Daily Papers

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

This article introduces idMotif, a visual analytics framework designed to aid domain experts in the identification of motifs within protein sequences. Motifs, short sequences of amino acids, are critical for understanding the distinct functions of proteins. Identifying these motifs is pivotal for predicting diseases or infections. idMotif employs a deep learning-based method for the categorization of protein sequences, enabling the discovery of potential motif candidates within protein groups through local explanations of deep learning model decisions. It offers multiple interactive views for the analysis of protein clusters or groups and their sequences. A case study, complemented by expert feedback, illustrates idMotif's utility in facilitating the analysis and identification of protein sequences and motifs.

We propose a new definition of higher-order DisCoCat (categorical compositional distributional) models where the meaning of a word is not a diagram, but a diagram-valued higher-order function. Our models can be seen as a variant of Montague semantics based on a lambda calculus where the primitives act on string diagrams rather than logical formulae. As a special case, we show how to translate from the Lambek calculus into Peirce's system beta for first-order logic. This allows us to give a purely diagrammatic treatment of higher-order and non-linear processes in natural language semantics: adverbs, prepositions, negation and quantifiers. The theoretical definition presented in this article comes with a proof-of-concept implementation in DisCoPy, the Python library for string diagrams.

Aiming at better representing multivariate relationships, this paper investigates a motif dimensional framework for higher-order graph learning. The graph learning effectiveness can be improved through OFFER. The proposed framework mainly aims at accelerating and improving higher-order graph learning results. We apply the acceleration procedure from the dimensional of network motifs. Specifically, the refined degree for nodes and edges are conducted in two stages: (1) employ motif degree of nodes to refine the adjacency matrix of the network; and (2) employ motif degree of edges to refine the transition probability matrix in the learning process. In order to assess the efficiency of the proposed framework, four popular network representation algorithms are modified and examined. By evaluating the performance of OFFER, both link prediction results and clustering results demonstrate that the graph representation learning algorithms enhanced with OFFER consistently outperform the original algorithms with higher efficiency.

The success of the GPT series proves that GPT can extract general information from sequences, thereby benefiting all downstream tasks. This motivates us to use pre-trained models to explore the hidden information in DNA sequences. However, data and task requirements in DNA sequence analysis are complexity and diversity as DNA relevant data includes different types of information, such as sequences, expression levels, etc, while there is currently no model specifically designed for these characteristics. Hereby, we present DNAGPT, a generalized foundation model pre-trained on over 10 billion base pairs from 9 species which can be fine-tuned for any DNA sequence analysis task. Our model can simultaneously process or output DNA sequences and numbers. In addition, our unique token design allows users to design prompts according to their own task requirements, making it applicable to any type of task. We have evaluated our model on classification, regression, and generation tasks. We demonstrate that DNAGPT benefits from pre-training, and therefore can bring performance gains to any downstream task. Our model is not only a new attempt in the field of genomes analysis, but also provides a new direction for the application of foundation models in biology.

Foundation language models obtain the instruction-following ability through supervised fine-tuning (SFT). Diversity and complexity are considered critical factors of a successful SFT dataset, while their definitions remain obscure and lack quantitative analyses. In this work, we propose InsTag, an open-set fine-grained tagger, to tag samples within SFT datasets based on semantics and intentions and define instruction diversity and complexity regarding tags. We obtain 6.6K tags to describe comprehensive user queries. Then we analyze popular open-sourced SFT datasets and find that the model ability grows with more diverse and complex data. Based on this observation, we propose a data selector based on InsTag to select 6K diverse and complex samples from open-source datasets and fine-tune models on InsTag-selected data. The resulting models, TagLM, outperform open-source models based on considerably larger SFT data evaluated by MT-Bench, echoing the importance of query diversity and complexity. We open-source InsTag in https://github.com/OFA-Sys/InsTag.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

Large pretrained language models (LLMs) can be rapidly adapted to a wide variety of tasks via a text-to-text approach, where the instruction and input are fed to the model in natural language. Combined with in-context learning (ICL), this paradigm is impressively flexible and powerful. However, it also burdens users with an overwhelming number of choices, many of them arbitrary. Inspired by markup languages like HTML, we contribute a method of using soft-token tags to compose prompt templates. This approach reduces arbitrary decisions and streamlines the application of ICL. Our method is a form of meta-learning for ICL; it learns these tags in advance during a parameter-efficient fine-tuning ``warm-up'' process. The tags can subsequently be used in templates for ICL on new, unseen tasks without any additional fine-tuning. Our experiments with this approach yield promising initial results, improving LLM performance on important enterprise applications such as few-shot and open-world intent detection, as well as text classification in news and legal domains.

Many tasks in natural language processing require the extraction of relationship information for a given condition, such as event argument extraction, relation extraction, and task-oriented semantic parsing. Recent works usually propose sophisticated models for each task independently and pay less attention to the commonality of these tasks and to have a unified framework for all the tasks. In this work, we propose to take a unified view of all these tasks and introduce TAGPRIME to address relational structure extraction problems. TAGPRIME is a sequence tagging model that appends priming words about the information of the given condition (such as an event trigger) to the input text. With the self-attention mechanism in pre-trained language models, the priming words make the output contextualized representations contain more information about the given condition, and hence become more suitable for extracting specific relationships for the condition. Extensive experiments and analyses on three different tasks that cover ten datasets across five different languages demonstrate the generality and effectiveness of TAGPRIME.

We enhance the calculus of string diagrams for monoidal categories with hierarchical features in order to capture closed monoidal (and cartesian closed) structure. Using this new syntax we formulate an automatic differentiation algorithm for (applied) simply typed lambda calculus in the style of [Pearlmutter and Siskind 2008] and we prove for the first time its soundness. To give an efficient yet principled implementation of the AD algorithm we define a sound and complete representation of hierarchical string diagrams as a class of hierarchical hypergraphs we call hypernets.

Pre-training (PT) followed by fine-tuning (FT) is an effective method for training neural networks, and has led to significant performance improvements in many domains. PT can incorporate various design choices such as task and data reweighting strategies, augmentation policies, and noise models, all of which can significantly impact the quality of representations learned. The hyperparameters introduced by these strategies therefore must be tuned appropriately. However, setting the values of these hyperparameters is challenging. Most existing methods either struggle to scale to high dimensions, are too slow and memory-intensive, or cannot be directly applied to the two-stage PT and FT learning process. In this work, we propose an efficient, gradient-based algorithm to meta-learn PT hyperparameters. We formalize the PT hyperparameter optimization problem and propose a novel method to obtain PT hyperparameter gradients by combining implicit differentiation and backpropagation through unrolled optimization. We demonstrate that our method improves predictive performance on two real-world domains. First, we optimize high-dimensional task weighting hyperparameters for multitask pre-training on protein-protein interaction graphs and improve AUROC by up to 3.9%. Second, we optimize a data augmentation neural network for self-supervised PT with SimCLR on electrocardiography data and improve AUROC by up to 1.9%.

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Creating layouts is a fundamental step in graphic design. In this work, we propose to use text as the guidance to create graphic layouts, i.e., Text-to-Layout, aiming to lower the design barriers. Text-to-Layout is a challenging task, because it needs to consider the implicit, combined, and incomplete layout constraints from text, each of which has not been studied in previous work. To address this, we present a two-stage approach, named parse-then-place. The approach introduces an intermediate representation (IR) between text and layout to represent diverse layout constraints. With IR, Text-to-Layout is decomposed into a parse stage and a place stage. The parse stage takes a textual description as input and generates an IR, in which the implicit constraints from the text are transformed into explicit ones. The place stage generates layouts based on the IR. To model combined and incomplete constraints, we use a Transformer-based layout generation model and carefully design a way to represent constraints and layouts as sequences. Besides, we adopt the pretrain-then-finetune strategy to boost the performance of the layout generation model with large-scale unlabeled layouts. To evaluate our approach, we construct two Text-to-Layout datasets and conduct experiments on them. Quantitative results, qualitative analysis, and user studies demonstrate the effectiveness of our approach.

Reordering is a preprocessing stage for Statistical Machine Translation (SMT) system where the words of the source sentence are reordered as per the syntax of the target language. We are proposing a rich set of rules for better reordering. The idea is to facilitate the training process by better alignments and parallel phrase extraction for a phrase-based SMT system. Reordering also helps the decoding process and hence improving the machine translation quality. We have observed significant improvements in the translation quality by using our approach over the baseline SMT. We have used BLEU, NIST, multi-reference word error rate, multi-reference position independent error rate for judging the improvements. We have exploited open source SMT toolkit MOSES to develop the system.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

This paper studies the topic modeling problem of tagged documents and images. Higher-order relations among tagged documents and images are major and ubiquitous characteristics, and play positive roles in extracting reliable and interpretable topics. In this paper, we propose the tag-topic models (TTM) to depict such higher-order topic structural dependencies within the Markov random field (MRF) framework. First, we use the novel factor graph representation of latent Dirichlet allocation (LDA)-based topic models from the MRF perspective, and present an efficient loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Second, we propose the factor hypergraph representation of TTM, and focus on both pairwise and higher-order relation modeling among tagged documents and images. Efficient loopy BP algorithm is developed to learn TTM, which encourages the topic labeling smoothness among tagged documents and images. Extensive experimental results confirm the incorporation of higher-order relations to be effective in enhancing the overall topic modeling performance, when compared with current state-of-the-art topic models, in many text and image mining tasks of broad interests such as word and link prediction, document classification, and tag recommendation.

Higher-order probabilistic programming languages allow programmers to write sophisticated models in machine learning and statistics in a succinct and structured way, but step outside the standard measure-theoretic formalization of probability theory. Programs may use both higher-order functions and continuous distributions, or even define a probability distribution on functions. But standard probability theory does not handle higher-order functions well: the category of measurable spaces is not cartesian closed. Here we introduce quasi-Borel spaces. We show that these spaces: form a new formalization of probability theory replacing measurable spaces; form a cartesian closed category and so support higher-order functions; form a well-pointed category and so support good proof principles for equational reasoning; and support continuous probability distributions. We demonstrate the use of quasi-Borel spaces for higher-order functions and probability by: showing that a well-known construction of probability theory involving random functions gains a cleaner expression; and generalizing de Finetti's theorem, that is a crucial theorem in probability theory, to quasi-Borel spaces.

We consider higher-order linear-chain conditional random fields (HO-LC-CRFs) for sequence modelling, and use sum-product networks (SPNs) for representing higher-order input- and output-dependent factors. SPNs are a recently introduced class of deep models for which exact and efficient inference can be performed. By combining HO-LC-CRFs with SPNs, expressive models over both the output labels and the hidden variables are instantiated while still enabling efficient exact inference. Furthermore, the use of higher-order factors allows us to capture relations of multiple input segments and multiple output labels as often present in real-world data. These relations can not be modelled by the commonly used first-order models and higher-order models with local factors including only a single output label. We demonstrate the effectiveness of our proposed models for sequence labeling. In extensive experiments, we outperform other state-of-the-art methods in optical character recognition and achieve competitive results in phone classification.

Current language models tailored for code tasks often adopt the pre-training-then-fine-tuning paradigm from natural language processing, modeling source code as plain text. This approach, however, overlooks the unambiguous structures inherent in programming languages. In this work, we explore data-efficient adaptation of pre-trained code models by further pre-training and fine-tuning them with program structures. Specifically, we represent programs as parse trees -- also known as concrete syntax trees (CSTs) -- and adapt pre-trained models on serialized CSTs. Although the models that we adapt have been pre-trained only on the surface form of programs, we find that a small amount of continual pre-training and fine-tuning on CSTs without changing the model architecture yields improvements over the baseline approach across various code tasks. The improvements are found to be particularly significant when there are limited training examples, demonstrating the effectiveness of integrating program structures with plain-text representation even when working with backbone models that have not been pre-trained with structures.

Pretext training followed by task-specific fine-tuning has been a successful approach in vision and language domains. This paper proposes a self-supervised pretext training framework tailored to event sequence data. We introduce a novel alignment verification task that is specialized to event sequences, building on good practices in masked reconstruction and contrastive learning. Our pretext tasks unlock foundational representations that are generalizable across different down-stream tasks, including next-event prediction for temporal point process models, event sequence classification, and missing event interpolation. Experiments on popular public benchmarks demonstrate the potential of the proposed method across different tasks and data domains.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

Set-of-Mark (SoM) Prompting unleashes the visual grounding capability of GPT-4V, by enabling the model to associate visual objects with tags inserted on the image. These tags, marked with alphanumerics, can be indexed via text tokens for easy reference. Despite the extraordinary performance from GPT-4V, we observe that other Multimodal Large Language Models (MLLMs) struggle to understand these visual tags. To promote the learning of SoM prompting for open-source models, we propose a new learning paradigm: "list items one by one," which asks the model to enumerate and describe all visual tags placed on the image following the alphanumeric orders of tags. By integrating our curated dataset with other visual instruction tuning datasets, we are able to equip existing MLLMs with the SoM prompting ability. Furthermore, we evaluate our finetuned SoM models on five MLLM benchmarks. We find that this new dataset, even in a relatively small size (10k-30k images with tags), significantly enhances visual reasoning capabilities and reduces hallucinations for MLLMs. Perhaps surprisingly, these improvements persist even when the visual tags are omitted from input images during inference. This suggests the potential of "list items one by one" as a new paradigm for training MLLMs, which strengthens the object-text alignment through the use of visual tags in the training stage. Finally, we conduct analyses by probing trained models to understand the working mechanism of SoM. Our code and data are available at https://github.com/zzxslp/SoM-LLaVA.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as a generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable. The source code of this work is released at https://github.com/sail-sg/autofd .

Fast and effective automated indexing is critical for search and personalized services. Key phrases that consist of one or more words and represent the main concepts of the document are often used for the purpose of indexing. In this paper, we investigate the use of additional semantic features and pre-processing steps to improve automatic key phrase extraction. These features include the use of signal words and freebase categories. Some of these features lead to significant improvements in the accuracy of the results. We also experimented with 2 forms of document pre-processing that we call light filtering and co-reference normalization. Light filtering removes sentences from the document, which are judged peripheral to its main content. Co-reference normalization unifies several written forms of the same named entity into a unique form. We also needed a "Gold Standard" - a set of labeled documents for training and evaluation. While the subjective nature of key phrase selection precludes a true "Gold Standard", we used Amazon's Mechanical Turk service to obtain a useful approximation. Our data indicates that the biggest improvements in performance were due to shallow semantic features, news categories, and rhetorical signals (nDCG 78.47% vs. 68.93%). The inclusion of deeper semantic features such as Freebase sub-categories was not beneficial by itself, but in combination with pre-processing, did cause slight improvements in the nDCG scores.

