, parameter-efficient methods like LoRA, and Reinforcement Learning from Human Feedback (RLHF) as well as Reinforced Self-Training (ReST). Additionally, it provides a comprehensive survey of transformer architectures and training techniques for LLMs. The toolbox for implementing these techniques is publicly available at https://github.com/giorgioroffo/large_language_models_open_suite

Large Language Models (LLMs), including GPT-x and LLaMA2, have achieved remarkable performance in multiple Natural Language Processing (NLP) tasks. Under the premise that protein sequences constitute the protein language, Protein Large Language Models (ProLLMs) trained on protein corpora excel at de novo protein sequence generation. However, as of now, unlike LLMs in NLP, no ProLLM is capable of multiple tasks in the Protein Language Processing (PLP) field. This prompts us to delineate the inherent limitations in current ProLLMs: (i) the lack of natural language capabilities, (ii) insufficient instruction understanding, and (iii) high training resource demands. To address these challenges, we introduce a training framework to transform any general LLM into a ProLLM capable of handling multiple PLP tasks. Specifically, our framework utilizes low-rank adaptation and employs a two-stage training approach, and it is distinguished by its universality, low overhead, and scalability. Through training under this framework, we propose the ProLLaMA model, the first known ProLLM to handle multiple PLP tasks simultaneously. Experiments show that ProLLaMA achieves state-of-the-art results in the unconditional protein sequence generation task. In the controllable protein sequence generation task, ProLLaMA can design novel proteins with desired functionalities. In the protein property prediction task, ProLLaMA achieves nearly 100\% accuracy across many categories. The latter two tasks are beyond the reach of other ProLLMs. Code is available at https://github.com/Lyu6PosHao/ProLLaMA.

Building a general-purpose task model similar to ChatGPT has been an important research direction for gene large language models. Instruction fine-tuning is a key component in building ChatGPT, but existing instructions are primarily based on natural language. Natural language and gene sequences have significant differences in tokenization and encoding. Therefore, constructing a multilingual model that can handle both natural language and gene sequences is crucial for solving this problem.In this paper, we expand the capabilities of the LLaMA large language model to include gene language. This involves expanding the vocabulary using the Byte Pair Encoding (BPE) method, specifically tailored for DNA and protein sequences, and conducting further pre-training on these sequences. We then convert various downstream gene task data into a unified format for instruction fine-tuning and further fine-tune the model on this data.Our study demonstrates that a mixed model of gene and natural language, fine-tuned with instructions, achieves results comparable to the current state-of-the-art (SOTA) in tasks such as gene classification and gene sequence interaction. This provides a promising direction for building a unified large language model for gene tasks.

We propose a general and efficient framework to control auto-regressive generation models with NeurAlly-Decomposed Oracle (NADO). Given a pre-trained base language model and a sequence-level boolean oracle function, we propose to decompose the oracle function into token-level guidance to steer the base model in text generation. Specifically, the token-level guidance is approximated by a neural model trained with examples sampled from the base model, demanding no additional auxiliary labeled data. Based on posterior regularization, we present the closed-form optimal solution to incorporate the token-level guidance into the base model for controllable generation. We further provide a theoretical analysis of how the approximation quality of NADO affects the controllable generation results. Experiments conducted on two applications: (1) text generation with lexical constraints and (2) machine translation with formality control demonstrate that our framework efficiently guides the base model towards the given oracle while maintaining high generation quality.

We introduce Chunk-Distilled Language Modeling (CD-LM), an approach to text generation that addresses two challenges in current large language models (LLMs): the inefficiency of token-level generation, and the difficulty of adapting to new data and knowledge. Our method combines deep network-based LLMs with a straightforward retrieval module, which allows the generation of multi-token text chunks at a single decoding step. Our retrieval framework enables flexible construction of model- or domain-specific datastores, either leveraging the internal knowledge of existing models, or incorporating expert insights from human-annotated corpora. This adaptability allows for enhanced control over the language model's distribution without necessitating additional training. We present the CD-LM formulation along with performance metrics demonstrating its ability to improve language model performance and efficiency across a diverse set of downstream tasks. Code and data will be made publicly available.

Recently, large language models such as GPT-2 have shown themselves to be extremely adept at text generation and have also been able to achieve high-quality results in many downstream NLP tasks such as text classification, sentiment analysis and question answering with the aid of fine-tuning. We present a useful technique for using a large language model to perform the task of paraphrasing on a variety of texts and subjects. Our approach is demonstrated to be capable of generating paraphrases not only at a sentence level but also for longer spans of text such as paragraphs without needing to break the text into smaller chunks.

Lexically constrained text generation is one of the constrained text generation tasks, which aims to generate text that covers all the given constraint lexicons. While the existing approaches tackle this problem using a lexically constrained beam search algorithm or dedicated model using non-autoregressive decoding, there is a trade-off between the generated text quality and the hard constraint satisfaction. We introduce AutoTemplate, a simple yet effective lexically constrained text generation framework divided into template generation and lexicalization tasks. The template generation is to generate the text with the placeholders, and lexicalization replaces them into the constraint lexicons to perform lexically constrained text generation. We conducted the experiments on two tasks: keywords-to-sentence generations and entity-guided summarization. Experimental results show that the AutoTemplate outperforms the competitive baselines on both tasks while satisfying the hard lexical constraints.

Recent approaches to large language model (LLM) alignment typically require millions of human annotations or rely on external aligned models for synthetic data generation. This paper introduces ALMA: Alignment with Minimal Annotation, demonstrating that effective alignment can be achieved using only 9,000 labeled examples -- less than 1% of conventional approaches. ALMA generates large amounts of high-quality synthetic alignment data through new techniques: diverse prompt synthesis via few-shot learning, diverse response generation with multiple model checkpoints, and judge (reward model) enhancement through score aggregation and self-distillation. Using only a pretrained Llama3 base model, 5,000 SFT examples, and 4,000 judge annotations, ALMA achieves performance close to Llama3-Instruct across diverse alignment benchmarks (e.g., 0.1% difference on AlpacaEval 2.0 score). These results are achieved with a multi-round, self-bootstrapped data synthesis and training recipe that continues to improve for 10 rounds, surpassing the typical 3-round ceiling of previous methods. These results suggest that base models already possess sufficient knowledge for effective alignment, and that synthetic data generation methods can expose it.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

In this study, we introduce Orion-14B, a collection of multilingual large language models with 14 billion parameters. We utilize a data scheduling approach to train a foundational model on a diverse corpus of 2.5 trillion tokens, sourced from texts in English, Chinese, Japanese, Korean, and other languages. Additionally, we fine-tuned a series of models tailored for conversational applications and other specific use cases. Our evaluation results demonstrate that Orion-14B achieves state-of-the-art performance across a broad spectrum of tasks. We make the Orion-14B model family and its associated code publicly accessible https://github.com/OrionStarAI/Orion, aiming to inspire future research and practical applications in the field.

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

We discover a robust self-supervised strategy tailored towards molecular representations for generative masked language models through a series of tailored, in-depth ablations. Using this pre-training strategy, we train BARTSmiles, a BART-like model with an order of magnitude more compute than previous self-supervised molecular representations. In-depth evaluations show that BARTSmiles consistently outperforms other self-supervised representations across classification, regression, and generation tasks setting a new state-of-the-art on 11 tasks. We then quantitatively show that when applied to the molecular domain, the BART objective learns representations that implicitly encode our downstream tasks of interest. For example, by selecting seven neurons from a frozen BARTSmiles, we can obtain a model having performance within two percentage points of the full fine-tuned model on task Clintox. Lastly, we show that standard attribution interpretability methods, when applied to BARTSmiles, highlight certain substructures that chemists use to explain specific properties of molecules. The code and the pretrained model are publicly available.

Large language models (LLMs) specializing in natural language generation (NLG) have recently started exhibiting promising capabilities across a variety of domains. However, gauging the trustworthiness of responses generated by LLMs remains an open challenge, with limited research on uncertainty quantification (UQ) for NLG. Furthermore, existing literature typically assumes white-box access to language models, which is becoming unrealistic either due to the closed-source nature of the latest LLMs or computational constraints. In this work, we investigate UQ in NLG for black-box LLMs. We first differentiate uncertainty vs confidence: the former refers to the "dispersion" of the potential predictions for a fixed input, and the latter refers to the confidence on a particular prediction/generation. We then propose and compare several confidence/uncertainty metrics, applying them to selective NLG where unreliable results could either be ignored or yielded for further assessment. Experiments were carried out with several popular LLMs on question-answering datasets (for evaluation purposes). Results reveal that a simple metric for the semantic dispersion can be a reliable predictor of the quality of LLM responses, providing valuable insights for practitioners on uncertainty management when adopting LLMs. The code to replicate our experiments is available at https://github.com/zlin7/UQ-NLG.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Large language models (LLMs) have proven to be remarkably efficient, both across a wide range of natural language processing tasks and well beyond them. However, a comprehensive theoretical analysis of the origins of their impressive performance remains elusive. In this paper, we approach this challenging task by drawing an equivalence between generic autoregressive language models with vocabulary of size T and context window of size K and Markov chains defined on a finite state space of size O(T^K). We derive several surprising findings related to the existence of a stationary distribution of Markov chains that capture the inference power of LLMs, their speed of convergence to it, and the influence of the temperature on the latter. We then prove pre-training and in-context generalization bounds and show how the drawn equivalence allows us to enrich their interpretation. Finally, we illustrate our theoretical guarantees with experiments on several recent LLMs to highlight how they capture the behavior observed in practice.

Large Language Models (LLMs), such as GPT3.5, have exhibited remarkable proficiency in comprehending and generating natural language. However, their unpersonalized generation paradigm may result in suboptimal user-specific outcomes. Typically, users converse differently based on their knowledge and preferences. This necessitates the task of enhancing user-oriented LLM which remains unexplored. While one can fully train an LLM for this objective, the resource consumption is unaffordable. Prior research has explored memory-based methods to store and retrieve knowledge to enhance generation without retraining for new queries. However, we contend that a mere memory module is inadequate to comprehend a user's preference, and fully training an LLM can be excessively costly. In this study, we propose a novel computational bionic memory mechanism, equipped with a parameter-efficient fine-tuning schema, to personalize LLMs. Our extensive experimental results demonstrate the effectiveness and superiority of the proposed approach. To encourage further research into this area, we are releasing a new conversation dataset generated entirely by LLM based on an open-source medical corpus, as well as our implementation code.

Large language model (LLM) decoding involves generating a sequence of tokens based on a given context, where each token is predicted one at a time using the model's learned probabilities. The typical autoregressive decoding method requires a separate forward pass through the model for each token generated, which is computationally inefficient and poses challenges for deploying LLMs in latency-sensitive scenarios. The main limitations of current decoding methods stem from their inefficiencies and resource demands. Existing approaches either necessitate fine-tuning smaller models, which is resource-intensive, or rely on fixed retrieval schemes to construct drafts for the next tokens, which lack adaptability and fail to generalize across different models and contexts. To address these issues, we introduce a novel methodology called ADED, which accelerates LLM decoding without requiring fine-tuning. Our approach involves an adaptive draft-verification process that evolves over time to improve efficiency. We utilize a tri-gram matrix-based LLM representation to dynamically approximate the output distribution of the LLM, allowing the model to adjust to changing token probabilities during the decoding process. Additionally, we implement a draft construction mechanism that effectively balances exploration and exploitation, ensuring that the drafts generated are both diverse and close to the true output distribution of the LLM. The importance of this design lies in its ability to optimize the draft distribution adaptively, leading to faster and more accurate decoding. Through extensive experiments on various benchmark datasets and LLM architectures, we demonstrate that ADED significantly accelerates the decoding process while maintaining high accuracy, making it suitable for deployment in a wide range of practical applications.

Personalized text generation is an emerging research area that has attracted much attention in recent years. Most studies in this direction focus on a particular domain by designing bespoke features or models. In this work, we propose a general approach for personalized text generation using large language models (LLMs). Inspired by the practice of writing education, we develop a multistage and multitask framework to teach LLMs for personalized generation. In writing instruction, the task of writing from sources is often decomposed into multiple steps that involve finding, evaluating, summarizing, synthesizing, and integrating information. Analogously, our approach to personalized text generation consists of multiple stages: retrieval, ranking, summarization, synthesis, and generation. In addition, we introduce a multitask setting that helps the model improve its generation ability further, which is inspired by the observation in education that a student's reading proficiency and writing ability are often correlated. We evaluate our approach on three public datasets, each of which covers a different and representative domain. Our results show significant improvements over a variety of baselines.

Pretrained language models have served as important backbones for natural language processing. Recently, in-domain pretraining has been shown to benefit various domain-specific downstream tasks. In the biomedical domain, natural language generation (NLG) tasks are of critical importance, while understudied. Approaching natural language understanding (NLU) tasks as NLG achieves satisfying performance in the general domain through constrained language generation or language prompting. We emphasize the lack of in-domain generative language models and the unsystematic generative downstream benchmarks in the biomedical domain, hindering the development of the research community. In this work, we introduce the generative language model BioBART that adapts BART to the biomedical domain. We collate various biomedical language generation tasks including dialogue, summarization, entity linking, and named entity recognition. BioBART pretrained on PubMed abstracts has enhanced performance compared to BART and set strong baselines on several tasks. Furthermore, we conduct ablation studies on the pretraining tasks for BioBART and find that sentence permutation has negative effects on downstream tasks.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

Large language models (LLMs) have shown remarkable ability on controllable text generation. However, the potential of LLMs in generating text from structured tables remains largely under-explored. In this paper, we study the capabilities of LLMs for table-to-text generation tasks, particularly aiming to investigate their performance in generating natural language statements that can be logically entailed by a provided table. First, we investigate how LLMs compare to state-of-the-art table-to-text fine-tuned models, and demonstrate that LLMs can generate statements with higher faithfulness compared with previous state-of-the-art fine-tuned models. Given this finding, we next explore whether LLMs can serve as faithfulness-level automated evaluation metrics. Through human evaluation, we show that evaluation metrics adopted from LLMs correlates better with human judgments compared with existing faithfulness-level metrics. Finally, we demonstrate that LLMs using chain-of-thought prompting can generate high-fidelity natural language feedback for other table-to-text models' generations, provide insights for future work regarding the distillation of text generation capabilities from LLMs to smaller models.

Large Language Models (LLMs) hold immense potential to generate synthetic data of high quality and utility, which has numerous applications from downstream model training to practical data utilisation. However, contemporary models, despite their impressive capacities, consistently struggle to produce both coherent and diverse data. To address the coherency issue, we introduce contrastive expert guidance, where the difference between the logit distributions of fine-tuned and base language models is emphasised to ensure domain adherence. In order to ensure diversity, we utilise existing real and synthetic examples as negative prompts to the model. We deem this dual-pronged approach to logit reshaping as STEER: Semantic Text Enhancement via Embedding Repositioning. STEER operates at inference-time and systematically guides the LLMs to strike a balance between adherence to the data distribution (ensuring semantic fidelity) and deviation from prior synthetic examples or existing real datasets (ensuring diversity and authenticity). This delicate balancing act is achieved by dynamically moving towards or away from chosen representations in the latent space. STEER demonstrates improved performance over previous synthetic data generation techniques, exhibiting better balance between data diversity and coherency across three distinct tasks: hypothesis generation, toxic and non-toxic comment generation, and commonsense reasoning task generation. We demonstrate how STEER allows for fine-tuned control over the diversity-coherency trade-off via its hyperparameters, highlighting its versatility.

Large language models (LLMs) have notably enhanced the fluency and diversity of machine-generated text. However, this progress also presents a significant challenge in detecting the origin of a given text, and current research on detection methods lags behind the rapid evolution of LLMs. Conventional training-based methods have limitations in flexibility, particularly when adapting to new domains, and they often lack explanatory power. To address this gap, we propose a novel training-free detection strategy called Divergent N-Gram Analysis (DNA-GPT). Given a text, we first truncate it in the middle and then use only the preceding portion as input to the LLMs to regenerate the new remaining parts. By analyzing the differences between the original and new remaining parts through N-gram analysis in black-box or probability divergence in white-box, we can clearly illustrate significant discrepancies between machine-generated and human-written text. We conducted extensive experiments on the most advanced LLMs from OpenAI, including text-davinci-003, GPT-3.5-turbo, and GPT-4, as well as open-source models such as GPT-NeoX-20B and LLaMa-13B. Results show that our zero-shot approach exhibits state-of-the-art performance in distinguishing between human and GPT-generated text on four English and one German dataset, outperforming OpenAI's own classifier, which is trained on millions of text. Additionally, our methods provide reasonable explanations and evidence to support our claim, which is a unique feature of explainable detection. Our method is also robust under the revised text attack and can additionally solve model sourcing. Codes are available at https://github.com/Xianjun-Yang/DNA-GPT.

Large Language Models (LLMs) have attracted extensive attention due to their remarkable performance across various tasks. However, the substantial computational and memory requirements of LLM inference pose challenges for deployment in resource-constrained scenarios. Efforts within the field have been directed towards developing techniques aimed at enhancing the efficiency of LLM inference. This paper presents a comprehensive survey of the existing literature on efficient LLM inference. We start by analyzing the primary causes of the inefficient LLM inference, i.e., the large model size, the quadratic-complexity attention operation, and the auto-regressive decoding approach. Then, we introduce a comprehensive taxonomy that organizes the current literature into data-level, model-level, and system-level optimization. Moreover, the paper includes comparative experiments on representative methods within critical sub-fields to provide quantitative insights. Last but not least, we provide some knowledge summary and discuss future research directions.

Large language models (LLMs) currently dominate the field of natural language processing (NLP), representing the state-of-the-art across a diverse array of tasks. Developing a model of this nature, from training to inference, requires making numerous decisions which define a combinatorial search problem. For example, selecting the optimal pre-trained LLM, prompt, or hyperparameters to attain the best performance for a task often requires evaluating multiple candidates on an entire test set. This exhaustive evaluation can be time-consuming and costly, as both inference and metric computation with LLMs are resource-intensive. In this paper, we address the challenge of identifying the best method within a limited budget for evaluating methods on test examples. By leveraging the well-studied multi-armed bandit framework, which sequentially selects the next method-example pair to evaluate, our approach, combining multi-armed bandit algorithms with low-rank factorization, significantly reduces the required resources. Experiments show that our algorithms can identify the top-performing method using only 5-15\% of the typically needed resources, resulting in an 85-95\% reduction in cost.

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

Large Language Models (LLMs) have drawn a lot of attention due to their strong performance on a wide range of natural language tasks, since the release of ChatGPT in November 2022. LLMs' ability of general-purpose language understanding and generation is acquired by training billions of model's parameters on massive amounts of text data, as predicted by scaling laws kaplan2020scaling,hoffmann2022training. The research area of LLMs, while very recent, is evolving rapidly in many different ways. In this paper, we review some of the most prominent LLMs, including three popular LLM families (GPT, LLaMA, PaLM), and discuss their characteristics, contributions and limitations. We also give an overview of techniques developed to build, and augment LLMs. We then survey popular datasets prepared for LLM training, fine-tuning, and evaluation, review widely used LLM evaluation metrics, and compare the performance of several popular LLMs on a set of representative benchmarks. Finally, we conclude the paper by discussing open challenges and future research directions.

Large language models (LLMs) can learn to perform a wide range of natural language tasks from just a handful of in-context examples. However, for generating strings from highly structured languages (e.g., semantic parsing to complex domain-specific languages), it is challenging for the LLM to generalize from just a few exemplars. We explore grammar prompting as a simple approach for enabling LLMs to use external knowledge and domain-specific constraints, expressed through a grammar expressed in Backus--Naur Form (BNF), during in-context learning. Grammar prompting augments each demonstration example with a specialized grammar that is minimally sufficient for generating the particular output example, where the specialized grammar is a subset of the full DSL grammar. For inference, the LLM first predicts a BNF grammar given a test input, and then generates the output according to the rules of the grammar. Experiments demonstrate that grammar prompting can enable LLMs to perform competitively on a diverse set of DSL generation tasks, including semantic parsing (SMCalFlow, Overnight, GeoQuery), PDDL planning, and even molecule generation (SMILES).

Large language models (LLMs) are versatile and can address many tasks, but for computational efficiency, it is often desirable to distill their capabilities into smaller student models. One way to do this for classification tasks is via dataset synthesis, which can be accomplished by generating examples of each label from the LLM. Prior approaches to synthesis use few-shot prompting, which relies on the LLM's parametric knowledge to generate usable examples. However, this leads to issues of repetition, bias towards popular entities, and stylistic differences from human text. In this work, we propose Synthesize by Retrieval and Refinement (SynthesizRR), which uses retrieval augmentation to introduce variety into the dataset synthesis process: as retrieved passages vary, the LLM is "seeded" with different content to generate its examples. We empirically study the synthesis of six datasets, covering topic classification, sentiment analysis, tone detection, and humor, requiring complex synthesis strategies. We find SynthesizRR greatly improves lexical and semantic diversity, similarity to human-written text, and distillation performance, when compared to standard 32-shot prompting and six baseline approaches.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Large Language Models (LLMs) exhibit impressive capabilities but require careful alignment with human preferences. Traditional training-time methods finetune LLMs using human preference datasets but incur significant training costs and require repeated training to handle diverse user preferences. Test-time alignment methods address this by using reward models (RMs) to guide frozen LLMs without retraining. However, existing test-time approaches rely on trajectory-level RMs which are designed to evaluate complete responses, making them unsuitable for autoregressive text generation that requires computing next-token rewards from partial responses. To address this, we introduce GenARM, a test-time alignment approach that leverages the Autoregressive Reward Model--a novel reward parametrization designed to predict next-token rewards for efficient and effective autoregressive generation. Theoretically, we demonstrate that this parametrization can provably guide frozen LLMs toward any distribution achievable by traditional RMs within the KL-regularized reinforcement learning framework. Experimental results show that GenARM significantly outperforms prior test-time alignment baselines and matches the performance of training-time methods. Additionally, GenARM enables efficient weak-to-strong guidance, aligning larger LLMs with smaller RMs without the high costs of training larger models. Furthermore, GenARM supports multi-objective alignment, allowing real-time trade-offs between preference dimensions and catering to diverse user preferences without retraining.

Sentence embedding is essential for many NLP tasks, with contrastive learning methods achieving strong performance using annotated datasets like NLI. Yet, the reliance on manual labels limits scalability. Recent studies leverage large language models (LLMs) to generate sentence pairs, reducing annotation dependency. However, they overlook ranking information crucial for fine-grained semantic distinctions. To tackle this challenge, we propose a method for controlling the generation direction of LLMs in the latent space. Unlike unconstrained generation, the controlled approach ensures meaningful semantic divergence. Then, we refine exist sentence embedding model by integrating ranking information and semantic information. Experiments on multiple benchmarks demonstrate that our method achieves new SOTA performance with a modest cost in ranking sentence synthesis.

Generative large language models (LLMs) can be a powerful tool for augmenting text annotation procedures, but their performance varies across annotation tasks due to prompt quality, text data idiosyncrasies, and conceptual difficulty. Because these challenges will persist even as LLM technology improves, we argue that any automated annotation process using an LLM must validate the LLM's performance against labels generated by humans. To this end, we outline a workflow to harness the annotation potential of LLMs in a principled, efficient way. Using GPT-4, we validate this approach by replicating 27 annotation tasks across 11 datasets from recent social science articles in high-impact journals. We find that LLM performance for text annotation is promising but highly contingent on both the dataset and the type of annotation task, which reinforces the necessity to validate on a task-by-task basis. We make available easy-to-use software designed to implement our workflow and streamline the deployment of LLMs for automated annotation.

Many information retrieval tasks require large labeled datasets for fine-tuning. However, such datasets are often unavailable, and their utility for real-world applications can diminish quickly due to domain shifts. To address this challenge, we develop and motivate a method for using large language models (LLMs) to generate large numbers of synthetic queries cheaply. The method begins by generating a small number of synthetic queries using an expensive LLM. After that, a much less expensive one is used to create large numbers of synthetic queries, which are used to fine-tune a family of reranker models. These rerankers are then distilled into a single efficient retriever for use in the target domain. We show that this technique boosts zero-shot accuracy in long-tail domains, even where only 2K synthetic queries are used for fine-tuning, and that it achieves substantially lower latency than standard reranking methods. We make our end-to-end approach, including our synthetic datasets and replication code, publicly available on Github: https://github.com/primeqa/primeqa.

We propose a new benchmark corpus to be used for measuring progress in statistical language modeling. With almost one billion words of training data, we hope this benchmark will be useful to quickly evaluate novel language modeling techniques, and to compare their contribution when combined with other advanced techniques. We show performance of several well-known types of language models, with the best results achieved with a recurrent neural network based language model. The baseline unpruned Kneser-Ney 5-gram model achieves perplexity 67.6; a combination of techniques leads to 35% reduction in perplexity, or 10% reduction in cross-entropy (bits), over that baseline. The benchmark is available as a code.google.com project; besides the scripts needed to rebuild the training/held-out data, it also makes available log-probability values for each word in each of ten held-out data sets, for each of the baseline n-gram models.

Relations such as "is influenced by", "is known for" or "is a competitor of" are inherently graded: we can rank entity pairs based on how well they satisfy these relations, but it is hard to draw a line between those pairs that satisfy them and those that do not. Such graded relations play a central role in many applications, yet they are typically not covered by existing Knowledge Graphs. In this paper, we consider the possibility of using Large Language Models (LLMs) to fill this gap. To this end, we introduce a new benchmark, in which entity pairs have to be ranked according to how much they satisfy a given graded relation. The task is formulated as a few-shot ranking problem, where models only have access to a description of the relation and five prototypical instances. We use the proposed benchmark to evaluate state-of-the-art relation embedding strategies as well as several recent LLMs, covering both publicly available LLMs and closed models such as GPT-4. Overall, we find a strong correlation between model size and performance, with smaller Language Models struggling to outperform a naive baseline. The results of the largest Flan-T5 and OPT models are remarkably strong, although a clear gap with human performance remains.

Many applications of text generation require incorporating different constraints to control the semantics or style of generated text. These constraints can be hard (e.g., ensuring certain keywords are included in the output) and soft (e.g., contextualizing the output with the left- or right-hand context). In this paper, we present Energy-based Constrained Decoding with Langevin Dynamics (COLD), a decoding framework which unifies constrained generation as specifying constraints through an energy function, then performing efficient differentiable reasoning over the constraints through gradient-based sampling. COLD decoding is a flexible framework that can be applied directly to off-the-shelf left-to-right language models without the need for any task-specific fine-tuning, as demonstrated through three challenging text generation applications: lexically-constrained generation, abductive reasoning, and counterfactual reasoning. Our experiments on these constrained generation tasks point to the effectiveness of our approach, both in terms of automatic and human evaluation.

Protein language models have shown remarkable success in learning biological information from protein sequences. However, most existing models are limited by either autoencoding or autoregressive pre-training objectives, which makes them struggle to handle protein understanding and generation tasks concurrently. We propose a unified protein language model, xTrimoPGLM, to address these two types of tasks simultaneously through an innovative pre-training framework. Our key technical contribution is an exploration of the compatibility and the potential for joint optimization of the two types of objectives, which has led to a strategy for training xTrimoPGLM at an unprecedented scale of 100 billion parameters and 1 trillion training tokens. Our extensive experiments reveal that 1) xTrimoPGLM significantly outperforms other advanced baselines in 18 protein understanding benchmarks across four categories. The model also facilitates an atomic-resolution view of protein structures, leading to an advanced 3D structural prediction model that surpasses existing language model-based tools. 2) xTrimoPGLM not only can generate de novo protein sequences following the principles of natural ones, but also can perform programmable generation after supervised fine-tuning (SFT) on curated sequences. These results highlight the substantial capability and versatility of xTrimoPGLM in understanding and generating protein sequences, contributing to the evolving landscape of foundation models in protein science.