This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they can be instructed by prompts to solve new tasks without any fine-tuning. Moreover, they can be applied to a wide range of different media and problem domains, ranging from image and video processing to robot control learning. Because they provide a blueprint for solving many tasks in artificial intelligence, they have been called Foundation Models. After a brief introduction to basic NLP models the main pre-trained language models BERT, GPT and sequence-to-sequence transformer are described, as well as the concepts of self-attention and context-sensitive embedding. Then, different approaches to improving these models are discussed, such as expanding the pre-training criteria, increasing the length of input texts, or including extra knowledge. An overview of the best-performing models for about twenty application areas is then presented, e.g., question answering, translation, story generation, dialog systems, generating images from text, etc. For each application area, the strengths and weaknesses of current models are discussed, and an outlook on further developments is given. In addition, links are provided to freely available program code. A concluding chapter summarizes the economic opportunities, mitigation of risks, and potential developments of AI.

The class of tree-adjoining languages can be characterized by various two-level formalisms, consisting of a context-free grammar (CFG) or pushdown automaton (PDA) controlling another CFG or PDA. These four formalisms are equivalent to tree-adjoining grammars (TAG), linear indexed grammars (LIG), pushdown-adjoining automata (PAA), and embedded pushdown automata (EPDA). We define semiring-weighted versions of the above two-level formalisms, and we design new algorithms for computing their stringsums (the weight of all derivations of a string) and allsums (the weight of all derivations). From these, we also immediately obtain stringsum and allsum algorithms for TAG, LIG, PAA, and EPDA. For LIG, our algorithm is more time-efficient by a factor of O(n|N|) (where n is the string length and |N| is the size of the nonterminal set) and more space-efficient by a factor of O(|Gamma|) (where |Gamma| is the size of the stack alphabet) than the algorithm of Vijay-Shanker and Weir (1989). For EPDA, our algorithm is both more space-efficient and time-efficient than the algorithm of Alonso et al. (2001) by factors of O(|Gamma|^2) and O(|Gamma|^3), respectively. Finally, we give the first PAA stringsum and allsum algorithms.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Pretext-based self-supervised learning learns the semantic representation via a handcrafted pretext task over unlabeled data and then uses the learned representation for downstream tasks, which effectively reduces the sample complexity of downstream tasks under Conditional Independence (CI) condition. However, the downstream sample complexity gets much worse if the CI condition does not hold. One interesting question is whether we can make the CI condition hold by using downstream data to refine the unlabeled data to boost self-supervised learning. At first glance, one might think that seeing downstream data in advance would always boost the downstream performance. However, we show that it is not intuitively true and point out that in some cases, it hurts the final performance instead. In particular, we prove both model-free and model-dependent lower bounds of the number of downstream samples used for data refinement. Moreover, we conduct various experiments on both synthetic and real-world datasets to verify our theoretical results.

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of sim120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

The pretrain-finetune paradigm has shown outstanding performance on many applications of deep learning, where a model is pre-trained on a upstream large dataset (e.g. ImageNet), and is then fine-tuned to different downstream tasks. Though for most cases, the pre-training stage is conducted based on supervised methods, recent works on self-supervised pre-training have shown powerful transferability and even outperform supervised pre-training on multiple downstream tasks. It thus remains an open question how to better generalize supervised pre-training model to downstream tasks. In this paper, we argue that the worse transferability of existing supervised pre-training methods arise from the negligence of valuable intra-class semantic difference. This is because these methods tend to push images from the same class close to each other despite of the large diversity in their visual contents, a problem to which referred as "overfit of upstream tasks". To alleviate this problem, we propose a new supervised pre-training method based on Leave-One-Out K-Nearest-Neighbor, or LOOK for short. It relieves the problem of overfitting upstream tasks by only requiring each image to share its class label with most of its k nearest neighbors, thus allowing each class to exhibit a multi-mode distribution and consequentially preserving part of intra-class difference for better transferring to downstream tasks. We developed efficient implementation of the proposed method that scales well to large datasets. Experimental studies on multiple downstream tasks show that LOOK outperforms other state-of-the-art methods for supervised and self-supervised pre-training.

For a long time, different recommendation tasks typically require designing task-specific architectures and training objectives. As a result, it is hard to transfer the learned knowledge and representations from one task to another, thus restricting the generalization ability of existing recommendation approaches, e.g., a sequential recommendation model can hardly be applied or transferred to a review generation method. To deal with such issues, considering that language can describe almost anything and language grounding is a powerful medium to represent various problems or tasks, we present a flexible and unified text-to-text paradigm called "Pretrain, Personalized Prompt, and Predict Paradigm" (P5) for recommendation, which unifies various recommendation tasks in a shared framework. In P5, all data such as user-item interactions, user descriptions, item metadata, and user reviews are converted to a common format -- natural language sequences. The rich information from natural language assists P5 to capture deeper semantics for personalization and recommendation. Specifically, P5 learns different tasks with the same language modeling objective during pretraining. Thus, it serves as the foundation model for various downstream recommendation tasks, allows easy integration with other modalities, and enables instruction-based recommendation based on prompts. P5 advances recommender systems from shallow model to deep model to big model, and will revolutionize the technical form of recommender systems towards universal recommendation engine. With adaptive personalized prompt for different users, P5 is able to make predictions in a zero-shot or few-shot manner and largely reduces the necessity for extensive fine-tuning. On several recommendation benchmarks, we conduct experiments to show the effectiveness of P5. We release the source code at https://github.com/jeykigung/P5.

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.

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

Causal precedence between biochemical interactions is crucial in the biomedical domain, because it transforms collections of individual interactions, e.g., bindings and phosphorylations, into the causal mechanisms needed to inform meaningful search and inference. Here, we analyze causal precedence in the biomedical domain as distinct from open-domain, temporal precedence. First, we describe a novel, hand-annotated text corpus of causal precedence in the biomedical domain. Second, we use this corpus to investigate a battery of models of precedence, covering rule-based, feature-based, and latent representation models. The highest-performing individual model achieved a micro F1 of 43 points, approaching the best performers on the simpler temporal-only precedence tasks. Feature-based and latent representation models each outperform the rule-based models, but their performance is complementary to one another. We apply a sieve-based architecture to capitalize on this lack of overlap, achieving a micro F1 score of 46 points.

Pre-trained Programming Language Models (PPLMs) achieved many recent states of the art results for many code-related software engineering tasks. Though some studies use data flow or propose tree-based models that utilize Abstract Syntax Tree (AST), most PPLMs do not fully utilize the rich syntactical information in source code. Still, the input is considered a sequence of tokens. There are two issues; the first is computational inefficiency due to the quadratic relationship between input length and attention complexity. Second, any syntactical information, when needed as an extra input to the current PPLMs, requires the model to be pre-trained from scratch, wasting all the computational resources already used for pre-training the current models. In this work, we propose Named Entity Recognition (NER) adapters, lightweight modules that can be inserted into Transformer blocks to learn type information extracted from the AST. These adapters can be used with current PPLMs such as CodeBERT, GraphCodeBERT, and CodeT5. We train the NER adapters using a novel Token Type Classification objective function (TTC). We insert our proposed work in CodeBERT, building CodeBERTER, and evaluate the performance on two tasks of code refinement and code summarization. CodeBERTER improves the accuracy of code refinement from 16.4 to 17.8 while using 20% of training parameter budget compared to the fully fine-tuning approach, and the BLEU score of code summarization from 14.75 to 15.90 while reducing 77% of training parameters compared to the fully fine-tuning approach.

Recent years have witnessed the rise and success of pre-training techniques in visually-rich document understanding. However, most existing methods lack the systematic mining and utilization of layout-centered knowledge, leading to sub-optimal performances. In this paper, we propose ERNIE-Layout, a novel document pre-training solution with layout knowledge enhancement in the whole workflow, to learn better representations that combine the features from text, layout, and image. Specifically, we first rearrange input sequences in the serialization stage, and then present a correlative pre-training task, reading order prediction, to learn the proper reading order of documents. To improve the layout awareness of the model, we integrate a spatial-aware disentangled attention into the multi-modal transformer and a replaced regions prediction task into the pre-training phase. Experimental results show that ERNIE-Layout achieves superior performance on various downstream tasks, setting new state-of-the-art on key information extraction, document image classification, and document question answering datasets. The code and models are publicly available at http://github.com/PaddlePaddle/PaddleNLP/tree/develop/model_zoo/ernie-layout.

Hypergraph neural networks (HNNs) using neural networks to encode hypergraphs provide a promising way to model higher-order relations in data and further solve relevant prediction tasks built upon such higher-order relations. However, higher-order relations in practice contain complex patterns and are often highly irregular. So, it is often challenging to design an HNN that suffices to express those relations while keeping computational efficiency. Inspired by hypergraph diffusion algorithms, this work proposes a new HNN architecture named ED-HNN, which provably represents any continuous equivariant hypergraph diffusion operators that can model a wide range of higher-order relations. ED-HNN can be implemented efficiently by combining star expansions of hypergraphs with standard message passing neural networks. ED-HNN further shows great superiority in processing heterophilic hypergraphs and constructing deep models. We evaluate ED-HNN for node classification on nine real-world hypergraph datasets. ED-HNN uniformly outperforms the best baselines over these nine datasets and achieves more than 2\%uparrow in prediction accuracy over four datasets therein.

The quality of training data impacts the performance of pre-trained large language models (LMs). Given a fixed budget of tokens, we study how to best select data that leads to good downstream model performance across tasks. We develop a new framework based on a simple hypothesis: just as humans acquire interdependent skills in a deliberate order, language models also follow a natural order when learning a set of skills from their training data. If such an order exists, it can be utilized for improved understanding of LMs and for data-efficient training. Using this intuition, our framework formalizes the notion of a skill and of an ordered set of skills in terms of the associated data. First, using both synthetic and real data, we demonstrate that these ordered skill sets exist, and that their existence enables more advanced skills to be learned with less data when we train on their prerequisite skills. Second, using our proposed framework, we introduce an online data sampling algorithm, Skill-It, over mixtures of skills for both continual pre-training and fine-tuning regimes, where the objective is to efficiently learn multiple skills in the former and an individual skill in the latter. On the LEGO synthetic in the continual pre-training setting, Skill-It obtains 36.5 points higher accuracy than random sampling. On the Natural Instructions dataset in the fine-tuning setting, Skill-It reduces the validation loss on the target skill by 13.6% versus training on data associated with the target skill itself. We apply our skills framework on the recent RedPajama dataset to continually pre-train a 3B-parameter LM, achieving higher accuracy on the LM Evaluation Harness with 1B tokens than the baseline approach of sampling uniformly over data sources with 3B tokens.

We propose a design pattern for tackling text ranking problems, dubbed "Expando-Mono-Duo", that has been empirically validated for a number of ad hoc retrieval tasks in different domains. At the core, our design relies on pretrained sequence-to-sequence models within a standard multi-stage ranking architecture. "Expando" refers to the use of document expansion techniques to enrich keyword representations of texts prior to inverted indexing. "Mono" and "Duo" refer to components in a reranking pipeline based on a pointwise model and a pairwise model that rerank initial candidates retrieved using keyword search. We present experimental results from the MS MARCO passage and document ranking tasks, the TREC 2020 Deep Learning Track, and the TREC-COVID challenge that validate our design. In all these tasks, we achieve effectiveness that is at or near the state of the art, in some cases using a zero-shot approach that does not exploit any training data from the target task. To support replicability, implementations of our design pattern are open-sourced in the Pyserini IR toolkit and PyGaggle neural reranking library.

The objective of pre-trained language models is to learn contextual representations of textual data. Pre-trained language models have become mainstream in natural language processing and code modeling. Using probes, a technique to study the linguistic properties of hidden vector spaces, previous works have shown that these pre-trained language models encode simple linguistic properties in their hidden representations. However, none of the previous work assessed whether these models encode the whole grammatical structure of a programming language. In this paper, we prove the existence of a syntactic subspace, lying in the hidden representations of pre-trained language models, which contain the syntactic information of the programming language. We show that this subspace can be extracted from the models' representations and define a novel probing method, the AST-Probe, that enables recovering the whole abstract syntax tree (AST) of an input code snippet. In our experimentations, we show that this syntactic subspace exists in five state-of-the-art pre-trained language models. In addition, we highlight that the middle layers of the models are the ones that encode most of the AST information. Finally, we estimate the optimal size of this syntactic subspace and show that its dimension is substantially lower than those of the models' representation spaces. This suggests that pre-trained language models use a small part of their representation spaces to encode syntactic information of the programming languages.

Malware family classification is a significant issue with public safety and research implications that has been hindered by the high cost of expert labels. The vast majority of corpora use noisy labeling approaches that obstruct definitive quantification of results and study of deeper interactions. In order to provide the data needed to advance further, we have created the Malware Open-source Threat Intelligence Family (MOTIF) dataset. MOTIF contains 3,095 malware samples from 454 families, making it the largest and most diverse public malware dataset with ground truth family labels to date, nearly 3x larger than any prior expert-labeled corpus and 36x larger than the prior Windows malware corpus. MOTIF also comes with a mapping from malware samples to threat reports published by reputable industry sources, which both validates the labels and opens new research opportunities in connecting opaque malware samples to human-readable descriptions. This enables important evaluations that are normally infeasible due to non-standardized reporting in industry. For example, we provide aliases of the different names used to describe the same malware family, allowing us to benchmark for the first time accuracy of existing tools when names are obtained from differing sources. Evaluation results obtained using the MOTIF dataset indicate that existing tasks have significant room for improvement, with accuracy of antivirus majority voting measured at only 62.10% and the well-known AVClass tool having just 46.78% accuracy. Our findings indicate that malware family classification suffers a type of labeling noise unlike that studied in most ML literature, due to the large open set of classes that may not be known from the sample under consideration

Generic pre-trained neural networks may struggle to produce good results in specialized domains like finance and insurance. This is due to a domain mismatch between training data and downstream tasks, as in-domain data are often scarce due to privacy constraints. In this work, we compare different pre-training strategies for LayoutLM. We show that using domain-relevant documents improves results on a named-entity recognition (NER) problem using a novel dataset of anonymized insurance-related financial documents called Payslips. Moreover, we show that we can achieve competitive results using a smaller and faster model.

Pre-trained language models have demonstrated impressive performance in both natural language processing and program understanding, which represent the input as a token sequence without explicitly modeling its structure. Some prior works show that pre-trained language models can capture the syntactic rules of natural languages without finetuning on syntax understanding tasks. However, there is limited understanding of how well pre-trained models understand the code structure so far. In this work, we perform the first thorough benchmarking of the state-of-the-art pre-trained models for identifying the syntactic structures of programs. Specifically, we introduce CodeSyntax, a large-scale dataset of programs annotated with the syntactic relationships in their corresponding abstract syntax trees. Our key observation is that existing language models pretrained on code still lack the understanding of code syntax. In fact, these pre-trained programming language models fail to match the performance of simple baselines based on positional offsets and keywords. We also present a natural language benchmark to highlight the differences between natural languages and programming languages in terms of syntactic structure understanding. Our findings point out key limitations of existing pre-training methods for programming languages, and suggest the importance of modeling code syntactic structures.