Large language models (LLMs) have garnered unprecedented advancements across diverse fields, ranging from natural language processing to computer vision and beyond. The prowess of LLMs is underpinned by their substantial model size, extensive and diverse datasets, and the vast computational power harnessed during training, all of which contribute to the emergent abilities of LLMs (e.g., in-context learning) that are not present in small models. Within this context, the mixture of experts (MoE) has emerged as an effective method for substantially scaling up model capacity with minimal computation overhead, gaining significant attention from academia and industry. Despite its growing prevalence, there lacks a systematic and comprehensive review of the literature on MoE. This survey seeks to bridge that gap, serving as an essential resource for researchers delving into the intricacies of MoE. We first briefly introduce the structure of the MoE layer, followed by proposing a new taxonomy of MoE. Next, we overview the core designs for various MoE models including both algorithmic and systemic aspects, alongside collections of available open-source implementations, hyperparameter configurations and empirical evaluations. Furthermore, we delineate the multifaceted applications of MoE in practice, and outline some potential directions for future research. To facilitate ongoing updates and the sharing of cutting-edge developments in MoE research, we have established a resource repository accessible at https://github.com/withinmiaov/A-Survey-on-Mixture-of-Experts.

Large Language Models (LLMs) are foundational in language technologies, particularly in information retrieval (IR). Previous studies have utilized LLMs for query expansion, achieving notable improvements in IR. In this paper, we thoroughly explore the best practice of leveraging LLMs for query expansion. To this end, we introduce a training-free, straightforward yet effective framework called Multi-Text Generation Integration (MuGI). It leverages LLMs to generate multiple pseudo-references, integrating them with queries to enhance both sparse and dense retrievers. Our empirical findings reveal that: (1) Increasing the number of samples from LLMs benefits IR systems; (2) A balance between the query and pseudo-documents, and an effective integration strategy, is critical for high performance; (3) Contextual information from LLMs is essential, even boost a 23M model to outperform a 7B baseline model; (4) Pseudo relevance feedback can further calibrate queries for improved performance; and (5) Query expansion is widely applicable and versatile, consistently enhancing models ranging from 23M to 7B parameters. Our code and all generated references are made available at https://github.com/lezhang7/Retrieval_MuGI

The development of state-of-the-art generative large language models (LLMs) disproportionately relies on English-centric tokenizers, vocabulary and pre-training data. Despite the fact that some LLMs have multilingual capabilities, recent studies have shown that their inference efficiency deteriorates when generating text in languages other than English. This results in increased inference time and costs. Cross-lingual vocabulary adaptation methods have been proposed for adapting models to a target language aiming to improve downstream performance. However, the effectiveness of these methods on increasing inference efficiency of generative LLMs has yet to be explored. In this paper, we perform an empirical study of various cross-lingual vocabulary adaptation methods on five generative LLMs (including monolingual and multilingual models) across four typologically-diverse languages and four natural language understanding tasks. We find that cross-lingual vocabulary adaptation substantially contributes to LLM inference speedups of up to 271.5%. We also show that adapting LLMs that have been pre-trained on more balanced multilingual data results in downstream performance comparable to the original models.

Large language models (LLMs) have established great success in the general domain of natural language processing. Their emerging task generalization and free-form dialogue capabilities can greatly help to design Chemical General Intelligence (CGI) to assist real-world research in chemistry. However, the existence of specialized language and knowledge in the field of chemistry, such as the highly informative SMILES notation, hinders the performance of general-domain LLMs in chemistry. To this end, we develop ChemDFM, the first LLM towards CGI. ChemDFM-13B is trained on 34B tokens from chemical literature, textbooks, and instructions as well as various data from the general domain. Therefore, it can store, understand, and reason over chemical knowledge and languages while still possessing advanced free-form language comprehension capabilities. Extensive quantitative evaluation shows that ChemDFM can significantly outperform the representative open-sourced LLMs. Moreover, ChemDFM can also surpass GPT-4 on a great portion of chemical tasks, despite the significant size difference. Further qualitative evaluations demonstrate the efficiency and effectiveness of ChemDFM in real-world research scenarios. We will open-source the ChemDFM model soon.

We propose a method to fuse frozen text-only large language models (LLMs) with pre-trained image encoder and decoder models, by mapping between their embedding spaces. Our model demonstrates a wide suite of multimodal capabilities: image retrieval, novel image generation, and multimodal dialogue. Ours is the first approach capable of conditioning on arbitrarily interleaved image and text inputs to generate coherent image (and text) outputs. To achieve strong performance on image generation, we propose an efficient mapping network to ground the LLM to an off-the-shelf text-to-image generation model. This mapping network translates hidden representations of text into the embedding space of the visual models, enabling us to leverage the strong text representations of the LLM for visual outputs. Our approach outperforms baseline generation models on tasks with longer and more complex language. In addition to novel image generation, our model is also capable of image retrieval from a prespecified dataset, and decides whether to retrieve or generate at inference time. This is done with a learnt decision module which conditions on the hidden representations of the LLM. Our model exhibits a wider range of capabilities compared to prior multimodal language models. It can process image-and-text inputs, and produce retrieved images, generated images, and generated text -- outperforming non-LLM based generation models across several text-to-image tasks that measure context dependence.

In this work we explore recent advances in Recurrent Neural Networks for large scale Language Modeling, a task central to language understanding. We extend current models to deal with two key challenges present in this task: corpora and vocabulary sizes, and complex, long term structure of language. We perform an exhaustive study on techniques such as character Convolutional Neural Networks or Long-Short Term Memory, on the One Billion Word Benchmark. Our best single model significantly improves state-of-the-art perplexity from 51.3 down to 30.0 (whilst reducing the number of parameters by a factor of 20), while an ensemble of models sets a new record by improving perplexity from 41.0 down to 23.7. We also release these models for the NLP and ML community to study and improve upon.

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

Large language models (LLMs) are capable of generating coherent summaries from very long contexts given a user query. Extracting and properly citing evidence spans could help improve the transparency and reliability of these summaries. At the same time, LLMs suffer from positional biases in terms of which information they understand and attend to, which could affect evidence citation. Whereas previous work has focused on evidence citation with predefined levels of granularity (e.g. sentence, paragraph, document, etc.), we propose the task of long-context query focused summarization with unstructured evidence citation. We show how existing systems struggle to generate and properly cite unstructured evidence from their context, and that evidence tends to be "lost-in-the-middle". To help mitigate this, we create the Summaries with Unstructured Evidence Text dataset (SUnsET), a synthetic dataset generated using a novel domain-agnostic pipeline which can be used as supervision to adapt LLMs to this task. We demonstrate across 5 LLMs of different sizes and 4 datasets with varying document types and lengths that LLMs adapted with SUnsET data generate more relevant and factually consistent evidence than their base models, extract evidence from more diverse locations in their context, and can generate more relevant and consistent summaries.

Large-scale pre-trained language models, such as BERT and GPT-2, have achieved excellent performance in language representation learning and free-form text generation. However, these models cannot be directly employed to generate text under specified lexical constraints. To address this challenge, we present POINTER (PrOgressive INsertion-based TransformER), a simple yet novel insertion-based approach for hard-constrained text generation. The proposed method operates by progressively inserting new tokens between existing tokens in a parallel manner. This procedure is recursively applied until a sequence is completed. The resulting coarse-to-fine hierarchy makes the generation process intuitive and interpretable. We pre-train our model with the proposed progressive insertion-based objective on a 12GB Wikipedia dataset, and fine-tune it on downstream hard-constrained generation tasks. Non-autoregressive decoding yields an empirically logarithmic time complexity during inference time. Experimental results on both News and Yelp datasets demonstrate that POINTER achieves state-of-the-art performance on constrained text generation. We released the pre-trained models and the source code to facilitate future research (https://github.com/dreasysnail/POINTER).

Large Language Models (LLMs) have emerged as powerful tools capable of accomplishing a broad spectrum of tasks. Their abilities span numerous areas, and one area where they have made a significant impact is in the domain of code generation. In this context, we view LLMs as mutation and crossover tools. Meanwhile, Quality-Diversity (QD) algorithms are known to discover diverse and robust solutions. By merging the code-generating abilities of LLMs with the diversity and robustness of QD solutions, we introduce LLMatic, a Neural Architecture Search (NAS) algorithm. While LLMs struggle to conduct NAS directly through prompts, LLMatic uses a procedural approach, leveraging QD for prompts and network architecture to create diverse and highly performant networks. We test LLMatic on the CIFAR-10 image classification benchmark, demonstrating that it can produce competitive networks with just 2,000 searches, even without prior knowledge of the benchmark domain or exposure to any previous top-performing models for the benchmark.

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

With the rapid development of NLP, large-scale language models (LLMs) excel in various tasks across multiple domains now. However, existing benchmarks may not adequately measure these models' capabilities, especially when faced with new knowledge. In this paper, we address the lack of benchmarks to evaluate LLMs' ability to handle new knowledge, an important and challenging aspect in the rapidly evolving world. We propose an approach called KnowGen that generates new knowledge by altering existing entity attributes and relationships, resulting in artificial entities that are distinct from real-world entities. With KnowGen, we introduce a benchmark named ALCUNA to assess LLMs' abilities in knowledge understanding, differentiation, and association. We benchmark several LLMs, reveals that their performance in face of new knowledge is not satisfactory, particularly in reasoning between new and internal knowledge. We also explore the impact of entity similarity on the model's understanding of entity knowledge and the influence of contextual entities. We appeal to the need for caution when using LLMs in new scenarios or with new knowledge, and hope that our benchmarks can help drive the development of LLMs in face of new knowledge.

Large language models (LLMs) have emerged as a widely-used tool for information seeking, but their generated outputs are prone to hallucination. In this work, we aim to enable LLMs to generate text with citations, improving their factual correctness and verifiability. Existing work mainly relies on commercial search engines and human evaluation, making it challenging to reproduce and compare with different modeling approaches. We propose ALCE, the first benchmark for Automatic LLMs' Citation Evaluation. ALCE collects a diverse set of questions and retrieval corpora and requires building end-to-end systems to retrieve supporting evidence and generate answers with citations. We build automatic metrics along three dimensions -- fluency, correctness, and citation quality -- and demonstrate their strong correlation with human judgements. Our experiments with state-of-the-art LLMs and novel prompting strategies show that current systems have considerable room for improvements -- for example, on the ELI5 dataset, even the best model has 49% of its generations lacking complete citation support. Our extensive analyses further highlight promising future directions, including developing better retrievers, advancing long-context LLMs, and improving the ability to synthesize information from multiple sources.

The ability of generative large language models (LLMs) to perform in-context learning has given rise to a large body of research into how best to prompt models for various natural language processing tasks. In this paper, we focus on machine translation (MT), a task that has been shown to benefit from in-context translation examples. However no systematic studies have been published on how best to select examples, and mixed results have been reported on the usefulness of similarity-based selection over random selection. We provide a study covering multiple LLMs and multiple in-context example retrieval strategies, comparing multilingual sentence embeddings. We cover several language directions, representing different levels of language resourcedness (English into French, German, Swahili and Wolof). Contrarily to previously published results, we find that sentence embedding similarity can improve MT, especially for low-resource language directions, and discuss the balance between selection pool diversity and quality. We also highlight potential problems with the evaluation of LLM-based MT and suggest a more appropriate evaluation protocol, adapting the COMET metric to the evaluation of LLMs. Code and outputs are freely available at https://github.com/ArmelRandy/ICL-MT.

Recent studies report that autoregressive language models can successfully solve many NLP tasks via zero- and few-shot learning paradigms, which opens up new possibilities for using the pre-trained language models. This paper introduces two autoregressive GPT-like models with 1.3 billion and 13 billion parameters trained on 60 languages from 25 language families using Wikipedia and Colossal Clean Crawled Corpus. We reproduce the GPT-3 architecture using GPT-2 sources and the sparse attention mechanism; Deepspeed and Megatron frameworks allow us to parallelize the training and inference steps effectively. The resulting models show performance on par with the recently released XGLM models by Facebook, covering more languages and enhancing NLP possibilities for low resource languages of CIS countries and Russian small nations. We detail the motivation for the choices of the architecture design, thoroughly describe the data preparation pipeline, and train five small versions of the model to choose the most optimal multilingual tokenization strategy. We measure the model perplexity in all covered languages and evaluate it on the wide spectre of multilingual tasks, including classification, generative, sequence labeling and knowledge probing. The models were evaluated with the zero-shot and few-shot methods. Furthermore, we compared the classification tasks with the state-of-the-art multilingual model XGLM. source code and the mGPT XL model are publicly released.

Large language models (LLMs) have been recently leveraged as training data generators for various natural language processing (NLP) tasks. While previous research has explored different approaches to training models using generated data, they generally rely on simple class-conditional prompts, which may limit the diversity of the generated data and inherit systematic biases of LLM. Thus, we investigate training data generation with diversely attributed prompts (e.g., specifying attributes like length and style), which have the potential to yield diverse and attributed generated data. Our investigation focuses on datasets with high cardinality and diverse domains, wherein we demonstrate that attributed prompts outperform simple class-conditional prompts in terms of the resulting model's performance. Additionally, we present a comprehensive empirical study on data generation encompassing vital aspects like bias, diversity, and efficiency, and highlight three key observations: firstly, synthetic datasets generated by simple prompts exhibit significant biases, such as regional bias; secondly, attribute diversity plays a pivotal role in enhancing model performance; lastly, attributed prompts achieve the performance of simple class-conditional prompts while utilizing only 5\% of the querying cost of ChatGPT associated with the latter. We release the generated dataset and used prompts to facilitate future research. The data and code will be available on https://github.com/yueyu1030/AttrPrompt.

Current literature, aiming to surpass the "Chain-of-Thought" approach, often resorts to an external modus operandi involving halting, modifying, and then resuming the generation process to boost Large Language Models' (LLMs) reasoning capacities. This mode escalates the number of query requests, leading to increased costs, memory, and computational overheads. Addressing this, we propose the Algorithm of Thoughts -- a novel strategy that propels LLMs through algorithmic reasoning pathways, pioneering a new mode of in-context learning. By employing algorithmic examples, we exploit the innate recurrence dynamics of LLMs, expanding their idea exploration with merely one or a few queries. Our technique outperforms earlier single-query methods and stands on par with a recent multi-query strategy that employs an extensive tree search algorithm. Intriguingly, our results suggest that instructing an LLM using an algorithm can lead to performance surpassing that of the algorithm itself, hinting at LLM's inherent ability to weave its intuition into optimized searches. We probe into the underpinnings of our method's efficacy and its nuances in application.

Large Language Models (LLMs) demonstrate impressive performance in diverse applications, yet they face significant drawbacks, including high inference latency, expensive training cost, and generation of hallucination. Collaborative decoding between large and small language models (SLMs) offers a novel approach to address these challenges. Inspired by dual-process cognitive theory, we integrate these methods into a unified framework termed Fast and Slow Generating (FS-GEN). This paper explores several techniques within the FS-GEN framework, including speculative decoding, contrastive decoding, and emulator or proxy fine-tuning. We provide a comprehensive analysis of these methodologies, offering insights into their similarities and differences under this framework. Our study delves into the differential knowledge capabilities of LLMs versus SLMs through the FS-GEN lens, revealing that fewer than 20% of collaborative interactions are required across various methods. These interactions adhere to a scaling law relative to the parameter ratios, thereby facilitating predictable collaboration. Furthermore, we investigate the specific positions where collaboration is most effective from an uncertainty perspective, yielding novel insights that could refine FS-GEN methods. Our findings reveal that the essential difference between models of different sizes lies in the uncertainty of the next token prediction, where interventions by larger models are most needed to assist the smaller ones. Code for Reproduction: https://github.com/TsinghuaC3I/FS-GEN

Pretrained using large amount of data, autoregressive language models are able to generate high quality sequences. However, these models do not perform well under hard lexical constraints as they lack fine control of content generation process. Progressive insertion-based transformers can overcome the above limitation and efficiently generate a sequence in parallel given some input tokens as constraint. These transformers however may fail to support hard lexical constraints as their generation process is more likely to terminate prematurely. The paper analyses such early termination problems and proposes the Entity-constrained insertion transformer (ENCONTER), a new insertion transformer that addresses the above pitfall without compromising much generation efficiency. We introduce a new training strategy that considers predefined hard lexical constraints (e.g., entities to be included in the generated sequence). Our experiments show that ENCONTER outperforms other baseline models in several performance metrics rendering it more suitable in practical applications. Our code is available at https://github.com/LARC-CMU-SMU/Enconter

This paper presents LOLA, a massively multilingual large language model trained on more than 160 languages using a sparse Mixture-of-Experts Transformer architecture. Our architectural and implementation choices address the challenge of harnessing linguistic diversity while maintaining efficiency and avoiding the common pitfalls of multilinguality. Our analysis of the evaluation results shows competitive performance in natural language generation and understanding tasks. Additionally, we demonstrate how the learned expert-routing mechanism exploits implicit phylogenetic linguistic patterns to potentially alleviate the curse of multilinguality. We provide an in-depth look at the training process, an analysis of the datasets, and a balanced exploration of the model's strengths and limitations. As an open-source model, LOLA promotes reproducibility and serves as a robust foundation for future research. Our findings enable the development of compute-efficient multilingual models with strong, scalable performance across languages.

Large Language Models (LLMs) rely on instruction samples for alignment, but creating these datasets poses challenges, particularly in expert-dependent tasks like coding, which can be cost-prohibitive. One approach to mitigate these challenges is synthesizing data using another LLM. In this paper, we introduce a scalable method for generating synthetic instructions to enhance the code generation capability of LLMs. The proposed algorithm, Genetic-Instruct, mimics evolutionary processes, utilizing self-instruction to create numerous synthetic samples from a limited number of seeds. Genetic-Instruct is designed for efficient scaling of the generation process. Fine-tuning multiple coding LLMs with the synthetic samples demonstrates a significant improvement in their code generation accuracy compared to the baselines.

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional finetuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. We release the ProGen2 models and code at https://github.com/salesforce/progen.

Large language models (LLMs) have emerged as pivotal contributors in contemporary natural language processing and are increasingly being applied across a diverse range of industries. However, these large-scale probabilistic statistical models cannot currently ensure the requisite quality in professional content generation. These models often produce hallucinated text, compromising their practical utility in professional contexts. To assess the authentic reliability of LLMs in text generation, numerous initiatives have developed benchmark evaluations for hallucination phenomena. Nevertheless, these benchmarks frequently utilize constrained generation techniques due to cost and temporal constraints. These techniques encompass the use of directed hallucination induction and strategies that deliberately alter authentic text to produce hallucinations. These approaches are not congruent with the unrestricted text generation demanded by real-world applications. Furthermore, a well-established Chinese-language dataset dedicated to the evaluation of hallucinations in text generation is presently lacking. Consequently, we have developed an Unconstrained Hallucination Generation Evaluation (UHGEval) benchmark, designed to compile outputs produced with minimal restrictions by LLMs. Concurrently, we have established a comprehensive benchmark evaluation framework to aid subsequent researchers in undertaking scalable and reproducible experiments. We have also executed extensive experiments, evaluating prominent Chinese language models and the GPT series models to derive professional performance insights regarding hallucination challenges.

Given an input sequence (or prefix), modern language models often assign high probabilities to output sequences that are repetitive, incoherent, or irrelevant to the prefix; as such, model-generated text also contains such artifacts. To address these issues we present RankGen, a 1.2B parameter encoder model for English that scores model generations given a prefix. RankGen can be flexibly incorporated as a scoring function in beam search and used to decode from any pretrained language model. We train RankGen using large-scale contrastive learning to map a prefix close to the ground-truth sequence that follows it and far away from two types of negatives: (1) random sequences from the same document as the prefix, and (2) sequences generated from a large language model conditioned on the prefix. Experiments across four different language models (345M-11B parameters) and two domains show that RankGen significantly outperforms decoding algorithms like nucleus, top-k, and typical sampling, as well as contrastive decoding and search, on both automatic metrics (85.0 vs 77.3 MAUVE over nucleus) as well as human evaluations with English writers (74.5% human preference over nucleus sampling). Analysis reveals that RankGen outputs are more relevant to the prefix and improve continuity and coherence compared to baselines. We release our model checkpoints, code, and human preference data with explanations to facilitate future research.

Large Language Models (LLMs) have demonstrated remarkable capabilities in important tasks such as natural language understanding, language generation, and complex reasoning and have the potential to make a substantial impact on our society. Such capabilities, however, come with the considerable resources they demand, highlighting the strong need to develop effective techniques for addressing their efficiency challenges. In this survey, we provide a systematic and comprehensive review of efficient LLMs research. We organize the literature in a taxonomy consisting of three main categories, covering distinct yet interconnected efficient LLMs topics from model-centric, data-centric, and framework-centric perspective, respectively. We have also created a GitHub repository where we compile the papers featured in this survey at https://github.com/AIoT-MLSys-Lab/EfficientLLMs, and will actively maintain this repository and incorporate new research as it emerges. We hope our survey can serve as a valuable resource to help researchers and practitioners gain a systematic understanding of the research developments in efficient LLMs and inspire them to contribute to this important and exciting field.

The ability of large language models (LLMs) to perform zero-shot classification makes them viable solutions for data annotation in rapidly evolving domains where quality labeled data is often scarce and costly to obtain. However, the large-scale deployment of LLMs can be prohibitively expensive. This paper introduces an LLM chain ensemble methodology that aligns multiple LLMs in a sequence, routing data subsets to subsequent models based on classification uncertainty. This approach leverages the strengths of individual LLMs within a broader system, allowing each model to handle data points where it exhibits the highest confidence, while forwarding more complex cases to potentially more robust models. Our results show that the chain ensemble method often exceeds the performance of the best individual model in the chain and achieves substantial cost savings, making LLM chain ensembles a practical and efficient solution for large-scale data annotation challenges.

This paper discusses the methods that we used for our submissions to the WMT 2023 Terminology Shared Task for German-to-English (DE-EN), English-to-Czech (EN-CS), and Chinese-to-English (ZH-EN) language pairs. The task aims to advance machine translation (MT) by challenging participants to develop systems that accurately translate technical terms, ultimately enhancing communication and understanding in specialised domains. To this end, we conduct experiments that utilise large language models (LLMs) for two purposes: generating synthetic bilingual terminology-based data, and post-editing translations generated by an MT model through incorporating pre-approved terms. Our system employs a four-step process: (i) using an LLM to generate bilingual synthetic data based on the provided terminology, (ii) fine-tuning a generic encoder-decoder MT model, with a mix of the terminology-based synthetic data generated in the first step and a randomly sampled portion of the original generic training data, (iii) generating translations with the fine-tuned MT model, and (iv) finally, leveraging an LLM for terminology-constrained automatic post-editing of the translations that do not include the required terms. The results demonstrate the effectiveness of our proposed approach in improving the integration of pre-approved terms into translations. The number of terms incorporated into the translations of the blind dataset increases from an average of 36.67% with the generic model to an average of 72.88% by the end of the process. In other words, successful utilisation of terms nearly doubles across the three language pairs.

It has always been an important yet challenging problem to control language models to avoid generating texts with undesirable attributes, such as toxic language and unnatural repetition. We introduce Click for controllable text generation, which needs no modification to the model architecture and facilitates out-of-the-box use of trained models. It employs a contrastive loss on sequence likelihood, which fundamentally decreases the generation probability of negative samples (i.e., generations with undesirable attributes). It also adopts a novel likelihood ranking-based strategy to construct contrastive samples from model generations. On the tasks of language detoxification, sentiment steering, and repetition reduction, we show that Click outperforms strong baselines of controllable text generation and demonstrate the superiority of Click's sample construction strategy.

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

We investigate the usefulness of generative Large Language Models (LLMs) in generating training data for cross-encoder re-rankers in a novel direction: generating synthetic documents instead of synthetic queries. We introduce a new dataset, ChatGPT-RetrievalQA, and compare the effectiveness of models fine-tuned on LLM-generated and human-generated data. Data generated with generative LLMs can be used to augment training data, especially in domains with smaller amounts of labeled data. We build ChatGPT-RetrievalQA based on an existing dataset, human ChatGPT Comparison Corpus (HC3), consisting of public question collections with human responses and answers from ChatGPT. We fine-tune a range of cross-encoder re-rankers on either human-generated or ChatGPT-generated data. Our evaluation on MS MARCO DEV, TREC DL'19, and TREC DL'20 demonstrates that cross-encoder re-ranking models trained on ChatGPT responses are statistically significantly more effective zero-shot re-rankers than those trained on human responses. In a supervised setting, the human-trained re-rankers outperform the LLM-trained re-rankers. Our novel findings suggest that generative LLMs have high potential in generating training data for neural retrieval models. Further work is needed to determine the effect of factually wrong information in the generated responses and test our findings' generalizability with open-source LLMs. We release our data, code, and cross-encoders checkpoints for future work.

In recent years, large language models (LLMs) have achieved remarkable success in natural language processing (NLP). LLMs require an extreme amount of parameters to attain high performance. As models grow into the trillion-parameter range, computational and memory costs increase significantly. This makes it difficult for many researchers to access the resources needed to train or apply these models. Optimizing LLM performance involves two main approaches: fine-tuning pre-trained models for specific tasks to achieve state-of-the-art performance, and reducing costs or improving training time while maintaining similar performance. This paper presents a systematic literature review (SLR) following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. We reviewed 65 publications out of 983 from 2017 to December 2023, retrieved from 5 databases. The study presents methods to optimize and accelerate LLMs while achieving cutting-edge results without sacrificing accuracy. We begin with an overview of the development of language modeling, followed by a detailed explanation of commonly used frameworks and libraries, and a taxonomy for improving and speeding up LLMs based on three classes: LLM training, LLM inference, and system serving. We then delve into recent optimization and acceleration strategies such as training optimization, hardware optimization, scalability and reliability, accompanied by the taxonomy and categorization of these strategies. Finally, we provide an in-depth comparison of each class and strategy, with two case studies on optimizing model training and enhancing inference efficiency. These case studies showcase practical approaches to address LLM resource limitations while maintaining performance.

While pretrained language models (PLMs) primarily serve as general-purpose text encoders that can be fine-tuned for a wide variety of downstream tasks, recent work has shown that they can also be rewired to produce high-quality word representations (i.e., static word embeddings) and yield good performance in type-level lexical tasks. While existing work primarily focused on the lexical specialization of monolingual PLMs with immense quantities of monolingual constraints, in this work we expose massively multilingual transformers (MMTs, e.g., mBERT or XLM-R) to multilingual lexical knowledge at scale, leveraging BabelNet as the readily available rich source of multilingual and cross-lingual type-level lexical knowledge. Concretely, we use BabelNet's multilingual synsets to create synonym pairs (or synonym-gloss pairs) across 50 languages and then subject the MMTs (mBERT and XLM-R) to a lexical specialization procedure guided by a contrastive objective. We show that such massively multilingual lexical specialization brings substantial gains in two standard cross-lingual lexical tasks, bilingual lexicon induction and cross-lingual word similarity, as well as in cross-lingual sentence retrieval. Crucially, we observe gains for languages unseen in specialization, indicating that multilingual lexical specialization enables generalization to languages with no lexical constraints. In a series of subsequent controlled experiments, we show that the number of specialization constraints plays a much greater role than the set of languages from which they originate.

The recent surge in research focused on generating synthetic data from large language models (LLMs), especially for scenarios with limited data availability, marks a notable shift in Generative Artificial Intelligence (AI). Their ability to perform comparably to real-world data positions this approach as a compelling solution to low-resource challenges. This paper delves into advanced technologies that leverage these gigantic LLMs for the generation of task-specific training data. We outline methodologies, evaluation techniques, and practical applications, discuss the current limitations, and suggest potential pathways for future research.

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Existing research on instruction following largely focuses on tasks with simple instructions and short responses. In this work, we explore multi-constraint instruction following for generating long-form text. We create Suri, a dataset with 20K human-written long-form texts paired with LLM-generated backtranslated instructions that contain multiple complex constraints. Because of prohibitive challenges associated with collecting human preference judgments on long-form texts, preference-tuning algorithms such as DPO are infeasible in our setting; thus, we propose Instructional ORPO (I-ORPO), an alignment method based on the ORPO algorithm. Instead of receiving negative feedback from dispreferred responses, I-ORPO obtains negative feedback from synthetically corrupted instructions generated by an LLM. Using Suri, we perform supervised and I-ORPO fine-tuning on Mistral-7b-Instruct-v0.2. The resulting models, Suri-SFT and Suri-I-ORPO, generate significantly longer texts (~5K tokens) than base models without significant quality deterioration. Our human evaluation shows that while both SFT and I-ORPO models satisfy most constraints, Suri-I-ORPO generations are generally preferred for their coherent and informative incorporation of the constraints. We release our code at https://github.com/chtmp223/suri.