Recent years have seen a paradigm shift in NLP towards using pretrained language models ({PLM}) for a wide range of tasks. However, there are many difficult design decisions to represent structures (e.g. tagged text, coreference chains) in a way such that they can be captured by PLMs. Prior work on structured prediction with PLMs typically flattens the structured output into a sequence, which limits the quality of structural information being learned and leads to inferior performance compared to classic discriminative models. In this work, we describe an approach to model structures as sequences of actions in an autoregressive manner with PLMs, allowing in-structure dependencies to be learned without any loss. Our approach achieves the new state-of-the-art on all the structured prediction tasks we looked at, namely, named entity recognition, end-to-end relation extraction, and coreference resolution.

Pretraining Large Language Models (LLMs) on large corpora of textual data is now a standard paradigm. When using these LLMs for many downstream applications, it is common to additionally bake in new knowledge (e.g., time-critical news, or private domain knowledge) into the pretrained model either through RAG-based-prompting, or fine-tuning. However, the optimal methodology for the model to gain such new knowledge remains an open question. In this paper, we present Retrieval Augmented FineTuning (RAFT), a training recipe that improves the model's ability to answer questions in a "open-book" in-domain settings. In RAFT, given a question, and a set of retrieved documents, we train the model to ignore those documents that don't help in answering the question, which we call, distractor documents. RAFT accomplishes this by citing verbatim the right sequence from the relevant document that would help answer the question. This coupled with RAFT's chain-of-thought-style response helps improve the model's ability to reason. In domain-specific RAG, RAFT consistently improves the model's performance across PubMed, HotpotQA, and Gorilla datasets, presenting a post-training recipe to improve pre-trained LLMs to in-domain RAG. RAFT's code and demo are open-sourced at github.com/ShishirPatil/gorilla.

Training keyphrase generation (KPG) models require a large amount of annotated data, which can be prohibitively expensive and often limited to specific domains. In this study, we first demonstrate that large distribution shifts among different domains severely hinder the transferability of KPG models. We then propose a three-stage pipeline, which gradually guides KPG models' learning focus from general syntactical features to domain-related semantics, in a data-efficient manner. With Domain-general Phrase pre-training, we pre-train Sequence-to-Sequence models with generic phrase annotations that are widely available on the web, which enables the models to generate phrases in a wide range of domains. The resulting model is then applied in the Transfer Labeling stage to produce domain-specific pseudo keyphrases, which help adapt models to a new domain. Finally, we fine-tune the model with limited data with true labels to fully adapt it to the target domain. Our experiment results show that the proposed process can produce good-quality keyphrases in new domains and achieve consistent improvements after adaptation with limited in-domain annotated data. All code and datasets are available at https://github.com/memray/OpenNMT-kpg-release.

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.

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

The goal of machine learning is generalization. While the No Free Lunch Theorem states that we cannot obtain theoretical guarantees for generalization without further assumptions, in practice we observe that simple models which explain the training data generalize best: a principle called Occam's razor. Despite the need for simple models, most current approaches in machine learning only minimize the training error, and at best indirectly promote simplicity through regularization or architecture design. Here, we draw a connection between Occam's razor and in-context learning: an emergent ability of certain sequence models like Transformers to learn at inference time from past observations in a sequence. In particular, we show that the next-token prediction loss used to train in-context learners is directly equivalent to a data compression technique called prequential coding, and that minimizing this loss amounts to jointly minimizing both the training error and the complexity of the model that was implicitly learned from context. Our theory and the empirical experiments we use to support it not only provide a normative account of in-context learning, but also elucidate the shortcomings of current in-context learning methods, suggesting ways in which they can be improved. We make our code available at https://github.com/3rdCore/PrequentialCode.

Large Language Models (LLMs) demonstrate remarkable generalizability across diverse tasks, yet genomic foundation models (GFMs) still require separate finetuning for each downstream application, creating significant overhead as model sizes grow. Moreover, existing GFMs are constrained by rigid output formats, limiting their applicability to various genomic tasks. In this work, we revisit the transformer-based auto-regressive models and introduce Omni-DNA, a family of cross-modal multi-task models ranging from 20 million to 1 billion parameters. Our approach consists of two stages: (i) pretraining on DNA sequences with next token prediction objective, and (ii) expanding the multi-modal task-specific tokens and finetuning for multiple downstream tasks simultaneously. When evaluated on the Nucleotide Transformer and GB benchmarks, Omni-DNA achieves state-of-the-art performance on 18 out of 26 tasks. Through multi-task finetuning, Omni-DNA addresses 10 acetylation and methylation tasks at once, surpassing models trained on each task individually. Finally, we design two complex genomic tasks, DNA2Function and Needle-in-DNA, which map DNA sequences to textual functional descriptions and images, respectively, indicating Omni-DNA's cross-modal capabilities to broaden the scope of genomic applications. All the models are available through https://huggingface.co/collections/zehui127

Gigantic pre-trained models have become central to natural language processing (NLP), serving as the starting point for fine-tuning towards a range of downstream tasks. However, two pain points persist for this paradigm: (a) as the pre-trained models grow bigger (e.g., 175B parameters for GPT-3), even the fine-tuning process can be time-consuming and computationally expensive; (b) the fine-tuned model has the same size as its starting point by default, which is neither sensible due to its more specialized functionality, nor practical since many fine-tuned models will be deployed in resource-constrained environments. To address these pain points, we propose a framework for resource- and parameter-efficient fine-tuning by leveraging the sparsity prior in both weight updates and the final model weights. Our proposed framework, dubbed Dually Sparsity-Embedded Efficient Tuning (DSEE), aims to achieve two key objectives: (i) parameter efficient fine-tuning - by enforcing sparsity-aware low-rank updates on top of the pre-trained weights; and (ii) resource-efficient inference - by encouraging a sparse weight structure towards the final fine-tuned model. We leverage sparsity in these two directions by exploiting both unstructured and structured sparse patterns in pre-trained language models via a unified approach. Extensive experiments and in-depth investigations, with diverse network backbones (i.e., BERT, RoBERTa, and GPT-2) on dozens of datasets, consistently demonstrate impressive parameter-/inference-efficiency, while maintaining competitive downstream performance. For instance, DSEE saves about 25% inference FLOPs while achieving comparable performance, with 0.5% trainable parameters on BERT. Codes are available in https://github.com/VITA-Group/DSEE.

Aspect Sentiment Triplet Extraction (ASTE) is the task of extracting the triplets of target entities, their associated sentiment, and opinion spans explaining the reason for the sentiment. Existing research efforts mostly solve this problem using pipeline approaches, which break the triplet extraction process into several stages. Our observation is that the three elements within a triplet are highly related to each other, and this motivates us to build a joint model to extract such triplets using a sequence tagging approach. However, how to effectively design a tagging approach to extract the triplets that can capture the rich interactions among the elements is a challenging research question. In this work, we propose the first end-to-end model with a novel position-aware tagging scheme that is capable of jointly extracting the triplets. Our experimental results on several existing datasets show that jointly capturing elements in the triplet using our approach leads to improved performance over the existing approaches. We also conducted extensive experiments to investigate the model effectiveness and robustness.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Visual language models (VLMs) rapidly progressed with the recent success of large language models. There have been growing efforts on visual instruction tuning to extend the LLM with visual inputs, but lacks an in-depth study of the visual language pre-training process, where the model learns to perform joint modeling on both modalities. In this work, we examine the design options for VLM pre-training by augmenting LLM towards VLM through step-by-step controllable comparisons. We introduce three main findings: (1) freezing LLMs during pre-training can achieve decent zero-shot performance, but lack in-context learning capability, which requires unfreezing the LLM; (2) interleaved pre-training data is beneficial whereas image-text pairs alone are not optimal; (3) re-blending text-only instruction data to image-text data during instruction fine-tuning not only remedies the degradation of text-only tasks, but also boosts VLM task accuracy. With an enhanced pre-training recipe we build VILA, a Visual Language model family that consistently outperforms the state-of-the-art models, e.g., LLaVA-1.5, across main benchmarks without bells and whistles. Multi-modal pre-training also helps unveil appealing properties of VILA, including multi-image reasoning, enhanced in-context learning, and better world knowledge.

Temporal graphs are widely used to model dynamic systems with time-varying interactions. In real-world scenarios, the underlying mechanisms of generating future interactions in dynamic systems are typically governed by a set of recurring substructures within the graph, known as temporal motifs. Despite the success and prevalence of current temporal graph neural networks (TGNN), it remains uncertain which temporal motifs are recognized as the significant indications that trigger a certain prediction from the model, which is a critical challenge for advancing the explainability and trustworthiness of current TGNNs. To address this challenge, we propose a novel approach, called Temporal Motifs Explainer (TempME), which uncovers the most pivotal temporal motifs guiding the prediction of TGNNs. Derived from the information bottleneck principle, TempME extracts the most interaction-related motifs while minimizing the amount of contained information to preserve the sparsity and succinctness of the explanation. Events in the explanations generated by TempME are verified to be more spatiotemporally correlated than those of existing approaches, providing more understandable insights. Extensive experiments validate the superiority of TempME, with up to 8.21% increase in terms of explanation accuracy across six real-world datasets and up to 22.96% increase in boosting the prediction Average Precision of current TGNNs.

Synthesizing inductive loop invariants is fundamental to automating program verification. In this work, we observe that Large Language Models (such as gpt-3.5 or gpt-4) are capable of synthesizing loop invariants for a class of programs in a 0-shot setting, yet require several samples to generate the correct invariants. This can lead to a large number of calls to a program verifier to establish an invariant. To address this issue, we propose a {\it re-ranking} approach for the generated results of LLMs. We have designed a ranker that can distinguish between correct inductive invariants and incorrect attempts based on the problem definition. The ranker is optimized as a contrastive ranker. Experimental results demonstrate that this re-ranking mechanism significantly improves the ranking of correct invariants among the generated candidates, leading to a notable reduction in the number of calls to a verifier.

In recent years, vision-language research has shifted to study tasks which require more complex reasoning, such as interactive question answering, visual common sense reasoning, and question-answer plausibility prediction. However, the datasets used for these problems fail to capture the complexity of real inputs and multimodal environments, such as ambiguous natural language requests and diverse digital domains. We introduce Mobile app Tasks with Iterative Feedback (MoTIF), a dataset with natural language commands for the greatest number of interactive environments to date. MoTIF is the first to contain natural language requests for interactive environments that are not satisfiable, and we obtain follow-up questions on this subset to enable research on task uncertainty resolution. We perform initial feasibility classification experiments and only reach an F1 score of 37.3, verifying the need for richer vision-language representations and improved architectures to reason about task feasibility.

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

We introduce "pointer-guided segment ordering" (SO), a novel pre-training technique aimed at enhancing the contextual understanding of paragraph-level text representations in large language models. Our methodology leverages a self-attention-driven pointer network to restore the original sequence of shuffled text segments, addressing the challenge of capturing the structural coherence and contextual dependencies within documents. This pre-training approach is complemented by a fine-tuning methodology that incorporates dynamic sampling, augmenting the diversity of training instances and improving sample efficiency for various downstream applications. We evaluate our method on a diverse set of datasets, demonstrating its efficacy in tasks requiring sequential text classification across scientific literature and financial reporting domains. Our experiments show that pointer-guided pre-training significantly enhances the model's ability to understand complex document structures, leading to state-of-the-art performance in downstream classification tasks.

A recently introduced classifier, called SS3, has shown to be well suited to deal with early risk detection (ERD) problems on text streams. It obtained state-of-the-art performance on early depression and anorexia detection on Reddit in the CLEF's eRisk open tasks. SS3 was created to deal with ERD problems naturally since: it supports incremental training and classification over text streams, and it can visually explain its rationale. However, SS3 processes the input using a bag-of-word model lacking the ability to recognize important word sequences. This aspect could negatively affect the classification performance and also reduces the descriptiveness of visual explanations. In the standard document classification field, it is very common to use word n-grams to try to overcome some of these limitations. Unfortunately, when working with text streams, using n-grams is not trivial since the system must learn and recognize which n-grams are important "on the fly". This paper introduces t-SS3, an extension of SS3 that allows it to recognize useful patterns over text streams dynamically. We evaluated our model in the eRisk 2017 and 2018 tasks on early depression and anorexia detection. Experimental results suggest that t-SS3 is able to improve both current results and the richness of visual explanations.

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

We introduce HTLM, a hyper-text language model trained on a large-scale web crawl. Modeling hyper-text has a number of advantages: (1) it is easily gathered at scale, (2) it provides rich document-level and end-task-adjacent supervision (e.g. class and id attributes often encode document category information), and (3) it allows for new structured prompting that follows the established semantics of HTML (e.g. to do zero-shot summarization by infilling title tags for a webpage that contains the input text). We show that pretraining with a BART-style denoising loss directly on simplified HTML provides highly effective transfer for a wide range of end tasks and supervision levels. HTLM matches or exceeds the performance of comparably sized text-only LMs for zero-shot prompting and fine-tuning for classification benchmarks, while also setting new state-of-the-art performance levels for zero-shot summarization. We also find that hyper-text prompts provide more value to HTLM, in terms of data efficiency, than plain text prompts do for existing LMs, and that HTLM is highly effective at auto-prompting itself, by simply generating the most likely hyper-text formatting for any available training data. We will release all code and models to support future HTLM research.

Retrieval-augmented Generation (RAG) has markedly enhanced the capabilities of Large Language Models (LLMs) in tackling knowledge-intensive tasks. The increasing demands of application scenarios have driven the evolution of RAG, leading to the integration of advanced retrievers, LLMs and other complementary technologies, which in turn has amplified the intricacy of RAG systems. However, the rapid advancements are outpacing the foundational RAG paradigm, with many methods struggling to be unified under the process of "retrieve-then-generate". In this context, this paper examines the limitations of the existing RAG paradigm and introduces the modular RAG framework. By decomposing complex RAG systems into independent modules and specialized operators, it facilitates a highly reconfigurable framework. Modular RAG transcends the traditional linear architecture, embracing a more advanced design that integrates routing, scheduling, and fusion mechanisms. Drawing on extensive research, this paper further identifies prevalent RAG patterns-linear, conditional, branching, and looping-and offers a comprehensive analysis of their respective implementation nuances. Modular RAG presents innovative opportunities for the conceptualization and deployment of RAG systems. Finally, the paper explores the potential emergence of new operators and paradigms, establishing a solid theoretical foundation and a practical roadmap for the continued evolution and practical deployment of RAG technologies.

Recent research in representation learning utilizes large databases of proteins or molecules to acquire knowledge of drug and protein structures through unsupervised learning techniques. These pre-trained representations have proven to significantly enhance the accuracy of subsequent tasks, such as predicting the affinity between drugs and target proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results on established benchmark datasets. We provide preprocessed and integrated data obtained from 7 public sources, which encompass over 30M triples. Additionally, we make available the pre-trained models based on this data, along with the reported outcomes of their performance on three widely-used benchmark datasets for drug-target binding affinity prediction found in the Therapeutic Data Commons (TDC) benchmarks. Additionally, we make the source code for training models on benchmark datasets publicly available. Our objective in releasing these pre-trained models, accompanied by clean data for model pretraining and benchmark results, is to encourage research in knowledge-enhanced representation learning.