Large Language Models (LLMs) have gained significant attention due to their high performance on a wide range of natural language tasks since the release of ChatGPT. The LLMs learn to understand and generate language by training billions of model parameters on vast volumes of text data. Despite being a relatively new field, LLM research is rapidly advancing in various directions. In this paper, we present an overview of LLM families, including LLaMA, PaLM, GPT, and MoE, and the methods developed to create and enhance LLMs for official European Union (EU) languages. We provide a comprehensive summary of common monolingual and multilingual datasets used for pretraining large language models.

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.

Despite their outstanding capabilities, large language models (LLMs) are prone to hallucination and producing factually incorrect information. This challenge has spurred efforts in attributed text generation, which prompts LLMs to generate content with supporting evidence. In this paper, we propose a novel framework, called Think&Cite, and formulate attributed text generation as a multi-step reasoning problem integrated with search. Specifically, we propose Self-Guided Monte Carlo Tree Search (SG-MCTS), which capitalizes on the self-reflection capability of LLMs to reflect on the intermediate states of MCTS for guiding the tree expansion process. To provide reliable and comprehensive feedback, we introduce Progress Reward Models to measure the progress of tree search from the root to the current state from two aspects, i.e., generation and attribution progress. We conduct extensive experiments on three datasets and the results show that our approach significantly outperforms baseline approaches.

Constituency parsing is a fundamental yet unsolved natural language processing task. In this paper, we explore the potential of recent large language models (LLMs) that have exhibited remarkable performance across various domains and tasks to tackle this task. We employ three linearization strategies to transform output trees into symbol sequences, such that LLMs can solve constituency parsing by generating linearized trees. We conduct experiments using a diverse range of LLMs, including ChatGPT, GPT-4, OPT, LLaMA, and Alpaca, comparing their performance against the state-of-the-art constituency parsers. Our experiments encompass zero-shot, few-shot, and full-training learning settings, and we evaluate the models on one in-domain and five out-of-domain test datasets. Our findings reveal insights into LLMs' performance, generalization abilities, and challenges in constituency parsing.

The pace of evolution of Large Language Models (LLMs) necessitates new approaches for rigorous and comprehensive evaluation. Traditional human annotation is increasingly impracticable due to the complexities and costs involved in generating high-quality, challenging problems. In this work, we introduce CHASE, a unified framework to synthetically generate challenging problems using LLMs without human involvement. For a given task, our approach builds a hard problem in a bottom-up manner from simpler components. Moreover, our framework decomposes the generation process into independently verifiable sub-tasks, thereby ensuring a high level of quality and correctness. We implement CHASE to create evaluation benchmarks across three diverse domains: (1) document-based question answering, (2) repository-level code completion, and (3) math reasoning. The performance of state-of-the-art LLMs on these synthetic benchmarks lies in the range of 40-60% accuracy, thereby demonstrating the effectiveness of our framework at generating challenging problems. We publicly release our benchmarks and code.

Large Language Models (LLMs) have recently demonstrated remarkable capabilities in natural language processing tasks and beyond. This success of LLMs has led to a large influx of research contributions in this direction. These works encompass diverse topics such as architectural innovations of the underlying neural networks, context length improvements, model alignment, training datasets, benchmarking, efficiency and more. With the rapid development of techniques and regular breakthroughs in LLM research, it has become considerably challenging to perceive the bigger picture of the advances in this direction. Considering the rapidly emerging plethora of literature on LLMs, it is imperative that the research community is able to benefit from a concise yet comprehensive overview of the recent developments in this field. This article provides that overview to the research community. It not only focuses on a systematic treatment of the existing literature on a broad range of LLM related concept, but also pays special attention to providing comprehensive summaries with extensive details about the individual existing models, datasets and major insights. We also pay heed to aligning our overview with the emerging outlook of this research direction by accounting for the other recently materializing reviews of the broader research direction of LLMs. Our self-contained comprehensive overview of LLMs discusses relevant background concepts along with covering the advanced topics at the frontier of this research direction. This review article is intended to not only provide a systematic survey, but also a quick comprehensive reference for the researchers and practitioners to draw insights from extensive informative summaries of the existing works to advance the LLM research direction.

The genome sequence contains the blueprint for governing cellular processes. While the availability of genomes has vastly increased over the last decades, experimental annotation of the various functional, non-coding and regulatory elements encoded in the DNA sequence remains both expensive and challenging. This has sparked interest in unsupervised language modeling of genomic DNA, a paradigm that has seen great success for protein sequence data. Although various DNA language models have been proposed, evaluation tasks often differ between individual works, and might not fully recapitulate the fundamental challenges of genome annotation, including the length, scale and sparsity of the data. In this study, we introduce BEND, a Benchmark for DNA language models, featuring a collection of realistic and biologically meaningful downstream tasks defined on the human genome. We find that embeddings from current DNA LMs can approach performance of expert methods on some tasks, but only capture limited information about long-range features. BEND is available at https://github.com/frederikkemarin/BEND.

Large language models (LLMs) have revolutionized Natural Language Processing (NLP) by minimizing the need for complex feature engineering. However, the application of LLMs in specialized domains like biopharmaceuticals and chemistry remains largely unexplored. These fields are characterized by intricate terminologies, specialized knowledge, and a high demand for precision areas where general purpose LLMs often fall short. In this study, we introduce PharmaGPT, a suite of domain specilized LLMs with 13 billion and 70 billion parameters, specifically trained on a comprehensive corpus tailored to the Bio-Pharmaceutical and Chemical domains. Our evaluation shows that PharmaGPT surpasses existing general models on specific-domain benchmarks such as NAPLEX, demonstrating its exceptional capability in domain-specific tasks. Remarkably, this performance is achieved with a model that has only a fraction, sometimes just one-tenth-of the parameters of general-purpose large models. This advancement establishes a new benchmark for LLMs in the bio-pharmaceutical and chemical fields, addressing the existing gap in specialized language modeling. It also suggests a promising path for enhanced research and development, paving the way for more precise and effective NLP applications in these areas.

Large language models (LLMs) are increasingly adopted for knowledge-intensive tasks and contexts. Existing approaches improve the knowledge capabilities of general-purpose LLMs through retrieval or generated knowledge prompting, but they fall short of reflecting two key properties of knowledge-rich models: knowledge should be modular, ever-growing, sourced from diverse domains; knowledge acquisition and production should be a collaborative process, where diverse stakeholders contribute new information. To this end, we propose CooK, a novel framework to empower general-purpose large language models with modular and collaboratively sourced knowledge. We first introduce specialized language models, autoregressive models trained on corpora from a wide range of domains and sources. These specialized LMs serve as parametric knowledge repositories that are later prompted to generate background knowledge for general-purpose LLMs. We then propose three knowledge filters to dynamically select and retain information in generated documents by controlling for relevance, brevity, and factuality. Finally, we propose bottom-up and top-down knowledge integration approaches to augment general-purpose LLMs with the curated (relevant, factual) knowledge from community-driven specialized LMs that enable multi-domain knowledge synthesis and on-demand knowledge requests. Through extensive experiments, we demonstrate that CooK achieves state-of-the-art performance on six benchmark datasets. Our results highlight the potential of enriching general-purpose LLMs with evolving and modular knowledge -- relevant knowledge that can be continuously updated through the collective efforts of the research community.

Large Language Models (LLMs) have demonstrated remarkable generation capabilities but often struggle to access up-to-date information, which can lead to hallucinations. Retrieval-Augmented Generation (RAG) addresses this issue by incorporating knowledge from external databases, enabling more accurate and relevant responses. Due to the context window constraints of LLMs, it is impractical to input the entire external database context directly into the model. Instead, only the most relevant information, referred to as chunks, is selectively retrieved. However, current RAG research faces three key challenges. First, existing solutions often select each chunk independently, overlooking potential correlations among them. Second, in practice the utility of chunks is non-monotonic, meaning that adding more chunks can decrease overall utility. Traditional methods emphasize maximizing the number of included chunks, which can inadvertently compromise performance. Third, each type of user query possesses unique characteristics that require tailored handling, an aspect that current approaches do not fully consider. To overcome these challenges, we propose a cost constrained retrieval optimization system CORAG for retrieval-augmented generation. We employ a Monte Carlo Tree Search (MCTS) based policy framework to find optimal chunk combinations sequentially, allowing for a comprehensive consideration of correlations among chunks. Additionally, rather than viewing budget exhaustion as a termination condition, we integrate budget constraints into the optimization of chunk combinations, effectively addressing the non-monotonicity of chunk utility.

Large language models (LLMs) have become ubiquitous in practice and are widely used for generation tasks such as translation, summarization and instruction following. However, their enormous size and reliance on autoregressive decoding increase deployment costs and complicate their use in latency-critical applications. In this work, we propose a hybrid approach that combines language models of different sizes to increase the efficiency of autoregressive decoding while maintaining high performance. Our method utilizes a pretrained frozen LLM that encodes all prompt tokens once in parallel, and uses the resulting representations to condition and guide a small language model (SLM), which then generates the response more efficiently. We investigate the combination of encoder-decoder LLMs with both encoder-decoder and decoder-only SLMs from different model families and only require fine-tuning of the SLM. Experiments with various benchmarks show substantial speedups of up to 4times, with minor performance penalties of 1-2% for translation and summarization tasks compared to the LLM.

As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule. Existing template-free approaches only consider the graph structures of the target molecule, which often cannot generalize well to rare reaction types and large molecules. Here, we propose T-Rex, a text-assisted retrosynthesis prediction approach that exploits pre-trained text language models, such as ChatGPT, to assist the generation of reactants. T-Rex first exploits ChatGPT to generate a description for the target molecule and rank candidate reaction centers based both the description and the molecular graph. It then re-ranks these candidates by querying the descriptions for each reactants and examines which group of reactants can best synthesize the target molecule. We observed that T-Rex substantially outperformed graph-based state-of-the-art approaches on two datasets, indicating the effectiveness of considering text information. We further found that T-Rex outperformed the variant that only use ChatGPT-based description without the re-ranking step, demonstrate how our framework outperformed a straightforward integration of ChatGPT and graph information. Collectively, we show that text generated by pre-trained language models can substantially improve retrosynthesis prediction, opening up new avenues for exploiting ChatGPT to advance computational chemistry. And the codes can be found at https://github.com/lauyikfung/T-Rex.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

In everyday life, humans often plan their actions by following step-by-step instructions in the form of goal-oriented scripts. Previous work has exploited language models (LMs) to plan for abstract goals of stereotypical activities (e.g., "make a cake"), but leaves more specific goals with multi-facet constraints understudied (e.g., "make a cake for diabetics"). In this paper, we define the task of constrained language planning for the first time. We propose an overgenerate-then-filter approach to improve large language models (LLMs) on this task, and use it to distill a novel constrained language planning dataset, CoScript, which consists of 55,000 scripts. Empirical results demonstrate that our method significantly improves the constrained language planning ability of LLMs, especially on constraint faithfulness. Furthermore, CoScript is demonstrated to be quite effective in endowing smaller LMs with constrained language planning ability.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Alignment is the most critical step in building large language models (LLMs) that meet human needs. With the rapid development of LLMs gradually surpassing human capabilities, traditional alignment methods based on human-annotation are increasingly unable to meet the scalability demands. Therefore, there is an urgent need to explore new sources of automated alignment signals and technical approaches. In this paper, we systematically review the recently emerging methods of automated alignment, attempting to explore how to achieve effective, scalable, automated alignment once the capabilities of LLMs exceed those of humans. Specifically, we categorize existing automated alignment methods into 4 major categories based on the sources of alignment signals and discuss the current status and potential development of each category. Additionally, we explore the underlying mechanisms that enable automated alignment and discuss the essential factors that make automated alignment technologies feasible and effective from the fundamental role of alignment.

Large Language Models (LLMs) excel in various tasks, but they rely on carefully crafted prompts that often demand substantial human effort. To automate this process, in this paper, we propose a novel framework for discrete prompt optimization, called EvoPrompt, which borrows the idea of evolutionary algorithms (EAs) as they exhibit good performance and fast convergence. To enable EAs to work on discrete prompts, which are natural language expressions that need to be coherent and human-readable, we connect LLMs with EAs. This approach allows us to simultaneously leverage the powerful language processing capabilities of LLMs and the efficient optimization performance of EAs. Specifically, abstaining from any gradients or parameters, EvoPrompt starts from a population of prompts and iteratively generates new prompts with LLMs based on the evolutionary operators, improving the population based on the development set. We optimize prompts for both closed- and open-source LLMs including GPT-3.5 and Alpaca, on 9 datasets spanning language understanding and generation tasks. EvoPrompt significantly outperforms human-engineered prompts and existing methods for automatic prompt generation by up to 25% and 14% respectively. Furthermore, EvoPrompt demonstrates that connecting LLMs with EAs creates synergies, which could inspire further research on the combination of LLMs and conventional algorithms.

Large language models (LLM) have recently emerged as a powerful tool for a variety of natural language processing tasks, bringing a new surge of combining LLM with recommendation systems, termed as LLM-based RS. Current approaches generally fall into two main paradigms, the ID direct usage paradigm and the ID translation paradigm, noting their core weakness stems from lacking recommendation knowledge and uniqueness. To address this limitation, we propose a new paradigm, ID representation, which incorporates pre-trained ID embeddings into LLMs in a complementary manner. In this work, we present RA-Rec, an efficient ID representation alignment framework for LLM-based recommendation, which is compatible with multiple ID-based methods and LLM architectures. Specifically, we treat ID embeddings as soft prompts and design an innovative alignment module and an efficient tuning method with tailored data construction for alignment. Extensive experiments demonstrate RA-Rec substantially outperforms current state-of-the-art methods, achieving up to 3.0% absolute HitRate@100 improvements while utilizing less than 10x training data.

Recent breakthroughs in large language modeling have facilitated rigorous exploration of their application in diverse tasks related to tabular data modeling, such as prediction, tabular data synthesis, question answering, and table understanding. Each task presents unique challenges and opportunities. However, there is currently a lack of comprehensive review that summarizes and compares the key techniques, metrics, datasets, models, and optimization approaches in this research domain. This survey aims to address this gap by consolidating recent progress in these areas, offering a thorough survey and taxonomy of the datasets, metrics, and methodologies utilized. It identifies strengths, limitations, unexplored territories, and gaps in the existing literature, while providing some insights for future research directions in this vital and rapidly evolving field. It also provides relevant code and datasets references. Through this comprehensive review, we hope to provide interested readers with pertinent references and insightful perspectives, empowering them with the necessary tools and knowledge to effectively navigate and address the prevailing challenges in the field.

Moderate-sized large language models (LLMs) -- those with 7B or 13B parameters -- exhibit promising machine translation (MT) performance. However, even the top-performing 13B LLM-based translation models, like ALMA, does not match the performance of state-of-the-art conventional encoder-decoder translation models or larger-scale LLMs such as GPT-4. In this study, we bridge this performance gap. We first assess the shortcomings of supervised fine-tuning for LLMs in the MT task, emphasizing the quality issues present in the reference data, despite being human-generated. Then, in contrast to SFT which mimics reference translations, we introduce Contrastive Preference Optimization (CPO), a novel approach that trains models to avoid generating adequate but not perfect translations. Applying CPO to ALMA models with only 22K parallel sentences and 12M parameters yields significant improvements. The resulting model, called ALMA-R, can match or exceed the performance of the WMT competition winners and GPT-4 on WMT'21, WMT'22 and WMT'23 test datasets.

Information extraction (IE) aims to extract structural knowledge (such as entities, relations, and events) from plain natural language texts. Recently, generative Large Language Models (LLMs) have demonstrated remarkable capabilities in text understanding and generation, allowing for generalization across various domains and tasks. As a result, numerous works have been proposed to harness abilities of LLMs and offer viable solutions for IE tasks based on a generative paradigm. To conduct a comprehensive systematic review and exploration of LLM efforts for IE tasks, in this study, we survey the most recent advancements in this field. We first present an extensive overview by categorizing these works in terms of various IE subtasks and learning paradigms, then we empirically analyze the most advanced methods and discover the emerging trend of IE tasks with LLMs. Based on thorough review conducted, we identify several insights in technique and promising research directions that deserve further exploration in future studies. We maintain a public repository and consistently update related resources at: https://github.com/quqxui/Awesome-LLM4IE-Papers.

General-purpose Large Language Models (LLMs) like GPT-4 have achieved remarkable advancements in machine translation (MT) by leveraging extensive web content. On the other hand, translation-specific LLMs are built by pre-training on domain-specific monolingual corpora and fine-tuning with human-annotated translation data. Despite the superior performance, these methods either demand an unprecedented scale of computing and data or substantial human editing and annotation efforts. In this paper, we develop MT-Ladder, a novel model-agnostic and cost-effective tool to refine the performance of general LLMs for MT. MT-Ladder is trained on pseudo-refinement triplets which can be easily obtained from existing LLMs without additional human cost. During training, we propose a hierarchical fine-tuning strategy with an easy-to-hard schema, improving MT-Ladder's refining performance progressively. The trained MT-Ladder can be seamlessly integrated with any general-purpose LLMs to boost their translation performance. By utilizing Gemma-2B/7B as the backbone, MT-Ladder-2B can elevate raw translations to the level of top-tier open-source models (e.g., refining BigTranslate-13B with +6.91 BLEU and +3.52 COMET for XX-En), and MT-Ladder-7B can further enhance model performance to be on par with the state-of-the-art GPT-4. Extensive ablation and analysis corroborate the effectiveness of MT-Ladder in diverse settings. Our code is available at https://github.com/fzp0424/Ladder

Large Language Models (LLMs) are being adopted at an unprecedented rate, yet still face challenges in knowledge-intensive domains like biomedicine. Solutions such as pre-training and domain-specific fine-tuning add substantial computational overhead, requiring further domain expertise. Here, we introduce a token-optimized and robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo and GPT-4, to generate meaningful biomedical text rooted in established knowledge. Compared to the existing RAG technique for Knowledge Graphs, the proposed method utilizes minimal graph schema for context extraction and uses embedding methods for context pruning. This optimization in context extraction results in more than 50% reduction in token consumption without compromising the accuracy, making a cost-effective and robust RAG implementation on proprietary LLMs. KG-RAG consistently enhanced the performance of LLMs across diverse biomedical prompts by generating responses rooted in established knowledge, accompanied by accurate provenance and statistical evidence (if available) to substantiate the claims. Further benchmarking on human curated datasets, such as biomedical true/false and multiple-choice questions (MCQ), showed a remarkable 71% boost in the performance of the Llama-2 model on the challenging MCQ dataset, demonstrating the framework's capacity to empower open-source models with fewer parameters for domain specific questions. Furthermore, KG-RAG enhanced the performance of proprietary GPT models, such as GPT-3.5 and GPT-4. In summary, the proposed framework combines explicit and implicit knowledge of KG and LLM in a token optimized fashion, thus enhancing the adaptability of general-purpose LLMs to tackle domain-specific questions in a cost-effective fashion.

Large Language Models have proven highly successful at modelling a variety of tasks. However, this comes at a steep computational cost that hinders wider industrial uptake. In this pa005 per, we present MWT: a Multi-Word Tokenizer that goes beyond word boundaries by representing frequent multi-word expressions as single tokens. MWTs produce a more compact and efficient tokenization that yields two benefits: (1) Increase in performance due to a greater coverage of input data given a fixed sequence length and budget; (2) Faster and lighter inference due to the ability to reduce the sequence length with negligible drops in performance. Our results show that MWT is more robust across shorter sequence lengths, thus allowing for major speedups via early sequence truncation.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

Large language models (LLMs) encode a diverse range of linguistic features within their latent representations, which can be harnessed to steer their output toward specific target characteristics. In this paper, we modify the internal structure of LLMs by training sparse autoencoders to learn a sparse representation of the query embedding, allowing precise control over the model's attention distribution. We demonstrate that manipulating this sparse representation effectively transforms the output toward different stylistic and cognitive targets. Specifically, in an educational setting, we show that the cognitive complexity of LLM-generated feedback can be systematically adjusted by modifying the encoded query representation at a specific layer. To achieve this, we guide the learned sparse embedding toward the representation of samples from the desired cognitive complexity level, using gradient-based optimization in the latent space.

Large Language Models (LLMs) have revolutionized the field of natural language processing, but they fall short in comprehending biological sequences such as proteins. To address this challenge, we propose InstructProtein, an innovative LLM that possesses bidirectional generation capabilities in both human and protein languages: (i) taking a protein sequence as input to predict its textual function description and (ii) using natural language to prompt protein sequence generation. To achieve this, we first pre-train an LLM on both protein and natural language corpora, enabling it to comprehend individual languages. Then supervised instruction tuning is employed to facilitate the alignment of these two distinct languages. Herein, we introduce a knowledge graph-based instruction generation framework to construct a high-quality instruction dataset, addressing annotation imbalance and instruction deficits in existing protein-text corpus. In particular, the instructions inherit the structural relations between proteins and function annotations in knowledge graphs, which empowers our model to engage in the causal modeling of protein functions, akin to the chain-of-thought processes in natural languages. Extensive experiments on bidirectional protein-text generation tasks show that InstructProtein outperforms state-of-the-art LLMs by large margins. Moreover, InstructProtein serves as a pioneering step towards text-based protein function prediction and sequence design, effectively bridging the gap between protein and human language understanding.

The dominant text generation models compose the output by sequentially selecting words from a fixed vocabulary. In this paper, we formulate text generation as progressively copying text segments (e.g., words or phrases) from an existing text collection. We compute the contextualized representations of meaningful text segments and index them using efficient vector search toolkits. The task of text generation is then decomposed into a series of copy-and-paste operations: at each time step, we seek suitable text spans from the text collection rather than selecting from a standalone vocabulary. Experiments on the standard language modeling benchmark (WikiText-103) show that our approach achieves better generation quality according to both automatic and human evaluations. Besides, its inference efficiency is comparable to token-level autoregressive models thanks to the reduction of decoding steps. We also show that our approach allows for effective domain adaptation by simply switching to domain-specific text collection without extra training. Finally, we observe that our approach attains additional performance gains by simply scaling up to larger text collections, again without further training.Our source codes are publicly available at \url{https://github.com/gmftbyGMFTBY/Copyisallyouneed.}

Large Language Models (LLMs) have sparked significant interest in their generative capabilities, leading to the development of various commercial applications. The high cost of using the models drives application builders to maximize the value of generation under a limited inference budget. This paper presents a study of optimizing inference hyperparameters such as the number of responses, temperature and max tokens, which significantly affects the utility/cost of text generation. We design a framework named EcoOptiGen which leverages economical hyperparameter optimization and cost-based pruning. Experiments with the GPT-3.5/GPT-4 models on a variety of tasks verify its effectiveness. EcoOptiGen is implemented in the `autogen' package of the FLAML library: https://aka.ms/autogen.

Large language models (LLMs) have significantly benefited from training on diverse, high-quality task-specific data, leading to impressive performance across a range of downstream applications. Current methods often rely on human-annotated data or predefined task templates to direct powerful LLMs in synthesizing task-relevant data for effective model training. However, this dependence on manually designed components may constrain the scope of generated data, potentially overlooking critical edge cases or novel scenarios that could challenge the model. In this paper, we present a novel approach, ReverseGen, designed to automatically generate effective training samples that expose the weaknesses of LLMs. Specifically, we introduce a dedicated proposer trained to produce queries that lead target models to generate unsatisfactory responses. These failure-inducing queries are then used to construct training data, helping to address the models' shortcomings and improve overall performance. Our approach is flexible and can be applied to models of various scales (3B, 7B, and 8B). We evaluate ReverseGen on three key applications (safety, honesty, and math), demonstrating that our generated data is both highly effective and diverse. Models fine-tuned with ReverseGen-generated data consistently outperform those trained on human-annotated or general model-generated data, offering a new perspective on data synthesis for task-specific LLM enhancement.

Large language models (LLMs) have demonstrated remarkable performance in diverse tasks using zero-shot and few-shot prompting. Even though their capabilities of data synthesis have been studied well in recent years, the generated data suffers from a lack of diversity, less adherence to the prompt, and potential biases that creep into the data from the generator model. In this work, we tackle the challenge of generating datasets with high diversity, upon which a student model is trained for downstream tasks. Taking the route of decoding-time guidance-based approaches, we propose CorrSynth, which generates data that is more diverse and faithful to the input prompt using a correlated sampling strategy. Further, our method overcomes the complexity drawbacks of some other guidance-based techniques like classifier-based guidance. With extensive experiments, we show the effectiveness of our approach and substantiate our claims. In particular, we perform intrinsic evaluation to show the improvements in diversity. Our experiments show that CorrSynth improves both student metrics and intrinsic metrics upon competitive baselines across four datasets, showing the innate advantage of our method.

Standard language models generate text by selecting tokens from a fixed, finite, and standalone vocabulary. We introduce a novel method that selects context-aware phrases from a collection of supporting documents. One of the most significant challenges for this paradigm shift is determining the training oracles, because a string of text can be segmented in various ways and each segment can be retrieved from numerous possible documents. To address this, we propose to initialize the training oracles using linguistic heuristics and, more importantly, bootstrap the oracles through iterative self-reinforcement. Extensive experiments show that our model not only outperforms standard language models on a variety of knowledge-intensive tasks but also demonstrates improved generation quality in open-ended text generation. For instance, compared to the standard language model counterpart, our model raises the accuracy from 23.47% to 36.27% on OpenbookQA, and improves the MAUVE score from 42.61% to 81.58% in open-ended text generation. Remarkably, our model also achieves the best performance and the lowest latency among several retrieval-augmented baselines. In conclusion, we assert that retrieval is more accurate generation and hope that our work will encourage further research on this new paradigm shift.

Large language models (LLMs) have achieved success in acting as agents, which interact with environments through tools like search engines. However, LLMs are not optimized specifically for tool use during training or alignment, limiting their effectiveness as agents. To resolve this problem, previous work has collected interaction trajectories between GPT-4 and environments, and fine-tuned smaller models with them. As part of this, the standard approach has been to simply discard trajectories that do not finish the task successfully, which, on the one hand, leads to a significant waste of data and resources, and on the other hand, has the potential to limit the possible optimization paths during fine-tuning. In this paper, we contend that large language models can learn from failures through appropriate data cleaning and fine-tuning strategies. We conduct experiments on mathematical reasoning, multi-hop question answering, and strategic question answering tasks. Experimental results demonstrate that compared to solely using positive examples, incorporating negative examples enhances model performance by a large margin.

Existing text simplification or paraphrase datasets mainly focus on sentence-level text generation in a general domain. These datasets are typically developed without using domain knowledge. In this paper, we release a novel dataset, VTechAGP, which is the first academic-to-general-audience text paraphrase dataset consisting of 4,938 document-level these and dissertation academic and general-audience abstract pairs from 8 colleges authored over 25 years. We also propose a novel dynamic soft prompt generative language model, DSPT5. For training, we leverage a contrastive-generative loss function to learn the keyword vectors in the dynamic prompt. For inference, we adopt a crowd-sampling decoding strategy at both semantic and structural levels to further select the best output candidate. We evaluate DSPT5 and various state-of-the-art large language models (LLMs) from multiple perspectives. Results demonstrate that the SOTA LLMs does not provide satisfactory outcomes, while the lightweight DSPT5 can achieve competitive results. To the best of our knowledge, we are the first to build a benchmark dataset and solutions for academic-to-general-audience text paraphrase dataset.