Designing pre-training objectives that more closely resemble the downstream tasks for pre-trained language models can lead to better performance at the fine-tuning stage, especially in the ad-hoc retrieval area. Existing pre-training approaches tailored for IR tried to incorporate weak supervised signals, such as query-likelihood based sampling, to construct pseudo query-document pairs from the raw textual corpus. However, these signals rely heavily on the sampling method. For example, the query likelihood model may lead to much noise in the constructed pre-training data. dagger This work was done during an internship at Huawei. In this paper, we propose to leverage the large-scale hyperlinks and anchor texts to pre-train the language model for ad-hoc retrieval. Since the anchor texts are created by webmasters and can usually summarize the target document, it can help to build more accurate and reliable pre-training samples than a specific algorithm. Considering different views of the downstream ad-hoc retrieval, we devise four pre-training tasks based on the hyperlinks. We then pre-train the Transformer model to predict the pair-wise preference, jointly with the Masked Language Model objective. Experimental results on two large-scale ad-hoc retrieval datasets show the significant improvement of our model compared with the existing methods.

The "pre-training rightarrow downstream adaptation" presents both new opportunities and challenges for Continual Learning (CL). Although the recent state-of-the-art in CL is achieved through Parameter-Efficient-Tuning (PET) adaptation paradigm, only prompt has been explored, limiting its application to Transformers only. In this paper, we position prompting as one instantiation of PET, and propose a unified CL framework with general PET, dubbed as Learning-Accumulation-Ensemble (LAE). PET, e.g., using Adapter, LoRA, or Prefix, can adapt a pre-trained model to downstream tasks with fewer parameters and resources. Given a PET method, our LAE framework incorporates it for CL with three novel designs. 1) Learning: the pre-trained model adapts to the new task by tuning an online PET module, along with our adaptation speed calibration to align different PET modules, 2) Accumulation: the task-specific knowledge learned by the online PET module is accumulated into an offline PET module through momentum update, 3) Ensemble: During inference, we respectively construct two experts with online/offline PET modules (which are favored by the novel/historical tasks) for prediction ensemble. We show that LAE is compatible with a battery of PET methods and gains strong CL capability. For example, LAE with Adaptor PET surpasses the prior state-of-the-art by 1.3% and 3.6% in last-incremental accuracy on CIFAR100 and ImageNet-R datasets, respectively. Code is available at https://github.com/gqk/LAE.

Pre-trained language models (LMs) are capable of in-context learning (ICL): they can adapt to a task with only a few examples given in the prompt without any parameter update. However, it is unclear where this capability comes from as there is a stark distribution shift between pre-training text and ICL prompts. In this work, we study what patterns of the pre-training data contribute to ICL. We find that LMs' ICL ability depends on parallel structures in the pre-training data -- pairs of phrases following similar templates in the same context window. Specifically, we detect parallel structures by checking whether training on one phrase improves prediction of the other, and conduct ablation experiments to study their effect on ICL. We show that removing parallel structures in the pre-training data reduces LMs' ICL accuracy by 51% (vs 2% from random ablation). This drop persists even when excluding common patterns such as n-gram repetitions and long-range dependency, showing the diversity and generality of parallel structures. A closer look at the detected parallel structures indicates that they cover diverse linguistic tasks and span long distances in the data.

We propose pre-finetuning, an additional large-scale learning stage between language model pre-training and fine-tuning. Pre-finetuning is massively multi-task learning (around 50 datasets, over 4.8 million total labeled examples), and is designed to encourage learning of representations that generalize better to many different tasks. We show that pre-finetuning consistently improves performance for pretrained discriminators (e.g.~RoBERTa) and generation models (e.g.~BART) on a wide range of tasks (sentence prediction, commonsense reasoning, MRC, etc.), while also significantly improving sample efficiency during fine-tuning. We also show that large-scale multi-tasking is crucial; pre-finetuning can hurt performance when few tasks are used up until a critical point (usually above 15) after which performance improves linearly in the number of tasks.

Do state-of-the-art natural language understanding models care about word order - one of the most important characteristics of a sequence? Not always! We found 75% to 90% of the correct predictions of BERT-based classifiers, trained on many GLUE tasks, remain constant after input words are randomly shuffled. Despite BERT embeddings are famously contextual, the contribution of each individual word to downstream tasks is almost unchanged even after the word's context is shuffled. BERT-based models are able to exploit superficial cues (e.g. the sentiment of keywords in sentiment analysis; or the word-wise similarity between sequence-pair inputs in natural language inference) to make correct decisions when tokens are arranged in random orders. Encouraging classifiers to capture word order information improves the performance on most GLUE tasks, SQuAD 2.0 and out-of-samples. Our work suggests that many GLUE tasks are not challenging machines to understand the meaning of a sentence.

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

Language-image pre-training is an effective technique for learning powerful representations in general domains. However, when directly turning to person representation learning, these general pre-training methods suffer from unsatisfactory performance. The reason is that they neglect critical person-related characteristics, i.e., fine-grained attributes and identities. To address this issue, we propose a novel language-image pre-training framework for person representation learning, termed PLIP. Specifically, we elaborately design three pretext tasks: 1) Text-guided Image Colorization, aims to establish the correspondence between the person-related image regions and the fine-grained color-part textual phrases. 2) Image-guided Attributes Prediction, aims to mine fine-grained attribute information of the person body in the image; and 3) Identity-based Vision-Language Contrast, aims to correlate the cross-modal representations at the identity level rather than the instance level. Moreover, to implement our pre-train framework, we construct a large-scale person dataset with image-text pairs named SYNTH-PEDES by automatically generating textual annotations. We pre-train PLIP on SYNTH-PEDES and evaluate our models by spanning downstream person-centric tasks. PLIP not only significantly improves existing methods on all these tasks, but also shows great ability in the zero-shot and domain generalization settings. The code, dataset and weights will be released at~https://github.com/Zplusdragon/PLIP

This paper proposes a novel method for constructing instruction-tuned large language models (LLMs) for finance without instruction data. Traditionally, developing such domain-specific LLMs has been resource-intensive, requiring a large dataset and significant computational power for continual pretraining and instruction tuning. Our study proposes a simpler approach that combines domain-specific continual pretraining with model merging. Given that general-purpose pretrained LLMs and their instruction-tuned LLMs are often publicly available, they can be leveraged to obtain the necessary instruction task vector. By merging this with a domain-specific pretrained vector, we can effectively create instruction-tuned LLMs for finance without additional instruction data. Our process involves two steps: first, we perform continual pretraining on financial data; second, we merge the instruction-tuned vector with the domain-specific pretrained vector. Our experiments demonstrate the successful construction of instruction-tuned LLMs for finance. One major advantage of our method is that the instruction-tuned and domain-specific pretrained vectors are nearly independent. This independence makes our approach highly effective. The Japanese financial instruction-tuned LLMs we developed in this study are available at https://huggingface.co/pfnet/nekomata-14b-pfn-qfin-inst-merge.

With infinitely many high-quality data points, infinite computational power, an infinitely large foundation model with a perfect training algorithm and guaranteed zero generalization error on the pretext task, can the model be used for everything? This question cannot be answered by the existing theory of representation, optimization or generalization, because the issues they mainly investigate are assumed to be nonexistent here. In this paper, we show that category theory provides powerful machinery to answer this question. We have proved three results. The first one limits the power of prompt-based learning, saying that the model can solve a downstream task with prompts if and only if the task is representable. The second one says fine tuning does not have this limit, as a foundation model with the minimum required power (up to symmetry) can theoretically solve downstream tasks for the category defined by pretext task, with fine tuning and enough resources. Our final result can be seen as a new type of generalization theorem, showing that the foundation model can generate unseen objects from the target category (e.g., images) using the structural information from the source category (e.g., texts). Along the way, we provide a categorical framework for supervised and self-supervised learning, which might be of independent interest.

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.

There is a compelling necessity from enterprises for fine tuning LLMs (Large Language Models) o get them trained on proprietary domain knowledge. The challenge is to imbibe the LLMs with domain specific knowledge using the most optimial resource and cost and in the best possible time. Many enterprises rely on RAG (Retrieval Augmented Generation) which does not need LLMs to be ine-tuned but they are limited by the quality of vector databases and their retrieval capabilities rather than the intrinsic capabilities of the LLMs themselves. In our current work we focus on fine tuning LLaMA, an open source LLM using proprietary documents and code from an enterprise repository and use the fine tuned models to evaluate the quality of responses. As part of this work, we aim to guide beginners on how to start with fine tuning an LLM for documentation and code by making educated guesses on size of GPU required and options that are available for formatting the data. We also propose pre processing recipes for both documentation and code to prepare dataset in different formats. The proposed methods of data preparation for document datasets are forming paragraph chunks, forming question and answer pairs and forming keyword and paragraph chunk pairs. For code dataset we propose forming summary and function pairs. Further, we qualitatively evaluate the results of the models for domain specific queries. Finally, we also propose practical guidelines and recommendations for fine tuning LLMs.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

In recent years, pretrained language models have revolutionized the NLP world, while achieving state of the art performance in various downstream tasks. However, in many cases, these models do not perform well when labeled data is scarce and the model is expected to perform in the zero or few shot setting. Recently, several works have shown that continual pretraining or performing a second phase of pretraining (inter-training) which is better aligned with the downstream task, can lead to improved results, especially in the scarce data setting. Here, we propose to leverage sentiment-carrying discourse markers to generate large-scale weakly-labeled data, which in turn can be used to adapt language models for sentiment analysis. Extensive experimental results show the value of our approach on various benchmark datasets, including the finance domain. Code, models and data are available at https://github.com/ibm/tslm-discourse-markers.

Higher-order interactions (HOIs) are ubiquitous in real-world complex systems and applications. Investigation of deep learning for HOIs, thus, has become a valuable agenda for the data mining and machine learning communities. As networks of HOIs are expressed mathematically as hypergraphs, hypergraph neural networks (HNNs) have emerged as a powerful tool for representation learning on hypergraphs. Given the emerging trend, we present the first survey dedicated to HNNs, with an in-depth and step-by-step guide. Broadly, the present survey overviews HNN architectures, training strategies, and applications. First, we break existing HNNs down into four design components: (i) input features, (ii) input structures, (iii) message-passing schemes, and (iv) training strategies. Second, we examine how HNNs address and learn HOIs with each of their components. Third, we overview the recent applications of HNNs in recommendation, bioinformatics and medical science, time series analysis, and computer vision. Lastly, we conclude with a discussion on limitations and future directions.

An ability that underlies human syntactic knowledge is determining which words can appear in the similar structures (i.e. grouping words by their syntactic categories). These groupings enable humans to combine structures in order to communicate complex meanings. A foundational question is how do children acquire this ability underlying syntactic knowledge. In exploring this process, we will review various engineering approaches whose goal is similar to that of a child's -- without prior syntactic knowledge, correctly identify the parts of speech (POS) of the words in a sample of text. In reviewing these unsupervised tagging efforts, we will discuss common themes that support the advances in the models and their relevance for language acquisition. For example, we discuss how each model judges success (evaluation metrics), the "additional information" that constrains the POS learning (such as orthographic information), and the context used to determine POS (only previous word, words before and after the target, etc). The identified themes pave the way for future investigations into the cognitive processes that underpin the acquisition of syntactic categories and provide a useful layout of current state of the art unsupervised POS tagging models.

The pre-training and fine-tuning paradigm has contributed to a number of breakthroughs in Natural Language Processing (NLP). Instead of directly training on a downstream task, language models are first pre-trained on large datasets with cross-domain knowledge (e.g., Pile, MassiveText, etc.) and then fine-tuned on task-specific data (e.g., natural language generation, text summarization, etc.). Scaling the model and dataset size has helped improve the performance of LLMs, but unfortunately, this also lead to highly prohibitive computational costs. Pre-training LLMs often require orders of magnitude more FLOPs than fine-tuning and the model capacity often remains the same between the two phases. To achieve training efficiency w.r.t training FLOPs, we propose to decouple the model capacity between the two phases and introduce Sparse Pre-training and Dense Fine-tuning (SPDF). In this work, we show the benefits of using unstructured weight sparsity to train only a subset of weights during pre-training (Sparse Pre-training) and then recover the representational capacity by allowing the zeroed weights to learn (Dense Fine-tuning). We demonstrate that we can induce up to 75% sparsity into a 1.3B parameter GPT-3 XL model resulting in a 2.5x reduction in pre-training FLOPs, without a significant loss in accuracy on the downstream tasks relative to the dense baseline. By rigorously evaluating multiple downstream tasks, we also establish a relationship between sparsity, task complexity and dataset size. Our work presents a promising direction to train large GPT models at a fraction of the training FLOPs using weight sparsity, while retaining the benefits of pre-trained textual representations for downstream tasks.

Autoregressive models, such as the GPT family, use a fixed order, usually left-to-right, to generate sequences. However, this is not a necessity. In this paper, we challenge this assumption and show that by simply adding a positional encoding for the output, this order can be modulated on-the-fly per-sample which offers key advantageous properties. It allows for the sampling of and conditioning on arbitrary subsets of tokens, and it also allows sampling in one shot multiple tokens dynamically according to a rejection strategy, leading to a sub-linear number of model evaluations. We evaluate our method across various domains, including language modeling, path-solving, and aircraft vertical rate prediction, decreasing the number of steps required for generation by an order of magnitude.

We study the pre-train + fine-tune strategy for data-to-text tasks. Our experiments indicate that text-to-text pre-training in the form of T5, enables simple, end-to-end transformer based models to outperform pipelined neural architectures tailored for data-to-text generation, as well as alternative language model based pre-training techniques such as BERT and GPT-2. Importantly, T5 pre-training leads to better generalization, as evidenced by large improvements on out-of-domain test sets. We hope our work serves as a useful baseline for future research, as transfer learning becomes ever more prevalent for data-to-text 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.

The goal of self-supervised learning from images is to construct image representations that are semantically meaningful via pretext tasks that do not require semantic annotations for a large training set of images. Many pretext tasks lead to representations that are covariant with image transformations. We argue that, instead, semantic representations ought to be invariant under such transformations. Specifically, we develop Pretext-Invariant Representation Learning (PIRL, pronounced as "pearl") that learns invariant representations based on pretext tasks. We use PIRL with a commonly used pretext task that involves solving jigsaw puzzles. We find that PIRL substantially improves the semantic quality of the learned image representations. Our approach sets a new state-of-the-art in self-supervised learning from images on several popular benchmarks for self-supervised learning. Despite being unsupervised, PIRL outperforms supervised pre-training in learning image representations for object detection. Altogether, our results demonstrate the potential of self-supervised learning of image representations with good invariance properties.

Understanding the relations between entities denoted by NPs in a text is a critical part of human-like natural language understanding. However, only a fraction of such relations is covered by standard NLP tasks and benchmarks nowadays. In this work, we propose a novel task termed text-based NP enrichment (TNE), in which we aim to enrich each NP in a text with all the preposition-mediated relations -- either explicit or implicit -- that hold between it and other NPs in the text. The relations are represented as triplets, each denoted by two NPs related via a preposition. Humans recover such relations seamlessly, while current state-of-the-art models struggle with them due to the implicit nature of the problem. We build the first large-scale dataset for the problem, provide the formal framing and scope of annotation, analyze the data, and report the results of fine-tuned language models on the task, demonstrating the challenge it poses to current technology. A webpage with a data-exploration UI, a demo, and links to the code, models, and leaderboard, to foster further research into this challenging problem can be found at: yanaiela.github.io/TNE/.