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

The rapid growth of biomedical knowledge has outpaced our ability to efficiently extract insights and generate novel hypotheses. Large language models (LLMs) have emerged as a promising tool to revolutionize knowledge interaction and potentially accelerate biomedical discovery. In this paper, we present a comprehensive evaluation of LLMs as biomedical hypothesis generators. We construct a dataset of background-hypothesis pairs from biomedical literature, carefully partitioned into training, seen, and unseen test sets based on publication date to mitigate data contamination. Using this dataset, we assess the hypothesis generation capabilities of top-tier instructed models in zero-shot, few-shot, and fine-tuning settings. To enhance the exploration of uncertainty, a crucial aspect of scientific discovery, we incorporate tool use and multi-agent interactions in our evaluation framework. Furthermore, we propose four novel metrics grounded in extensive literature review to evaluate the quality of generated hypotheses, considering both LLM-based and human assessments. Our experiments yield two key findings: 1) LLMs can generate novel and validated hypotheses, even when tested on literature unseen during training, and 2) Increasing uncertainty through multi-agent interactions and tool use can facilitate diverse candidate generation and improve zero-shot hypothesis generation performance. However, we also observe that the integration of additional knowledge through few-shot learning and tool use may not always lead to performance gains, highlighting the need for careful consideration of the type and scope of external knowledge incorporated. These findings underscore the potential of LLMs as powerful aids in biomedical hypothesis generation and provide valuable insights to guide further research in this area.

With the development of large language models (LLMs), zero-shot learning has attracted much attention for various NLP tasks. Different from prior works that generate training data with billion-scale natural language generation (NLG) models, we propose a retrieval-enhanced framework to create training data from a general-domain unlabeled corpus. To realize this, we first conduct contrastive pretraining to learn an unsupervised dense retriever for extracting the most relevant documents using class-descriptive verbalizers. We then further propose two simple strategies, namely Verbalizer Augmentation with Demonstrations and Self-consistency Guided Filtering to improve the topic coverage of the dataset while removing noisy examples. Experiments on nine datasets demonstrate that REGEN achieves 4.3% gain over the strongest baselines and saves around 70% of the time compared to baselines using large NLG models. Besides, REGEN can be naturally integrated with recently proposed large language models to boost performance.

This paper presents a comprehensive and practical guide for practitioners and end-users working with Large Language Models (LLMs) in their downstream natural language processing (NLP) tasks. We provide discussions and insights into the usage of LLMs from the perspectives of models, data, and downstream tasks. Firstly, we offer an introduction and brief summary of current GPT- and BERT-style LLMs. Then, we discuss the influence of pre-training data, training data, and test data. Most importantly, we provide a detailed discussion about the use and non-use cases of large language models for various natural language processing tasks, such as knowledge-intensive tasks, traditional natural language understanding tasks, natural language generation tasks, emergent abilities, and considerations for specific tasks.We present various use cases and non-use cases to illustrate the practical applications and limitations of LLMs in real-world scenarios. We also try to understand the importance of data and the specific challenges associated with each NLP task. Furthermore, we explore the impact of spurious biases on LLMs and delve into other essential considerations, such as efficiency, cost, and latency, to ensure a comprehensive understanding of deploying LLMs in practice. This comprehensive guide aims to provide researchers and practitioners with valuable insights and best practices for working with LLMs, thereby enabling the successful implementation of these models in a wide range of NLP tasks. A curated list of practical guide resources of LLMs, regularly updated, can be found at https://github.com/Mooler0410/LLMsPracticalGuide.

The adeptness of Large Language Models (LLMs) in comprehending and following natural language instructions is critical for their deployment in sophisticated real-world applications. Existing evaluations mainly focus on fragmented constraints or narrow scenarios, but they overlook the comprehensiveness and authenticity of constraints from the user's perspective. To bridge this gap, we propose CFBench, a large-scale Comprehensive Constraints Following Benchmark for LLMs, featuring 1,000 curated samples that cover more than 200 real-life scenarios and over 50 NLP tasks. CFBench meticulously compiles constraints from real-world instructions and constructs an innovative systematic framework for constraint types, which includes 10 primary categories and over 25 subcategories, and ensures each constraint is seamlessly integrated within the instructions. To make certain that the evaluation of LLM outputs aligns with user perceptions, we propose an advanced methodology that integrates multi-dimensional assessment criteria with requirement prioritization, covering various perspectives of constraints, instructions, and requirement fulfillment. Evaluating current leading LLMs on CFBench reveals substantial room for improvement in constraints following, and we further investigate influencing factors and enhancement strategies. The data and code are publicly available at https://github.com/PKU-Baichuan-MLSystemLab/CFBench

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Large language models (LLMs) have demonstrated remarkable capabilities across a wide range of tasks in various domains. Despite their impressive performance, they can be unreliable due to factual errors in their generations. Assessing their confidence and calibrating them across different tasks can help mitigate risks and enable LLMs to produce better generations. There has been a lot of recent research aiming to address this, but there has been no comprehensive overview to organize it and outline the main lessons learned. The present survey aims to bridge this gap. In particular, we outline the challenges and we summarize recent technical advancements for LLM confidence estimation and calibration. We further discuss their applications and suggest promising directions for future work.

Information extraction(IE) is a crucial subfield within natural language processing. In this study, we introduce a Sentence Classification and Named Entity Recognition Multi-task (SCNM) approach that combines Sentence Classification (SC) and Named Entity Recognition (NER). We develop a Sentence-to-Label Generation (SLG) framework for SCNM and construct a Wikipedia dataset containing both SC and NER. Using a format converter, we unify input formats and employ a generative model to generate SC-labels, NER-labels, and associated text segments. We propose a Constraint Mechanism (CM) to improve generated format accuracy. Our results show SC accuracy increased by 1.13 points and NER by 1.06 points in SCNM compared to standalone tasks, with CM raising format accuracy from 63.61 to 100. The findings indicate mutual reinforcement effects between SC and NER, and integration enhances both tasks' performance.

Recently, large language models (LLMs) have shown remarkable capabilities including understanding context, engaging in logical reasoning, and generating responses. However, this is achieved at the expense of stringent computational and memory requirements, hindering their ability to effectively support long input sequences. This survey provides an inclusive review of the recent techniques and methods devised to extend the sequence length in LLMs, thereby enhancing their capacity for long-context understanding. In particular, we review and categorize a wide range of techniques including architectural modifications, such as modified positional encoding and altered attention mechanisms, which are designed to enhance the processing of longer sequences while avoiding a proportional increase in computational requirements. The diverse methodologies investigated in this study can be leveraged across different phases of LLMs, i.e., training, fine-tuning and inference. This enables LLMs to efficiently process extended sequences. The limitations of the current methodologies is discussed in the last section along with the suggestions for future research directions, underscoring the importance of sequence length in the continued advancement of LLMs.

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

When scaled to hundreds of billions of parameters, pretrained language models such as GPT-3 (Brown et al., 2020) achieve remarkable few-shot performance. However, enormous amounts of compute are required for training and applying such big models, resulting in a large carbon footprint and making it difficult for researchers and practitioners to use them. We show that performance similar to GPT-3 can be obtained with language models that are much "greener" in that their parameter count is several orders of magnitude smaller. This is achieved by converting textual inputs into cloze questions that contain a task description, combined with gradient-based optimization; exploiting unlabeled data gives further improvements. We identify key factors required for successful natural language understanding with small language models.

Large Language Models (LLMs) have achieved state-of-the-art performance across various language tasks but pose challenges for practical deployment due to their substantial memory requirements. Furthermore, the latest generative models suffer from high inference costs caused by the memory bandwidth bottleneck in the auto-regressive decoding process. To address these issues, we propose an efficient weight-only quantization method that reduces memory consumption and accelerates inference for LLMs. To ensure minimal quality degradation, we introduce a simple and effective heuristic approach that utilizes only the model weights of a pre-trained model. This approach is applicable to both Mixture-of-Experts (MoE) and dense models without requiring additional fine-tuning. To demonstrate the effectiveness of our proposed method, we first analyze the challenges and issues associated with LLM quantization. Subsequently, we present our heuristic approach, which adaptively finds the granularity of quantization, effectively addressing these problems. Furthermore, we implement highly efficient GPU GEMMs that perform on-the-fly matrix multiplication and dequantization, supporting the multiplication of fp16 or bf16 activations with int8 or int4 weights. We evaluate our approach on large-scale open source models such as OPT-175B and internal MoE models, showcasing minimal accuracy loss while achieving up to 3.65 times higher throughput on the same number of GPUs.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

This paper presents novel systems and methodologies for the development of efficient large language models (LLMs). It explores the trade-offs between model size, performance, and computational resources, with the aim of maximizing the efficiency of these AI systems. The research explores novel methods that allow different parts of the model to share parameters, reducing the total number of unique parameters required. This approach ensures that the model remains compact without sacrificing its ability to learn and represent complex language structures. This study provides valuable insights and tools for creating more efficient and effective LLMs, contributing to a more sustainable and accessible future for AI language modeling.

Knowledge Graphs (KGs) can serve as reliable knowledge sources for question answering (QA) due to their structured representation of knowledge. Existing research on the utilization of KG for large language models (LLMs) prevalently relies on subgraph retriever or iterative prompting, overlooking the potential synergy of LLMs' step-wise reasoning capabilities and KGs' structural nature. In this paper, we present DoG (Decoding on Graphs), a novel framework that facilitates a deep synergy between LLMs and KGs. We first define a concept, well-formed chain, which consists of a sequence of interrelated fact triplets on the KGs, starting from question entities and leading to answers. We argue that this concept can serve as a principle for making faithful and sound reasoning for KGQA. To enable LLMs to generate well-formed chains, we propose graph-aware constrained decoding, in which a constraint derived from the topology of the KG regulates the decoding process of the LLMs. This constrained decoding method ensures the generation of well-formed chains while making full use of the step-wise reasoning capabilities of LLMs. Based on the above, DoG, a training-free approach, is able to provide faithful and sound reasoning trajectories grounded on the KGs. Experiments across various KGQA tasks with different background KGs demonstrate that DoG achieves superior and robust performance. DoG also shows general applicability with various open-source LLMs.

Large language models (LLMs) have ushered in a new era for processing complex information in various fields, including science. The increasing amount of scientific literature allows these models to acquire and understand scientific knowledge effectively, thus improving their performance in a wide range of tasks. Due to the power of LLMs, they require extremely expensive computational resources, intense amounts of data, and training time. Therefore, in recent years, researchers have proposed various methodologies to make scientific LLMs more affordable. The most well-known approaches align in two directions. It can be either focusing on the size of the models or enhancing the quality of data. To date, a comprehensive review of these two families of methods has not yet been undertaken. In this paper, we (I) summarize the current advances in the emerging abilities of LLMs into more accessible AI solutions for science, and (II) investigate the challenges and opportunities of developing affordable solutions for scientific domains using LLMs.

Large language models (LLMs) with extended context windows have made significant strides yet remain a challenge due to the scarcity of long documents. Existing methods tend to synthesize long-context data but lack a clear mechanism to reinforce the long-range dependency modeling. To address this limitation, we propose NExtLong, a novel framework for synthesizing long-context data through Negative document Extension. NExtLong decomposes a document into multiple meta-chunks and extends the context by interleaving hard negative distractors retrieved from pretraining corpora. This approach compels the model to discriminate long-range dependent context from distracting content, enhancing its ability to model long-range dependencies. Extensive experiments demonstrate that NExtLong achieves significant performance improvements on the HELMET and RULER benchmarks compared to existing long-context synthesis approaches and leading models, which are trained on non-synthetic long documents. These findings highlight NExtLong's ability to reduce reliance on non-synthetic long documents, making it an effective framework for developing advanced long-context LLMs.

Automatic music captioning, which generates natural language descriptions for given music tracks, holds significant potential for enhancing the understanding and organization of large volumes of musical data. Despite its importance, researchers face challenges due to the costly and time-consuming collection process of existing music-language datasets, which are limited in size. To address this data scarcity issue, we propose the use of large language models (LLMs) to artificially generate the description sentences from large-scale tag datasets. This results in approximately 2.2M captions paired with 0.5M audio clips. We term it Large Language Model based Pseudo music caption dataset, shortly, LP-MusicCaps. We conduct a systemic evaluation of the large-scale music captioning dataset with various quantitative evaluation metrics used in the field of natural language processing as well as human evaluation. In addition, we trained a transformer-based music captioning model with the dataset and evaluated it under zero-shot and transfer-learning settings. The results demonstrate that our proposed approach outperforms the supervised baseline model.

This paper embarks on an exploration into the Large Language Model (LLM) datasets, which play a crucial role in the remarkable advancements of LLMs. The datasets serve as the foundational infrastructure analogous to a root system that sustains and nurtures the development of LLMs. Consequently, examination of these datasets emerges as a critical topic in research. In order to address the current lack of a comprehensive overview and thorough analysis of LLM datasets, and to gain insights into their current status and future trends, this survey consolidates and categorizes the fundamental aspects of LLM datasets from five perspectives: (1) Pre-training Corpora; (2) Instruction Fine-tuning Datasets; (3) Preference Datasets; (4) Evaluation Datasets; (5) Traditional Natural Language Processing (NLP) Datasets. The survey sheds light on the prevailing challenges and points out potential avenues for future investigation. Additionally, a comprehensive review of the existing available dataset resources is also provided, including statistics from 444 datasets, covering 8 language categories and spanning 32 domains. Information from 20 dimensions is incorporated into the dataset statistics. The total data size surveyed surpasses 774.5 TB for pre-training corpora and 700M instances for other datasets. We aim to present the entire landscape of LLM text datasets, serving as a comprehensive reference for researchers in this field and contributing to future studies. Related resources are available at: https://github.com/lmmlzn/Awesome-LLMs-Datasets.