Instruction fine-tuning is crucial for today's large language models (LLMs) to learn to follow instructions and align with human preferences. Conventionally, supervised data, including the instruction and the correct response, is required for instruction fine-tuning. To obtain such data, some researchers prompted well-trained models like GPT-4 to generate instructions and correct responses. In this paper, we propose a novel approach that uses the first half of a random text from OpenWebText as the instruction and GPT-3.5-turbo or GPT-4-turbo to complete the text as the response. Despite the data being "non-instructional", we found that pre-trained LLMs fine-tuned on this data can gain instruction-following capabilities. This observation is verified by fine-tuning several well-known pre-trained LLMs (e.g., LLaMA-2-7B, LLaMA-3-8B, LLaMA-3-70B, Mistral-7B-v0.1). The "non-instructional data" also improved some models that underwent supervised fine-tuning and human preference alignment. Our LLaMA-3-70B-Instruct fine-tuned through "non-instructional data" is comparable with LLaMA-3.1-70B-Instruct on the Arena Hard leaderboard. We analyzed the "non-instructional data" and ensured it is devoid of content related to instruction fine-tuning. Our findings will inspire further investigation into how to develop instruction-following capabilities without explicit instruction-related data.

Multimodal pre-training with text, layout, and image has made significant progress for Visually Rich Document Understanding (VRDU), especially the fixed-layout documents such as scanned document images. While, there are still a large number of digital documents where the layout information is not fixed and needs to be interactively and dynamically rendered for visualization, making existing layout-based pre-training approaches not easy to apply. In this paper, we propose MarkupLM for document understanding tasks with markup languages as the backbone, such as HTML/XML-based documents, where text and markup information is jointly pre-trained. Experiment results show that the pre-trained MarkupLM significantly outperforms the existing strong baseline models on several document understanding tasks. The pre-trained model and code will be publicly available at https://aka.ms/markuplm.

We propose Strongly Supervised pre-training with ScreenShots (S4) - a novel pre-training paradigm for Vision-Language Models using data from large-scale web screenshot rendering. Using web screenshots unlocks a treasure trove of visual and textual cues that are not present in using image-text pairs. In S4, we leverage the inherent tree-structured hierarchy of HTML elements and the spatial localization to carefully design 10 pre-training tasks with large scale annotated data. These tasks resemble downstream tasks across different domains and the annotations are cheap to obtain. We demonstrate that, compared to current screenshot pre-training objectives, our innovative pre-training method significantly enhances performance of image-to-text model in nine varied and popular downstream tasks - up to 76.1% improvements on Table Detection, and at least 1% on Widget Captioning.

Recommendation is the task of ranking items (e.g. movies or products) according to individual user needs. Current systems rely on collaborative filtering and content-based techniques, which both require structured training data. We propose a framework for recommendation with off-the-shelf pretrained language models (LM) that only used unstructured text corpora as training data. If a user u liked Matrix and Inception, we construct a textual prompt, e.g. "Movies like Matrix, Inception, {<m{>}"} to estimate the affinity between u and m with LM likelihood. We motivate our idea with a corpus analysis, evaluate several prompt structures, and we compare LM-based recommendation with standard matrix factorization trained on different data regimes. The code for our experiments is publicly available (https://colab.research.google.com/drive/1f1mlZ-FGaLGdo5rPzxf3vemKllbh2esT?usp=sharing).

Recent advancements in biological research leverage the integration of molecules, proteins, and natural language to enhance drug discovery. However, current models exhibit several limitations, such as the generation of invalid molecular SMILES, underutilization of contextual information, and equal treatment of structured and unstructured knowledge. To address these issues, we propose BioT5, a comprehensive pre-training framework that enriches cross-modal integration in biology with chemical knowledge and natural language associations. BioT5 utilizes SELFIES for 100% robust molecular representations and extracts knowledge from the surrounding context of bio-entities in unstructured biological literature. Furthermore, BioT5 distinguishes between structured and unstructured knowledge, leading to more effective utilization of information. After fine-tuning, BioT5 shows superior performance across a wide range of tasks, demonstrating its strong capability of capturing underlying relations and properties of bio-entities. Our code is available at https://github.com/QizhiPei/BioT5{Github}.

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

The growing prevalence of visually rich documents, such as webpages and scanned/digital-born documents (images, PDFs, etc.), has led to increased interest in automatic document understanding and information extraction across academia and industry. Although various document modalities, including image, text, layout, and structure, facilitate human information retrieval, the interconnected nature of these modalities presents challenges for neural networks. In this paper, we introduce WebLM, a multimodal pre-training network designed to address the limitations of solely modeling text and structure modalities of HTML in webpages. Instead of processing document images as unified natural images, WebLM integrates the hierarchical structure of document images to enhance the understanding of markup-language-based documents. Additionally, we propose several pre-training tasks to model the interaction among text, structure, and image modalities effectively. Empirical results demonstrate that the pre-trained WebLM significantly surpasses previous state-of-the-art pre-trained models across several webpage understanding tasks. The pre-trained models and code are available at https://github.com/X-LANCE/weblm.

Sentiment is a pervasive feature in natural language text, yet it is an open question how sentiment is represented within Large Language Models (LLMs). In this study, we reveal that across a range of models, sentiment is represented linearly: a single direction in activation space mostly captures the feature across a range of tasks with one extreme for positive and the other for negative. Through causal interventions, we isolate this direction and show it is causally relevant in both toy tasks and real world datasets such as Stanford Sentiment Treebank. Through this case study we model a thorough investigation of what a single direction means on a broad data distribution. We further uncover the mechanisms that involve this direction, highlighting the roles of a small subset of attention heads and neurons. Finally, we discover a phenomenon which we term the summarization motif: sentiment is not solely represented on emotionally charged words, but is additionally summarized at intermediate positions without inherent sentiment, such as punctuation and names. We show that in Stanford Sentiment Treebank zero-shot classification, 76% of above-chance classification accuracy is lost when ablating the sentiment direction, nearly half of which (36%) is due to ablating the summarized sentiment direction exclusively at comma positions.

Pretraining is the preliminary and fundamental step in developing capable language models (LM). Despite this, pretraining data design is critically under-documented and often guided by empirically unsupported intuitions. To address this, we pretrain 28 1.5B parameter decoder-only models, training on data curated (1) at different times, (2) with varying toxicity and quality filters, and (3) with different domain compositions. First, we quantify the effect of pretraining data age. A temporal shift between evaluation data and pretraining data leads to performance degradation, which is not overcome by finetuning. Second, we explore the effect of quality and toxicity filters, showing a trade-off between performance on standard benchmarks and risk of toxic generations. Our findings indicate there does not exist a one-size-fits-all solution to filtering training data. We also find that the effects of different types of filtering are not predictable from text domain characteristics. Lastly, we empirically validate that the inclusion of heterogeneous data sources, like books and web, is broadly beneficial and warrants greater prioritization. These findings constitute the largest set of experiments to validate, quantify, and expose many undocumented intuitions about text pretraining, which we hope will help support more informed data-centric decisions in LM development.

Pre-training techniques have been verified successfully in a variety of NLP tasks in recent years. Despite the widespread use of pre-training models for NLP applications, they almost exclusively focus on text-level manipulation, while neglecting layout and style information that is vital for document image understanding. In this paper, we propose the LayoutLM to jointly model interactions between text and layout information across scanned document images, which is beneficial for a great number of real-world document image understanding tasks such as information extraction from scanned documents. Furthermore, we also leverage image features to incorporate words' visual information into LayoutLM. To the best of our knowledge, this is the first time that text and layout are jointly learned in a single framework for document-level pre-training. It achieves new state-of-the-art results in several downstream tasks, including form understanding (from 70.72 to 79.27), receipt understanding (from 94.02 to 95.24) and document image classification (from 93.07 to 94.42). The code and pre-trained LayoutLM models are publicly available at https://aka.ms/layoutlm.

Learning specific hands-on skills such as cooking, car maintenance, and home repairs increasingly happens via instructional videos. The user experience with such videos is known to be improved by meta-information such as time-stamped annotations for the main steps involved. Generating such annotations automatically is challenging, and we describe here two relevant contributions. First, we construct and release a new dense video captioning dataset, Video Timeline Tags (ViTT), featuring a variety of instructional videos together with time-stamped annotations. Second, we explore several multimodal sequence-to-sequence pretraining strategies that leverage large unsupervised datasets of videos and caption-like texts. We pretrain and subsequently finetune dense video captioning models using both YouCook2 and ViTT. We show that such models generalize well and are robust over a wide variety of instructional videos.

Large language models (LLMs) have made significant advancements in code-related tasks, yet many LLMs treat code as simple sequences, neglecting its structured nature. We introduce AST-T5, a novel pretraining paradigm that leverages the Abstract Syntax Tree (AST) for enhanced code generation, transpilation, and understanding. Using dynamic programming, our AST-Aware Segmentation retains code structure, while our AST-Aware Span Corruption objective equips the model to reconstruct various code structures. Unlike other models, AST-T5 avoids intricate program analyses or architectural changes, so it integrates seamlessly with any encoder-decoder Transformer. Evaluations show that AST-T5 consistently outperforms similar-sized LMs across various code-related tasks. Structure-awareness makes AST-T5 particularly powerful in code-to-code tasks, surpassing CodeT5 by 2 points in exact match score for the Bugs2Fix task and by 3 points in exact match score for Java-C# Transpilation in CodeXGLUE. Our code and model are publicly available at https://github.com/gonglinyuan/ast_t5.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

In Greek mythology, Pistis symbolized good faith, trust, and reliability, echoing the core principles of RAG in LLM systems. Pistis-RAG, a scalable multi-stage framework, effectively addresses the challenges of large-scale retrieval-augmented generation (RAG). Each stage plays a distinct role: matching refines the search space, pre-ranking prioritizes semantically relevant documents, and ranking aligns with the large language model's (LLM) preferences. The reasoning and aggregating stage supports the implementation of complex chain-of-thought (CoT) methods within this cascading structure. We argue that the lack of strong alignment between LLMs and the external knowledge ranking methods used in RAG tasks is relevant to the reliance on the model-centric paradigm in RAG frameworks. A content-centric approach would prioritize seamless integration between the LLMs and external information sources, optimizing the content transformation process for each specific task. Critically, our ranking stage deviates from traditional RAG approaches by recognizing that semantic relevance alone may not directly translate to improved generation. This is due to the sensitivity of the few-shot prompt order, as highlighted in prior work lu2021fantastically. Current RAG frameworks fail to account for this crucial factor. We introduce a novel ranking stage specifically designed for RAG systems. It adheres to information retrieval principles while considering the unique business scenario captured by LLM preferences and user feedback. Our approach integrates in-context learning (ICL) methods and reasoning steps to incorporate user feedback, ensuring efficient alignment. Experiments on the MMLU benchmark demonstrate a 9.3\% performance improvement. The model and code will be open-sourced on GitHub. Experiments on real-world, large-scale data validate our framework's scalability.

Instruction-following made modern large language models (LLMs) helpful assistants. However, the key to taming LLMs on complex instructions remains mysterious, for that there are huge gaps between models trained by open-source community and those trained by leading companies. To bridge the gap, we propose a simple and scalable approach UltraIF for building LLMs that can follow complex instructions with open-source data. UltraIF first decomposes real-world user prompts into simpler queries, constraints, and corresponding evaluation questions for the constraints. Then, we train an UltraComposer to compose constraint-associated prompts with evaluation questions. This prompt composer allows us to synthesize complicated instructions as well as filter responses with evaluation questions. In our experiment, for the first time, we successfully align LLaMA-3.1-8B-Base to catch up with its instruct version on 5 instruction-following benchmarks without any benchmark information, using only 8B model as response generator and evaluator. The aligned model also achieved competitive scores on other benchmarks. Moreover, we also show that UltraIF could further improve LLaMA-3.1-8B-Instruct through self-alignment, motivating broader use cases for the method. Our code will be available at https://github.com/kkk-an/UltraIF.

The surge of pre-training has witnessed the rapid development of document understanding recently. Pre-training and fine-tuning framework has been effectively used to tackle texts in various formats, including plain texts, document texts, and web texts. Despite achieving promising performance, existing pre-trained models usually target one specific document format at one time, making it difficult to combine knowledge from multiple document formats. To address this, we propose XDoc, a unified pre-trained model which deals with different document formats in a single model. For parameter efficiency, we share backbone parameters for different formats such as the word embedding layer and the Transformer layers. Meanwhile, we introduce adaptive layers with lightweight parameters to enhance the distinction across different formats. Experimental results have demonstrated that with only 36.7% parameters, XDoc achieves comparable or even better performance on a variety of downstream tasks compared with the individual pre-trained models, which is cost effective for real-world deployment. The code and pre-trained models will be publicly available at https://aka.ms/xdoc.

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.

Large language models have shown significant capabilities across various domains, including symbolic music generation. However, leveraging these pre-trained models for controllable music arrangement tasks, each requiring different forms of musical information as control, remains a novel challenge. In this paper, we propose a unified sequence-to-sequence framework that enables the fine-tuning of a symbolic music language model for multiple multi-track arrangement tasks, including band arrangement, piano reduction, drum arrangement, and voice separation. Our experiments demonstrate that the proposed approach consistently achieves higher musical quality compared to task-specific baselines across all four tasks. Furthermore, through additional experiments on probing analysis, we show the pre-training phase equips the model with essential knowledge to understand musical conditions, which is hard to acquired solely through task-specific fine-tuning.

Following natural instructions is crucial for the effective application of Retrieval-Augmented Generation (RAG) systems. Despite recent advancements in Large Language Models (LLMs), research on assessing and improving instruction-following (IF) alignment within the RAG domain remains limited. To address this issue, we propose VIF-RAG, the first automated, scalable, and verifiable synthetic pipeline for instruction-following alignment in RAG systems. We start by manually crafting a minimal set of atomic instructions (<100) and developing combination rules to synthesize and verify complex instructions for a seed set. We then use supervised models for instruction rewriting while simultaneously generating code to automate the verification of instruction quality via a Python executor. Finally, we integrate these instructions with extensive RAG and general data samples, scaling up to a high-quality VIF-RAG-QA dataset (>100k) through automated processes. To further bridge the gap in instruction-following auto-evaluation for RAG systems, we introduce FollowRAG Benchmark, which includes approximately 3K test samples, covering 22 categories of general instruction constraints and four knowledge-intensive QA datasets. Due to its robust pipeline design, FollowRAG can seamlessly integrate with different RAG benchmarks. Using FollowRAG and eight widely-used IF and foundational abilities benchmarks for LLMs, we demonstrate that VIF-RAG markedly enhances LLM performance across a broad range of general instruction constraints while effectively leveraging its capabilities in RAG scenarios. Further analysis offers practical insights for achieving IF alignment in RAG systems. Our code and datasets are released at https://FollowRAG.github.io.

Recent work has demonstrated that semantics specified by pretraining data influence how representations of different concepts are organized in a large language model (LLM). However, given the open-ended nature of LLMs, e.g., their ability to in-context learn, we can ask whether models alter these pretraining semantics to adopt alternative, context-specified ones. Specifically, if we provide in-context exemplars wherein a concept plays a different role than what the pretraining data suggests, do models reorganize their representations in accordance with these novel semantics? To answer this question, we take inspiration from the theory of conceptual role semantics and define a toy "graph tracing" task wherein the nodes of the graph are referenced via concepts seen during training (e.g., apple, bird, etc.) and the connectivity of the graph is defined via some predefined structure (e.g., a square grid). Given exemplars that indicate traces of random walks on the graph, we analyze intermediate representations of the model and find that as the amount of context is scaled, there is a sudden re-organization from pretrained semantic representations to in-context representations aligned with the graph structure. Further, we find that when reference concepts have correlations in their semantics (e.g., Monday, Tuesday, etc.), the context-specified graph structure is still present in the representations, but is unable to dominate the pretrained structure. To explain these results, we analogize our task to energy minimization for a predefined graph topology, providing evidence towards an implicit optimization process to infer context-specified semantics. Overall, our findings indicate scaling context-size can flexibly re-organize model representations, possibly unlocking novel capabilities.

Spreadsheets are widely used for table manipulation and presentation. Stylistic formatting of these tables is an important property for both presentation and analysis. As a result, popular spreadsheet software, such as Excel, supports automatically formatting tables based on rules. Unfortunately, writing such formatting rules can be challenging for users as it requires knowledge of the underlying rule language and data logic. We present CORNET, a system that tackles the novel problem of automatically learning such formatting rules from user examples in the form of formatted cells. CORNET takes inspiration from advances in inductive programming and combines symbolic rule enumeration with a neural ranker to learn conditional formatting rules. To motivate and evaluate our approach, we extracted tables with over 450K unique formatting rules from a corpus of over 1.8M real worksheets. Since we are the first to introduce conditional formatting, we compare CORNET to a wide range of symbolic and neural baselines adapted from related domains. Our results show that CORNET accurately learns rules across varying evaluation setups. Additionally, we show that CORNET finds shorter rules than those that a user has written and discovers rules in spreadsheets that users have manually formatted.

In this report, we present DNA 1.0 8B Instruct, a state-of-the-art bilingual language model optimized for Korean and English language tasks. By applying continual pre-training (CPT) with high-quality Korean datasets to Llama 3.1 8B and subsequent supervised fine-tuning (SFT), we create an instruction-following model with enhanced Korean language capabilities. This model is then merged with Llama 3.1 8B Instruct via spherical linear interpolation (SLERP) and undergoes further optimization through direct preference optimization (DPO) and knowledge distillation (KD). DNA 1.0 8B Instruct achieves state-of-the-art results on Korean-specific tasks, including KMMLU (53.26%), KoBEST (83.40%), and BELEBELE (57.99%), while maintaining strong English capabilities on MMLU (66.64%), MMLU-Pro (43.05%) and GSM8K (80.52%). As an open model, DNA 1.0 8B Instruct represents a significant advancement in bilingual language modeling. As an open model, DNA 1.0 8B Instruct is freely available through https://huggingface.co/dnotitia/Llama-DNA-1.0-8B-Instruct . For commercial licensing inquiries or feedback, please contact us at https://www.dnotitia.com/contact/post-form

We present semantic correctness proofs of automatic differentiation (AD). We consider a forward-mode AD method on a higher order language with algebraic data types, and we characterise it as the unique structure preserving macro given a choice of derivatives for basic operations. We describe a rich semantics for differentiable programming, based on diffeological spaces. We show that it interprets our language, and we phrase what it means for the AD method to be correct with respect to this semantics. We show that our characterisation of AD gives rise to an elegant semantic proof of its correctness based on a gluing construction on diffeological spaces. We explain how this is, in essence, a logical relations argument. Throughout, we show how the analysis extends to AD methods for computing higher order derivatives using a Taylor approximation.

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.

Ordinal regression refers to classifying object instances into ordinal categories. It has been widely studied in many scenarios, such as medical disease grading, movie rating, etc. Known methods focused only on learning inter-class ordinal relationships, but still incur limitations in distinguishing adjacent categories thus far. In this paper, we propose a simple sequence prediction framework for ordinal regression called Ord2Seq, which, for the first time, transforms each ordinal category label into a special label sequence and thus regards an ordinal regression task as a sequence prediction process. In this way, we decompose an ordinal regression task into a series of recursive binary classification steps, so as to subtly distinguish adjacent categories. Comprehensive experiments show the effectiveness of distinguishing adjacent categories for performance improvement and our new approach exceeds state-of-the-art performances in four different scenarios. Codes are available at https://github.com/wjh892521292/Ord2Seq.

In this article we describe an efficient approach to guiding language model text generation with regular expressions and context-free grammars. Our approach adds little to no overhead to the token sequence generation process, and makes guided generation feasible in practice. An implementation is provided in the open source Python library Outlines.

Text style transfer techniques are gaining popularity in Natural Language Processing, finding various applications such as text detoxification, sentiment, or formality transfer. However, the majority of the existing approaches were tested on such domains as online communications on public platforms, music, or entertainment yet none of them were applied to the domains which are typical for task-oriented production systems, such as personal plans arrangements (e.g. booking of flights or reserving a table in a restaurant). We fill this gap by studying formality transfer in this domain. We noted that the texts in this domain are full of named entities, which are very important for keeping the original sense of the text. Indeed, if for example, someone communicates the destination city of a flight it must not be altered. Thus, we concentrate on the role of named entities in content preservation for formality text style transfer. We collect a new dataset for the evaluation of content similarity measures in text style transfer. It is taken from a corpus of task-oriented dialogues and contains many important entities related to realistic requests that make this dataset particularly useful for testing style transfer models before using them in production. Besides, we perform an error analysis of a pre-trained formality transfer model and introduce a simple technique to use information about named entities to enhance the performance of baseline content similarity measures used in text style transfer.

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level properties. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP that aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that generates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We empirically verify the effectiveness of ProteinDT from three aspects: (1) consistently superior performance on four out of six protein property prediction benchmarks; (2) over 90% accuracy for text-guided protein generation; and (3) promising results for zero-shot text-guided protein editing.

Recently pre-trained language representation models such as BERT have shown great success when fine-tuned on downstream tasks including information retrieval (IR). However, pre-training objectives tailored for ad-hoc retrieval have not been well explored. In this paper, we propose Pre-training with Representative wOrds Prediction (PROP) for ad-hoc retrieval. PROP is inspired by the classical statistical language model for IR, specifically the query likelihood model, which assumes that the query is generated as the piece of text representative of the "ideal" document. Based on this idea, we construct the representative words prediction (ROP) task for pre-training. Given an input document, we sample a pair of word sets according to the document language model, where the set with higher likelihood is deemed as more representative of the document. We then pre-train the Transformer model to predict the pairwise preference between the two word sets, jointly with the Masked Language Model (MLM) objective. By further fine-tuning on a variety of representative downstream ad-hoc retrieval tasks, PROP achieves significant improvements over baselines without pre-training or with other pre-training methods. We also show that PROP can achieve exciting performance under both the zero- and low-resource IR settings. The code and pre-trained models are available at https://github.com/Albert-Ma/PROP.

The impressive capabilities of recent language models can be largely attributed to the multi-trillion token pretraining datasets that they are trained on. However, model developers fail to disclose their construction methodology which has lead to a lack of open information on how to develop effective pretraining sets. To address this issue, we perform the first systematic study across the entire pipeline of pretraining set construction. First, we run ablations on existing techniques for pretraining set development to identify which methods translate to the largest gains in model accuracy on downstream evaluations. Then, we categorize the most widely used data source, web crawl snapshots, across the attributes of toxicity, quality, type of speech, and domain. Finally, we show how such attribute information can be used to further refine and improve the quality of a pretraining set. These findings constitute an actionable set of steps that practitioners can use to develop high quality pretraining sets.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Recent studies have identified one aggravating factor of LLM hallucinations as the knowledge inconsistency between pre-training and fine-tuning, where unfamiliar fine-tuning data mislead the LLM to fabricate plausible but wrong outputs. In this paper, we propose a novel fine-tuning strategy called Prereq-Tune to address this knowledge inconsistency and reduce hallucinations. Fundamentally, Prereq-Tune disentangles the learning of skills and knowledge, so the model learns only the task skills without being impacted by the knowledge inconsistency. To achieve this, Prereq-Tune introduces an additional prerequisite learning stage to learn the necessary knowledge for SFT, allowing subsequent SFT to focus only on task skills. Prereq-Tune can also be combined with fictitious synthetic data to enhance the grounding of LLM outputs to their internal knowledge. Experiments show that Prereq-Tune outperforms existing baselines in improving LLM's factuality across short QA and long-form generation tasks. It also opens new possibilities for knowledge-controlled generation in LLMs. Our code is available at https://github.com/UCSB-NLP-Chang/Prereq_tune.git.

Self-supervised representation learning solves auxiliary prediction tasks (known as pretext tasks) without requiring labeled data to learn useful semantic representations. These pretext tasks are created solely using the input features, such as predicting a missing image patch, recovering the color channels of an image from context, or predicting missing words in text; yet predicting this known information helps in learning representations effective for downstream prediction tasks. We posit a mechanism exploiting the statistical connections between certain {\em reconstruction-based} pretext tasks that guarantee to learn a good representation. Formally, we quantify how the approximate independence between the components of the pretext task (conditional on the label and latent variables) allows us to learn representations that can solve the downstream task by just training a linear layer on top of the learned representation. We prove the linear layer yields small approximation error even for complex ground truth function class and will drastically reduce labeled sample complexity. Next, we show a simple modification of our method leads to nonlinear CCA, analogous to the popular SimSiam algorithm, and show similar guarantees for nonlinear CCA.

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.

Compositional generalization is crucial for artificial intelligence agents to solve complex vision-language reasoning tasks. Neuro-symbolic approaches have demonstrated promise in capturing compositional structures, but they face critical challenges: (a) reliance on predefined predicates for symbolic representations that limit adaptability, (b) difficulty in extracting predicates from raw data, and (c) using non-differentiable operations for combining primitive concepts. To address these issues, we propose NeSyCoCo, a neuro-symbolic framework that leverages large language models (LLMs) to generate symbolic representations and map them to differentiable neural computations. NeSyCoCo introduces three innovations: (a) augmenting natural language inputs with dependency structures to enhance the alignment with symbolic representations, (b) employing distributed word representations to link diverse, linguistically motivated logical predicates to neural modules, and (c) using the soft composition of normalized predicate scores to align symbolic and differentiable reasoning. Our framework achieves state-of-the-art results on the ReaSCAN and CLEVR-CoGenT compositional generalization benchmarks and demonstrates robust performance with novel concepts in the CLEVR-SYN benchmark.

The web contains large-scale, diverse, and abundant information to satisfy the information-seeking needs of humans. Through meticulous data collection, preprocessing, and curation, webpages can be used as a fundamental data resource for language model pretraining. However, when confronted with the progressively revolutionized and intricate nature of webpages, rule-based/feature-based web scrapers are becoming increasingly inadequate. This paper presents a simple, fast, and effective Neural web Scraper (NeuScraper) to help extract primary and clean text contents from webpages. Experimental results show that NeuScraper surpasses the baseline scrapers by achieving more than a 20% improvement, demonstrating its potential in extracting higher-quality data to facilitate the language model pretraining. All of the code is available at https://github.com/OpenMatch/NeuScraper.

We present POTATO, a task- and languageindependent framework for human-in-the-loop (HITL) learning of rule-based text classifiers using graph-based features. POTATO handles any type of directed graph and supports parsing text into Abstract Meaning Representations (AMR), Universal Dependencies (UD), and 4lang semantic graphs. A streamlit-based user interface allows users to build rule systems from graph patterns, provides real-time evaluation based on ground truth data, and suggests rules by ranking graph features using interpretable machine learning models. Users can also provide patterns over graphs using regular expressions, and POTATO can recommend refinements of such rules. POTATO is applied in projects across domains and languages, including classification tasks on German legal text and English social media data. All components of our system are written in Python, can be installed via pip, and are released under an MIT License on GitHub.

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance. Code is released at https://github.com/bytedance/dplm.

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 have exhibited robust performance across diverse natural language processing tasks. This report introduces TechGPT-2.0, a project designed to enhance the capabilities of large language models specifically in knowledge graph construction tasks, including named entity recognition (NER) and relationship triple extraction (RTE) tasks in NLP applications. Additionally, it serves as a LLM accessible for research within the Chinese open-source model community. We offer two 7B large language model weights and a QLoRA weight specialized for processing lengthy texts.Notably, TechGPT-2.0 is trained on Huawei's Ascend server. Inheriting all functionalities from TechGPT-1.0, it exhibits robust text processing capabilities, particularly in the domains of medicine and law. Furthermore, we introduce new capabilities to the model, enabling it to process texts in various domains such as geographical areas, transportation, organizations, literary works, biology, natural sciences, astronomical objects, and architecture. These enhancements also fortified the model's adeptness in handling hallucinations, unanswerable queries, and lengthy texts. This report provides a comprehensive and detailed introduction to the full fine-tuning process on Huawei's Ascend servers, encompassing experiences in Ascend server debugging, instruction fine-tuning data processing, and model training. Our code is available at https://github.com/neukg/TechGPT-2.0

Large Language Models (LLMs) for public use require continuous pre-training to remain up-to-date with the latest data. The models also need to be fine-tuned with specific instructions to maintain their ability to follow instructions accurately. Typically, LLMs are released in two versions: the Base LLM, pre-trained on diverse data, and the instruction-refined LLM, additionally trained with specific instructions for better instruction following. The question arises as to which model should undergo continuous pre-training to maintain its instruction-following abilities while also staying current with the latest data. In this study, we delve into the intricate relationship between continuous pre-training and instruction fine-tuning of the LLMs and investigate the impact of continuous pre-training on the instruction following abilities of both the base and its instruction finetuned model. Further, the instruction fine-tuning process is computationally intense and requires a substantial number of hand-annotated examples for the model to learn effectively. This study aims to find the most compute-efficient strategy to gain up-to-date knowledge and instruction-following capabilities without requiring any instruction data and fine-tuning. We empirically prove our findings on the LLaMa 3, 3.1 and Qwen 2, 2.5 family of base and instruction models, providing a comprehensive exploration of our hypotheses across varying sizes of pre-training data corpus and different LLMs settings.

Even though term-based methods such as BM25 provide strong baselines in ranking, under certain conditions they are dominated by large pre-trained masked language models (MLMs) such as BERT. To date, the source of their effectiveness remains unclear. Is it their ability to truly understand the meaning through modeling syntactic aspects? We answer this by manipulating the input order and position information in a way that destroys the natural sequence order of query and passage and shows that the model still achieves comparable performance. Overall, our results highlight that syntactic aspects do not play a critical role in the effectiveness of re-ranking with BERT. We point to other mechanisms such as query-passage cross-attention and richer embeddings that capture word meanings based on aggregated context regardless of the word order for being the main attributions for its superior performance.