Reliably generating structured outputs has become a critical capability for modern language model (LM) applications. Constrained decoding has emerged as the dominant technology across sectors for enforcing structured outputs during generation. Despite its growing adoption, little has been done with the systematic evaluation of the behaviors and performance of constrained decoding. Constrained decoding frameworks have standardized around JSON Schema as a structured data format, with most uses guaranteeing constraint compliance given a schema. However, there is poor understanding of the effectiveness of the methods in practice. We present an evaluation framework to assess constrained decoding approaches across three critical dimensions: efficiency in generating constraint-compliant outputs, coverage of diverse constraint types, and quality of the generated outputs. To facilitate this evaluation, we introduce JSONSchemaBench, a benchmark for constrained decoding comprising 10K real-world JSON schemas that encompass a wide range of constraints with varying complexity. We pair the benchmark with the existing official JSON Schema Test Suite and evaluate six state-of-the-art constrained decoding frameworks, including Guidance, Outlines, Llamacpp, XGrammar, OpenAI, and Gemini. Through extensive experiments, we gain insights into the capabilities and limitations of constrained decoding on structured generation with real-world JSON schemas. Our work provides actionable insights for improving constrained decoding frameworks and structured generation tasks, setting a new standard for evaluating constrained decoding and structured generation. We release JSONSchemaBench at https://github.com/guidance-ai/jsonschemabench

Large language models (LLMs) are highly capable at a variety of tasks given the right prompt, but writing one is still a difficult and tedious process. In this work, we introduce ConstitutionalExperts, a method for learning a prompt consisting of constitutional principles (i.e. rules), given a training dataset. Unlike prior methods that optimize the prompt as a single entity, our method incrementally improves the prompt by surgically editing individual principles. We also show that we can improve overall performance by learning unique prompts for different semantic regions of the training data and using a mixture-of-experts (MoE) architecture to route inputs at inference time. We compare our method to other state of the art prompt-optimization techniques across six benchmark datasets. We also investigate whether MoE improves these other techniques. Our results suggest that ConstitutionalExperts outperforms other prompt optimization techniques by 10.9% (F1) and that mixture-of-experts improves all techniques, suggesting its broad applicability.

As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization. Although the proportionality between the language model size and the richness of its learned representations is validated, we prioritize accessibility and pursue a path of data-efficient, cost-reduced, and knowledge-guided optimization. Through over twenty experiments ranging from masking, architecture, and pre-training data, we derive insights from protein-specific experimentation into building a model that interprets the language of life, optimally. We present Ankh, the first general-purpose PLM trained on Google's TPU-v4 surpassing the state-of-the-art performance with fewer parameters (<10% for pre-training, <7% for inference, and <30% for the embedding dimension). We provide a representative range of structure and function benchmarks where Ankh excels. We further provide a protein variant generation analysis on High-N and One-N input data scales where Ankh succeeds in learning protein evolutionary conservation-mutation trends and introducing functional diversity while retaining key structural-functional characteristics. We dedicate our work to promoting accessibility to research innovation via attainable resources.

Large language models (LLMs) are commonly trained on datasets consisting of fixed-length token sequences. These datasets are created by randomly concatenating documents of various lengths and then chunking them into sequences of a predetermined target length. However, this method of concatenation can lead to cross-document attention within a sequence, which is neither a desirable learning signal nor computationally efficient. Additionally, training on long sequences becomes computationally prohibitive due to the quadratic cost of attention. In this study, we introduce dataset decomposition, a novel variable sequence length training technique, to tackle these challenges. We decompose a dataset into a union of buckets, each containing sequences of the same size extracted from a unique document. During training, we use variable sequence length and batch size, sampling simultaneously from all buckets with a curriculum. In contrast to the concat-and-chunk baseline, which incurs a fixed attention cost at every step of training, our proposed method incurs a penalty proportional to the actual document lengths at each step, resulting in significant savings in training time. We train an 8k context-length 1B model at the same cost as a 2k context-length model trained with the baseline approach. Experiments on a web-scale corpus demonstrate that our approach significantly enhances performance on standard language evaluations and long-context benchmarks, reaching target accuracy 3x faster compared to the baseline. Our method not only enables efficient pretraining on long sequences but also scales effectively with dataset size. Lastly, we shed light on a critical yet less studied aspect of training large language models: the distribution and curriculum of sequence lengths, which results in a non-negligible difference in performance.

Large language models are typically trained densely: all parameters are updated with respect to all inputs. This requires synchronization of billions of parameters across thousands of GPUs. We introduce a simple but effective method to asynchronously train large, sparse language models on arbitrary text corpora. Our method clusters a corpus into sets of related documents, trains a separate expert language model on each cluster, and combines them in a sparse ensemble for inference. This approach generalizes embarrassingly parallel training by automatically discovering the domains for each expert, and eliminates nearly all the communication overhead of existing sparse language models. Our technique outperforms dense baselines on multiple corpora and few-shot tasks, and our analysis shows that specializing experts to meaningful clusters is key to these gains. Performance also improves with the number of experts and size of training data, suggesting this is a highly efficient and accessible approach to training large language models.

Large language models (LLMs) have shown remarkable capabilities in language understanding and generation. However, such impressive capability typically comes with a substantial model size, which presents significant challenges in both the deployment, inference, and training stages. With LLM being a general-purpose task solver, we explore its compression in a task-agnostic manner, which aims to preserve the multi-task solving and language generation ability of the original LLM. One challenge to achieving this is the enormous size of the training corpus of LLM, which makes both data transfer and model post-training over-burdensome. Thus, we tackle the compression of LLMs within the bound of two constraints: being task-agnostic and minimizing the reliance on the original training dataset. Our method, named LLM-Pruner, adopts structural pruning that selectively removes non-critical coupled structures based on gradient information, maximally preserving the majority of the LLM's functionality. To this end, the performance of pruned models can be efficiently recovered through tuning techniques, LoRA, in merely 3 hours, requiring only 50K data. We validate the LLM-Pruner on three LLMs, including LLaMA, Vicuna, and ChatGLM, and demonstrate that the compressed models still exhibit satisfactory capabilities in zero-shot classification and generation. The code is available at: https://github.com/horseee/LLM-Pruner

In the past year, MultiModal Large Language Models (MM-LLMs) have undergone substantial advancements, augmenting off-the-shelf LLMs to support MM inputs or outputs via cost-effective training strategies. The resulting models not only preserve the inherent reasoning and decision-making capabilities of LLMs but also empower a diverse range of MM tasks. In this paper, we provide a comprehensive survey aimed at facilitating further research of MM-LLMs. Specifically, we first outline general design formulations for model architecture and training pipeline. Subsequently, we provide brief introductions of 26 existing MM-LLMs, each characterized by its specific formulations. Additionally, we review the performance of MM-LLMs on mainstream benchmarks and summarize key training recipes to enhance the potency of MM-LLMs. Lastly, we explore promising directions for MM-LLMs while concurrently maintaining a real-time tracking website for the latest developments in the field. We hope that this survey contributes to the ongoing advancement of the MM-LLMs domain.

Large Language Models (LLMs) excel in various natural language processing tasks, but leveraging them for dense passage embedding remains challenging. This is due to their causal attention mechanism and the misalignment between their pre-training objectives and the text ranking tasks. Despite some recent efforts to address these issues, existing frameworks for LLM-based text embeddings have been limited by their support for only a limited range of LLM architectures and fine-tuning strategies, limiting their practical application and versatility. In this work, we introduce the Unified framework for Large Language Model Embedding (ULLME), a flexible, plug-and-play implementation that enables bidirectional attention across various LLMs and supports a range of fine-tuning strategies. We also propose Generation-augmented Representation Learning (GRL), a novel fine-tuning method to boost LLMs for text embedding tasks. GRL enforces consistency between representation-based and generation-based relevance scores, leveraging LLMs' powerful generative abilities for learning passage embeddings. To showcase our framework's flexibility and effectiveness, we release three pre-trained models from ULLME with different backbone architectures, ranging from 1.5B to 8B parameters, all of which demonstrate strong performance on the Massive Text Embedding Benchmark. Our framework is publicly available at: https://github.com/nlp-uoregon/ullme. A demo video for ULLME can also be found at https://rb.gy/ws1ile.

Large Language Models (LLMs) have revolutionized natural language processing tasks with remarkable success. However, their formidable size and computational demands present significant challenges for practical deployment, especially in resource-constrained environments. As these challenges become increasingly pertinent, the field of model compression has emerged as a pivotal research area to alleviate these limitations. This paper presents a comprehensive survey that navigates the landscape of model compression techniques tailored specifically for LLMs. Addressing the imperative need for efficient deployment, we delve into various methodologies, encompassing quantization, pruning, knowledge distillation, and more. Within each of these techniques, we highlight recent advancements and innovative approaches that contribute to the evolving landscape of LLM research. Furthermore, we explore benchmarking strategies and evaluation metrics that are essential for assessing the effectiveness of compressed LLMs. By providing insights into the latest developments and practical implications, this survey serves as an invaluable resource for both researchers and practitioners. As LLMs continue to evolve, this survey aims to facilitate enhanced efficiency and real-world applicability, establishing a foundation for future advancements in the field.

Domain-general semantic parsing is a long-standing goal in natural language processing, where the semantic parser is capable of robustly parsing sentences from domains outside of which it was trained. Current approaches largely rely on additional supervision from new domains in order to generalize to those domains. We present a generative model of natural language utterances and logical forms and demonstrate its application to semantic parsing. Our approach relies on domain-independent supervision to generalize to new domains. We derive and implement efficient algorithms for training, parsing, and sentence generation. The work relies on a novel application of hierarchical Dirichlet processes (HDPs) for structured prediction, which we also present in this manuscript. This manuscript is an excerpt of chapter 4 from the Ph.D. thesis of Saparov (2022), where the model plays a central role in a larger natural language understanding system. This manuscript provides a new simplified and more complete presentation of the work first introduced in Saparov, Saraswat, and Mitchell (2017). The description and proofs of correctness of the training algorithm, parsing algorithm, and sentence generation algorithm are much simplified in this new presentation. We also describe the novel application of hierarchical Dirichlet processes for structured prediction. In addition, we extend the earlier work with a new model of word morphology, which utilizes the comprehensive morphological data from Wiktionary.

This study investigates the consequences of training large language models (LLMs) on synthetic data generated by their predecessors, an increasingly prevalent practice aimed at addressing the limited supply of human-generated training data. Diverging from the usual emphasis on performance metrics, we focus on the impact of this training methodology on linguistic diversity, especially when conducted recursively over time. To assess this, we developed a set of novel metrics targeting lexical, syntactic, and semantic diversity, applying them in recursive fine-tuning experiments across various natural language generation tasks. Our findings reveal a marked decrease in the diversity of the models' outputs through successive iterations. This trend underscores the potential risks of training LLMs on predecessor-generated text, particularly concerning the preservation of linguistic richness. Our study highlights the need for careful consideration of the long-term effects of such training approaches on the linguistic capabilities of LLMs.

Large language models (LLMs) have revolutionized the field of natural language processing, extending their strong capabilities into multi-modal domains. Thus, it is vital to define proper and diversified metrics for the evaluation of LLMs. In this paper, we introduce matrix entropy, a novel metric rooted in information theory and geometry principles to quantify the data compression proficiency in LLMs. It reflects the model's ability to extract relevant information and eliminate unnecessary elements, thereby providing insight into the language model's intrinsic capability. Specifically, we demonstrate its applicability in both single-modal (language) and multi-modal settings. For language models, our findings reveal that the matrix entropy of representations follows a scaling law type reduction when the model scales up, serving as a complement to the traditional loss scaling law. For the multi-modal setting, we also propose an evaluation method based on matrix entropy for assessing alignment quality and we find that modern large multi-modal models exhibit great alignment performance.

Recently, Multi-Modal(MM) Large Language Models(LLMs) have unlocked many complex use-cases that require MM understanding (e.g., image captioning or visual question answering) and MM generation (e.g., text-guided image generation or editing) capabilities. To further improve the output fidelity of MM-LLMs we introduce the model-agnostic UniRAG technique that adds relevant retrieved information to prompts as few-shot examples during inference. Unlike the common belief that Retrieval Augmentation (RA) mainly improves generation or understanding of uncommon entities, our evaluation results on the MSCOCO dataset with common entities show that both proprietary models like GPT4 and Gemini-Pro and smaller open-source models like Llava, LaVIT, and Emu2 significantly enhance their generation quality when their input prompts are augmented with relevant information retrieved by MM retrievers like UniIR models.

Large Language Models (LLMs) have revolutionized natural language processing by unifying tasks into text generation, yet their large parameter sizes and autoregressive nature limit inference speed. SAM-Decoding addresses this by introducing a novel retrieval-based speculative decoding method that uses a suffix automaton for efficient and accurate draft generation. Unlike n-gram matching used by the existing method, SAM-Decoding finds the longest suffix match in generating text and text corpuss, achieving an average time complexity of O(1) per generation step. SAM-Decoding constructs static and dynamic suffix automatons for the text corpus and input prompts, respectively, enabling fast and precise draft generation. Meanwhile, it is designed as an approach that can be combined with existing methods, allowing SAM-Decoding to adaptively select a draft generation strategy based on the matching length, thus increasing the inference speed of the LLM. When combined with Token Recycling, evaluations show SAM-Decoding outperforms existing model-free methods, achieving a speedup of 2.27times over autoregressive decoding on Spec-Bench. When combined with EAGLE2, it reaches a speedup of 2.49times, surpassing all current approaches. Our code is available at https://github.com/hyx1999/SAM-Decoding.

Recently, large language models (LLMs) have emerged as a groundbreaking technology and their unparalleled text generation capabilities have sparked interest in their application to the fundamental sentence representation learning task. Existing methods have explored utilizing LLMs as data annotators to generate synthesized data for training contrastive learning based sentence embedding models such as SimCSE. However, since contrastive learning models are sensitive to the quality of sentence pairs, the effectiveness of these methods is largely influenced by the content generated from LLMs, highlighting the need for more refined generation in the context of sentence representation learning. Building upon this premise, we propose MultiCSR, a multi-level contrastive sentence representation learning framework that decomposes the process of prompting LLMs to generate a corpus for training base sentence embedding models into three stages (i.e., sentence generation, sentence pair construction, in-batch training) and refines the generated content at these three distinct stages, ensuring only high-quality sentence pairs are utilized to train a base contrastive learning model. Our extensive experiments reveal that MultiCSR enables a less advanced LLM to surpass the performance of ChatGPT, while applying it to ChatGPT achieves better state-of-the-art results. Comprehensive analyses further underscore the potential of our framework in various application scenarios and achieving better sentence representation learning with LLMs.