Online education platforms are powered by various NLP pipelines, which utilize models like BERT to aid in content curation. Since the inception of the pre-trained language models like BERT, there have also been many efforts toward adapting these pre-trained models to specific domains. However, there has not been a model specifically adapted for the education domain (particularly K-12) across subjects to the best of our knowledge. In this work, we propose to train a language model on a corpus of data curated by us across multiple subjects from various sources for K-12 education. We also evaluate our model, K12-BERT, on downstream tasks like hierarchical taxonomy tagging.

Seminal research in the field of graph neural networks (GNNs) has revealed a direct correspondence between the expressive capabilities of GNNs and the k-dimensional Weisfeiler-Leman (kWL) test, a widely-recognized method for verifying graph isomorphism. This connection has reignited interest in comprehending the specific graph properties effectively distinguishable by the kWL test. A central focus of research in this field revolves around determining the least dimensionality k, for which kWL can discern graphs with different number of occurrences of a pattern graph P. We refer to such a least k as the WL-dimension of this pattern counting problem. This inquiry traditionally delves into two distinct counting problems related to patterns: subgraph counting and induced subgraph counting. Intriguingly, despite their initial appearance as separate challenges with seemingly divergent approaches, both of these problems are interconnected components of a more comprehensive problem: "graph motif parameters". In this paper, we provide a precise characterization of the WL-dimension of labeled graph motif parameters. As specific instances of this result, we obtain characterizations of the WL-dimension of the subgraph counting and induced subgraph counting problem for every labeled pattern P. We additionally demonstrate that in cases where the kWL test distinguishes between graphs with varying occurrences of a pattern P, the exact number of occurrences of P can be computed uniformly using only local information of the last layer of a corresponding GNN. We finally delve into the challenge of recognizing the WL-dimension of various graph parameters. We give a polynomial time algorithm for determining the WL-dimension of the subgraph counting problem for given pattern P, answering an open question from previous work.

For a complicated algorithm, its implementation by a human programmer usually starts with outlining a rough control flow followed by iterative enrichments, eventually yielding carefully generated syntactic structures and variables in a hierarchy. However, state-of-the-art large language models generate codes in a single pass, without intermediate warm-ups to reflect the structured thought process of "outline-then-detail". Inspired by the recent success of chain-of-thought prompting, we propose ChainCoder, a program synthesis language model that generates Python code progressively, i.e. from coarse to fine in multiple passes. We first decompose source code into layout frame components and accessory components via abstract syntax tree parsing to construct a hierarchical representation. We then reform our prediction target into a multi-pass objective, each pass generates a subsequence, which is concatenated in the hierarchy. Finally, a tailored transformer architecture is leveraged to jointly encode the natural language descriptions and syntactically aligned I/O data samples. Extensive evaluations show that ChainCoder outperforms state-of-the-arts, demonstrating that our progressive generation eases the reasoning procedure and guides the language model to generate higher-quality solutions. Our codes are available at: https://github.com/VITA-Group/ChainCoder.

The quality and size of a pretraining dataset significantly influence the performance of large language models (LLMs). While there have been numerous efforts in the curation of such a dataset for English users, there is a relative lack of similar initiatives for Traditional Chinese. Building upon this foundation of FineWeb, we introduce FineWeb-zhtw, a dataset tailored specifically for Traditional Chinese users. We came up with multiple stages of meticulously designed filters to cater to the linguistic difference between English and Traditional Chinese, to ensure comprehensiveness and quality. We determined effectiveness from querying dataset samples with three main objectives. Our code and datasets are publicly available.

Pre-training Transformers has shown promising results on open-domain and domain-specific downstream tasks. However, state-of-the-art Transformers require an unreasonably large amount of pre-training data and compute. In this paper, we propose FPDM (Fast Pre-training Technique using Document Level Metadata), a novel, compute-efficient framework that utilizes Document metadata and Domain-Specific Taxonomy as supervision signals to pre-train transformer encoder on a domain-specific corpus. The main innovation is that during domain-specific pretraining, an open-domain encoder is continually pre-trained using sentence-level embeddings as inputs (to accommodate long documents), however, fine-tuning is done with token-level embeddings as inputs to this encoder. We show that FPDM outperforms several transformer-based baselines in terms of character-level F1 scores and other automated metrics in the Customer Support, Scientific, and Legal Domains, and shows a negligible drop in performance on open-domain benchmarks. Importantly, the novel use of document-level supervision along with sentence-level embedding input for pre-training reduces pre-training compute by around 1,000, 4,500, and 500 times compared to MLM and/or NSP in Customer Support, Scientific, and Legal Domains, respectively. Code and datasets are available at https://bit.ly/FPDMCode.

In the field of language modeling, models augmented with retrieval components have emerged as a promising solution to address several challenges faced in the natural language processing (NLP) field, including knowledge grounding, interpretability, and scalability. Despite the primary focus on NLP, we posit that the paradigm of retrieval-enhancement can be extended to a broader spectrum of machine learning (ML) such as computer vision, time series prediction, and computational biology. Therefore, this work introduces a formal framework of this paradigm, Retrieval-Enhanced Machine Learning (REML), by synthesizing the literature in various domains in ML with consistent notations which is missing from the current literature. Also, we found that while a number of studies employ retrieval components to augment their models, there is a lack of integration with foundational Information Retrieval (IR) research. We bridge this gap between the seminal IR research and contemporary REML studies by investigating each component that comprises the REML framework. Ultimately, the goal of this work is to equip researchers across various disciplines with a comprehensive, formally structured framework of retrieval-enhanced models, thereby fostering interdisciplinary future research.

The heterogeneous network is a robust data abstraction that can model entities of different types interacting in various ways. Such heterogeneity brings rich semantic information but presents nontrivial challenges in aggregating the heterogeneous relationships between objects - especially those of higher-order indirect relations. Recent graph neural network approaches for representation learning on heterogeneous networks typically employ the attention mechanism, which is often only optimized for predictions based on direct links. Furthermore, even though most deep learning methods can aggregate higher-order information by building deeper models, such a scheme can diminish the degree of interpretability. To overcome these challenges, we explore an architecture - Layer-stacked ATTention Embedding (LATTE) - that automatically decomposes higher-order meta relations at each layer to extract the relevant heterogeneous neighborhood structures for each node. Additionally, by successively stacking layer representations, the learned node embedding offers a more interpretable aggregation scheme for nodes of different types at different neighborhood ranges. We conducted experiments on several benchmark heterogeneous network datasets. In both transductive and inductive node classification tasks, LATTE can achieve state-of-the-art performance compared to existing approaches, all while offering a lightweight model. With extensive experimental analyses and visualizations, the framework can demonstrate the ability to extract informative insights on heterogeneous networks.

Abstract meaning representation (AMR) highlights the core semantic information of text in a graph structure. Recently, pre-trained language models (PLMs) have advanced tasks of AMR parsing and AMR-to-text generation, respectively. However, PLMs are typically pre-trained on textual data, thus are sub-optimal for modeling structural knowledge. To this end, we investigate graph self-supervised training to improve the structure awareness of PLMs over AMR graphs. In particular, we introduce two graph auto-encoding strategies for graph-to-graph pre-training and four tasks to integrate text and graph information during pre-training. We further design a unified framework to bridge the gap between pre-training and fine-tuning tasks. Experiments on both AMR parsing and AMR-to-text generation show the superiority of our model. To our knowledge, we are the first to consider pre-training on semantic graphs.

Phrase representations play an important role in data science and natural language processing, benefiting various tasks like Entity Alignment, Record Linkage, Fuzzy Joins, and Paraphrase Classification. The current state-of-the-art method involves fine-tuning pre-trained language models for phrasal embeddings using contrastive learning. However, we have identified areas for improvement. First, these pre-trained models tend to be unnecessarily complex and require to be pre-trained on a corpus with context sentences. Second, leveraging the phrase type and morphology gives phrase representations that are both more precise and more flexible. We propose an improved framework to learn phrase representations in a context-free fashion. The framework employs phrase type classification as an auxiliary task and incorporates character-level information more effectively into the phrase representation. Furthermore, we design three granularities of data augmentation to increase the diversity of training samples. Our experiments across a wide range of tasks show that our approach generates superior phrase embeddings compared to previous methods while requiring a smaller model size. The code is available at \faGithub~ https://github.com/tigerchen52/PEARL abstract

Prompt-learning has become a new paradigm in modern natural language processing, which directly adapts pre-trained language models (PLMs) to cloze-style prediction, autoregressive modeling, or sequence to sequence generation, resulting in promising performances on various tasks. However, no standard implementation framework of prompt-learning is proposed yet, and most existing prompt-learning codebases, often unregulated, only provide limited implementations for specific scenarios. Since there are many details such as templating strategy, initializing strategy, and verbalizing strategy, etc. need to be considered in prompt-learning, practitioners face impediments to quickly adapting the desired prompt learning methods to their applications. In this paper, we present {OpenPrompt}, a unified easy-to-use toolkit to conduct prompt-learning over PLMs. OpenPrompt is a research-friendly framework that is equipped with efficiency, modularity, and extendibility, and its combinability allows the freedom to combine different PLMs, task formats, and prompting modules in a unified paradigm. Users could expediently deploy prompt-learning frameworks and evaluate the generalization of them on different NLP tasks without constraints. OpenPrompt is publicly released at { https://github.com/thunlp/OpenPrompt}.

Prompting and fine-tuning have emerged as two competing paradigms for augmenting language models with new capabilities, such as the use of tools. Prompting approaches are quick to set up but rely on providing explicit demonstrations of each tool's usage in the model's prompt, thus coupling tool use to the task at hand and limiting generalisation. Fine-tuning removes the need for task-specific demonstrations of tool usage at runtime; however, this ties new capabilities to a single model, thus making already-heavier setup costs a recurring expense. In this paper, we introduce language hooks, a novel framework for augmenting language models with new capabilities that is decoupled both from the model's task-specific prompt and from the model itself. The language hook algorithm interleaves text generation by the base model with the execution of modular programs that trigger conditionally based on the existing text and the available capabilities. Upon triggering, programs may call external tools, auxiliary language models (e.g. using tool specific prompts), and modify the existing context. We benchmark our method against state-of-the-art baselines, find that it outperforms task-aware approaches, and demonstrate its ability to generalise to novel tasks.

The performance of a large language model (LLM) depends heavily on the quality and size of its pretraining dataset. However, the pretraining datasets for state-of-the-art open LLMs like Llama 3 and Mixtral are not publicly available and very little is known about how they were created. In this work, we introduce FineWeb, a 15-trillion token dataset derived from 96 Common Crawl snapshots that produces better-performing LLMs than other open pretraining datasets. To advance the understanding of how best to curate high-quality pretraining datasets, we carefully document and ablate all of the design choices used in FineWeb, including in-depth investigations of deduplication and filtering strategies. In addition, we introduce FineWeb-Edu, a 1.3-trillion token collection of educational text filtered from FineWeb. LLMs pretrained on FineWeb-Edu exhibit dramatically better performance on knowledge- and reasoning-intensive benchmarks like MMLU and ARC. Along with our datasets, we publicly release our data curation codebase and all of the models trained during our ablation experiments.

We extend Textual Inversion to learn pseudo-words that represent a concept at different resolutions. This allows us to generate images that use the concept with different levels of detail and also to manipulate different resolutions using language. Once learned, the user can generate images at different levels of agreement to the original concept; "A photo of S^*(0)" produces the exact object while the prompt "A photo of S^*(0.8)" only matches the rough outlines and colors. Our framework allows us to generate images that use different resolutions of an image (e.g. details, textures, styles) as separate pseudo-words that can be composed in various ways. We open-soure our code in the following URL: https://github.com/giannisdaras/multires_textual_inversion

Relation extraction (RE) has achieved remarkable progress with the help of pre-trained language models. However, existing RE models are usually incapable of handling two situations: implicit expressions and long-tail relation classes, caused by language complexity and data sparsity. Further, these approaches and models are largely inaccessible to users who don't have direct access to large language models (LLMs) and/or infrastructure for supervised training or fine-tuning. Rule-based systems also struggle with implicit expressions. Apart from this, Real world financial documents such as various 10-X reports (including 10-K, 10-Q, etc.) of publicly traded companies pose another challenge to rule-based systems in terms of longer and complex sentences. In this paper, we introduce a simple approach that consults training relations at test time through a nearest-neighbor search over dense vectors of lexico-syntactic patterns and provides a simple yet effective means to tackle the above issues. We evaluate our approach on REFinD and show that our method achieves state-of-the-art performance. We further show that it can provide a good start for human in the loop setup when a small number of annotations are available and it is also beneficial when domain experts can provide high quality patterns.

Large language models typically undergo two training stages, pretraining and finetuning. Despite that large-scale pretraining endows the model with strong capabilities to generate natural language responses, these pretrained models can still fail to understand human instructions at times. To enhance language models' ability of interpreting and responding to instructions, instruction finetuning has emerged as a critical method in this area. Recent studies found that large language models can be finetuned to perform well even with a small amount of high-quality instruction-following data. However, the selection of high-quality datasets for finetuning language models still lacks clear guidelines to follow. In this paper, we propose InstructMining, a linear rule for evaluating instruction-following data quality. We formulate InstructMining using specific natural language indicators. To investigate the relationship between data quality and these indicators, we further conduct extensive finetuning experiments. The experiment results are then applied to estimating parameters in InstructMining. To further investigate its performance, we use InstructMining to select high-quality data from unseen datasets. Results demonstrate that InstructMining can help select relatively high-quality samples from various instruction-following datasets. Compared to models finetuned on unfiltered datasets, models finetuned on InstructMining selected datasets perform better on 42.5% cases.

Pre-trained models have achieved state-of-the-art results in various Natural Language Processing (NLP) tasks. Recent works such as T5 and GPT-3 have shown that scaling up pre-trained language models can improve their generalization abilities. Particularly, the GPT-3 model with 175 billion parameters shows its strong task-agnostic zero-shot/few-shot learning capabilities. Despite their success, these large-scale models are trained on plain texts without introducing knowledge such as linguistic knowledge and world knowledge. In addition, most large-scale models are trained in an auto-regressive way. As a result, this kind of traditional fine-tuning approach demonstrates relatively weak performance when solving downstream language understanding tasks. In order to solve the above problems, we propose a unified framework named ERNIE 3.0 for pre-training large-scale knowledge enhanced models. It fuses auto-regressive network and auto-encoding network, so that the trained model can be easily tailored for both natural language understanding and generation tasks with zero-shot learning, few-shot learning or fine-tuning. We trained the model with 10 billion parameters on a 4TB corpus consisting of plain texts and a large-scale knowledge graph. Empirical results show that the model outperforms the state-of-the-art models on 54 Chinese NLP tasks, and its English version achieves the first place on the SuperGLUE benchmark (July 3, 2021), surpassing the human performance by +0.8% (90.6% vs. 89.8%).

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

In this paper, we study the problem of inference in high-order structured prediction tasks. In the context of Markov random fields, the goal of a high-order inference task is to maximize a score function on the space of labels, and the score function can be decomposed into sum of unary and high-order potentials. We apply a generative model approach to study the problem of high-order inference, and provide a two-stage convex optimization algorithm for exact label recovery. We also provide a new class of hypergraph structural properties related to hyperedge expansion that drives the success in general high-order inference problems. Finally, we connect the performance of our algorithm and the hyperedge expansion property using a novel hypergraph Cheeger-type inequality.

Learning to capture text-table alignment is essential for tasks like text-to-SQL. A model needs to correctly recognize natural language references to columns and values and to ground them in the given database schema. In this paper, we present a novel weakly supervised Structure-Grounded pretraining framework (StruG) for text-to-SQL that can effectively learn to capture text-table alignment based on a parallel text-table corpus. We identify a set of novel prediction tasks: column grounding, value grounding and column-value mapping, and leverage them to pretrain a text-table encoder. Additionally, to evaluate different methods under more realistic text-table alignment settings, we create a new evaluation set Spider-Realistic based on Spider dev set with explicit mentions of column names removed, and adopt eight existing text-to-SQL datasets for cross-database evaluation. STRUG brings significant improvement over BERT-LARGE in all settings. Compared with existing pretraining methods such as GRAPPA, STRUG achieves similar performance on Spider, and outperforms all baselines on more realistic sets. The Spider-Realistic dataset is available at https://doi.org/10.5281/zenodo.5205322.

Pre-trained LLMs have demonstrated substantial capabilities across a range of conventional natural language processing (NLP) tasks, such as summarization and entity recognition. In this paper, we explore the application of LLMs in the generation of high-quality protein sequences. Specifically, we adopt a suite of pre-trained LLMs, including Mistral-7B1, Llama-2-7B2, Llama-3-8B3, and gemma-7B4, to produce valid protein sequences. All of these models are publicly available.5 Unlike previous work in this field, our approach utilizes a relatively small dataset comprising 42,000 distinct human protein sequences. We retrain these models to process protein-related data, ensuring the generation of biologically feasible protein structures. Our findings demonstrate that even with limited data, the adapted models exhibit efficiency comparable to established protein-focused models such as ProGen varieties, ProtGPT2, and ProLLaMA, which were trained on millions of protein sequences. To validate and quantify the performance of our models, we conduct comparative analyses employing standard metrics such as pLDDT, RMSD, TM-score, and REU. Furthermore, we commit to making the trained versions of all four models publicly available, fostering greater transparency and collaboration in the field of computational biology.

This paper investigates the ability of transformer-based models to learn structural recursion from examples. Recursion is a universal concept in both natural and formal languages. Structural recursion is central to the programming language and formal mathematics tasks where symbolic tools currently excel beyond neural models, such as inferring semantic relations between datatypes and emulating program behavior. We introduce a general framework that nicely connects the abstract concepts of structural recursion in the programming language domain to concrete sequence modeling problems and learned models' behavior. The framework includes a representation that captures the general syntax of structural recursion, coupled with two different frameworks for understanding their semantics -- one that is more natural from a programming languages perspective and one that helps bridge that perspective with a mechanistic understanding of the underlying transformer architecture. With our framework as a powerful conceptual tool, we identify different issues under various set-ups. The models trained to emulate recursive computations cannot fully capture the recursion yet instead fit short-cut algorithms and thus cannot solve certain edge cases that are under-represented in the training distribution. In addition, it is difficult for state-of-the-art large language models (LLMs) to mine recursive rules from in-context demonstrations. Meanwhile, these LLMs fail in interesting ways when emulating reduction (step-wise computation) of the recursive function.

This work focuses on leveraging and selecting from vast, unlabeled, open data to pre-fine-tune a pre-trained language model. The goal is to minimize the need for costly domain-specific data for subsequent fine-tuning while achieving desired performance levels. While many data selection algorithms have been designed for small-scale applications, rendering them unsuitable for our context, some emerging methods do cater to language data scales. However, they often prioritize data that aligns with the target distribution. While this strategy may be effective when training a model from scratch, it can yield limited results when the model has already been pre-trained on a different distribution. Differing from prior work, our key idea is to select data that nudges the pre-training distribution closer to the target distribution. We show the optimality of this approach for fine-tuning tasks under certain conditions. We demonstrate the efficacy of our methodology across a diverse array of tasks (NLU, NLG, zero-shot) with models up to 2.7B, showing that it consistently surpasses other selection methods. Moreover, our proposed method is significantly faster than existing techniques, scaling to millions of samples within a single GPU hour. Our code is open-sourced (Code repository: https://anonymous.4open.science/r/DV4LLM-D761/ ). While fine-tuning offers significant potential for enhancing performance across diverse tasks, its associated costs often limit its widespread adoption; with this work, we hope to lay the groundwork for cost-effective fine-tuning, making its benefits more accessible.

Transformer-based Language Models are widely used in Natural Language Processing related tasks. Thanks to their pre-training, they have been successfully adapted to Information Extraction in business documents. However, most pre-training tasks proposed in the literature for business documents are too generic and not sufficient to learn more complex structures. In this paper, we use LayoutLM, a language model pre-trained on a collection of business documents, and introduce two new pre-training tasks that further improve its capacity to extract relevant information. The first is aimed at better understanding the complex layout of documents, and the second focuses on numeric values and their order of magnitude. These tasks force the model to learn better-contextualized representations of the scanned documents. We further introduce a new post-processing algorithm to decode BIESO tags in Information Extraction that performs better with complex entities. Our method significantly improves extraction performance on both public (from 93.88 to 95.50 F1 score) and private (from 84.35 to 84.84 F1 score) datasets composed of expense receipts, invoices, and purchase orders.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

We introduce model editing with canonical examples, a setting in which (1) a single learning example is provided per desired behavior, (2) evaluation is performed exclusively out-of-distribution, and (3) deviation from an initial model is strictly limited. A canonical example is a simple instance of good behavior, e.g., The capital of Mauritius is Port Louis) or bad behavior, e.g., An aspect of researchers is coldhearted). The evaluation set contains more complex examples of each behavior (like a paragraph in which the capital of Mauritius is called for.) We create three datasets and modify three more for model editing with canonical examples, covering knowledge-intensive improvements, social bias mitigation, and syntactic edge cases. In our experiments on Pythia language models, we find that LoRA outperforms full finetuning and MEMIT. We then turn to the Backpack language model architecture because it is intended to enable targeted improvement. The Backpack defines a large bank of sense vectors--a decomposition of the different uses of each word--which are weighted and summed to form the output logits of the model. We propose sense finetuning, which selects and finetunes a few (approx 10) sense vectors for each canonical example, and find that it outperforms other finetuning methods, e.g., 4.8% improvement vs 0.3%. Finally, we improve GPT-J-6B by an inference-time ensemble with just the changes from sense finetuning of a 35x smaller Backpack, in one setting outperforming editing GPT-J itself (4.1% vs 1.0%).

Contextual pretrained language models, such as BERT (Devlin et al., 2019), have made significant breakthrough in various NLP tasks by training on large scale of unlabeled text re-sources.Financial sector also accumulates large amount of financial communication text.However, there is no pretrained finance specific language models available. In this work,we address the need by pretraining a financial domain specific BERT models, FinBERT, using a large scale of financial communication corpora. Experiments on three financial sentiment classification tasks confirm the advantage of FinBERT over generic domain BERT model. The code and pretrained models are available at https://github.com/yya518/FinBERT. We hope this will be useful for practitioners and researchers working on financial NLP tasks.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

English to Indian language machine translation poses the challenge of structural and morphological divergence. This paper describes English to Indian language statistical machine translation using pre-ordering and suffix separation. The pre-ordering uses rules to transfer the structure of the source sentences prior to training and translation. This syntactic restructuring helps statistical machine translation to tackle the structural divergence and hence better translation quality. The suffix separation is used to tackle the morphological divergence between English and highly agglutinative Indian languages. We demonstrate that the use of pre-ordering and suffix separation helps in improving the quality of English to Indian Language machine translation.

Large pretrained language models are widely used in downstream NLP tasks via task-specific fine-tuning, but such procedures can be costly. Recently, Parameter-Efficient Fine-Tuning (PEFT) methods have achieved strong task performance while updating a much smaller number of parameters compared to full model fine-tuning (FFT). However, it is non-trivial to make informed design choices on the PEFT configurations, such as their architecture, the number of tunable parameters, and even the layers in which the PEFT modules are inserted. Consequently, it is highly likely that the current, manually designed configurations are suboptimal in terms of their performance-efficiency trade-off. Inspired by advances in neural architecture search, we propose AutoPEFT for automatic PEFT configuration selection: we first design an expressive configuration search space with multiple representative PEFT modules as building blocks. Using multi-objective Bayesian optimisation in a low-cost setup, we then discover a Pareto-optimal set of configurations with strong performance-cost trade-offs across different numbers of parameters that are also highly transferable across different tasks. Empirically, on GLUE and SuperGLUE tasks, we show that AutoPEFT-discovered configurations significantly outperform existing PEFT methods and are on par or better than FFT, without incurring substantial training efficiency costs.

We investigate the capability of a transformer pretrained on natural language to generalize to other modalities with minimal finetuning -- in particular, without finetuning of the self-attention and feedforward layers of the residual blocks. We consider such a model, which we call a Frozen Pretrained Transformer (FPT), and study finetuning it on a variety of sequence classification tasks spanning numerical computation, vision, and protein fold prediction. In contrast to prior works which investigate finetuning on the same modality as the pretraining dataset, we show that pretraining on natural language can improve performance and compute efficiency on non-language downstream tasks. Additionally, we perform an analysis of the architecture, comparing the performance of a random initialized transformer to a random LSTM. Combining the two insights, we find language-pretrained transformers can obtain strong performance on a variety of non-language tasks.

Analysis of pre-trained code models also has revealed that they can effectively learn program syntax. However, these works are limited in analyzing code syntax and their distance-based approaches are not accurate due to the curse of high dimensionality. Furthermore, the study of the learnt program semantics of these models is rarely discussed. To further understand the code features learnt by these models, in this paper, we target two well-known representative code pre-trained models (i.e., CodeBERT and GraphCodeBERT) and devise a set of probing tasks for the syntax and semantics analysis. Specifically, on one hand, we design two probing tasks (i.e., syntax pair node prediction and token tagging prediction) to manipulate AST for the understanding of learnt program syntax. On the other hand, we design two tasks (i.e., semantic relationship prediction and semantic propagation prediction(inGraph) ) on the constructed control flow graph (CFG), data dependency graph (DDG) and control dependency graph (CDG) for the learnt program semantic analysis. In addition, to understand which kind of program semantics these pre-trained models can comprehend well, we conduct the statistical analysis for attention weights learnt by different heads and layers. Through extensive analysis in terms of program syntax and semantics, we have the following findings: 1) Both CodeBERT and GraphCodeBERT can learn the program syntax well. 2) Both CodeBERT and GraphCodeBERT can learn program semantics to different extents. GraphCodeBERT is superior to CodeBERT in learning program control flow and data dependency information but has a similar capability to CodeBERT in learning control dependency information. 3) Both CodeBERT and GraphCodeBERT can capture program semantics in the final layer of representation, but different attention heads and layers exhibit different roles in learning program semantics.

This paper presents Okapi, a new dataset for Natural Language to executable web Application Programming Interfaces (NL2API). This dataset is in English and contains 22,508 questions and 9,019 unique API calls, covering three domains. We define new compositional generalization tasks for NL2API which explore the models' ability to extrapolate from simple API calls in the training set to new and more complex API calls in the inference phase. Also, the models are required to generate API calls that execute correctly as opposed to the existing approaches which evaluate queries with placeholder values. Our dataset is different than most of the existing compositional semantic parsing datasets because it is a non-synthetic dataset studying the compositional generalization in a low-resource setting. Okapi is a step towards creating realistic datasets and benchmarks for studying compositional generalization alongside the existing datasets and tasks. We report the generalization capabilities of sequence-to-sequence baseline models trained on a variety of the SCAN and Okapi datasets tasks. The best model achieves 15\% exact match accuracy when generalizing from simple API calls to more complex API calls. This highlights some challenges for future research. Okapi dataset and tasks are publicly available at https://aka.ms/nl2api/data.

Language models pretrained on text from a wide variety of sources form the foundation of today's NLP. In light of the success of these broad-coverage models, we investigate whether it is still helpful to tailor a pretrained model to the domain of a target task. We present a study across four domains (biomedical and computer science publications, news, and reviews) and eight classification tasks, showing that a second phase of pretraining in-domain (domain-adaptive pretraining) leads to performance gains, under both high- and low-resource settings. Moreover, adapting to the task's unlabeled data (task-adaptive pretraining) improves performance even after domain-adaptive pretraining. Finally, we show that adapting to a task corpus augmented using simple data selection strategies is an effective alternative, especially when resources for domain-adaptive pretraining might be unavailable. Overall, we consistently find that multi-phase adaptive pretraining offers large gains in task performance.

Recently, pre-trained models have achieved state-of-the-art results in various language understanding tasks, which indicates that pre-training on large-scale corpora may play a crucial role in natural language processing. Current pre-training procedures usually focus on training the model with several simple tasks to grasp the co-occurrence of words or sentences. However, besides co-occurring, there exists other valuable lexical, syntactic and semantic information in training corpora, such as named entity, semantic closeness and discourse relations. In order to extract to the fullest extent, the lexical, syntactic and semantic information from training corpora, we propose a continual pre-training framework named ERNIE 2.0 which builds and learns incrementally pre-training tasks through constant multi-task learning. Experimental results demonstrate that ERNIE 2.0 outperforms BERT and XLNet on 16 tasks including English tasks on GLUE benchmarks and several common tasks in Chinese. The source codes and pre-trained models have been released at https://github.com/PaddlePaddle/ERNIE.

Pre-trained models for Natural Languages (NL) like BERT and GPT have been recently shown to transfer well to Programming Languages (PL) and largely benefit a broad set of code-related tasks. Despite their success, most current methods either rely on an encoder-only (or decoder-only) pre-training that is suboptimal for generation (resp. understanding) tasks or process the code snippet in the same way as NL, neglecting the special characteristics of PL such as token types. We present CodeT5, a unified pre-trained encoder-decoder Transformer model that better leverages the code semantics conveyed from the developer-assigned identifiers. Our model employs a unified framework to seamlessly support both code understanding and generation tasks and allows for multi-task learning. Besides, we propose a novel identifier-aware pre-training task that enables the model to distinguish which code tokens are identifiers and to recover them when they are masked. Furthermore, we propose to exploit the user-written code comments with a bimodal dual generation task for better NL-PL alignment. Comprehensive experiments show that CodeT5 significantly outperforms prior methods on understanding tasks such as code defect detection and clone detection, and generation tasks across various directions including PL-NL, NL-PL, and PL-PL. Further analysis reveals that our model can better capture semantic information from code. Our code and pre-trained models are released at https: //github.com/salesforce/CodeT5 .

The ability to generate natural language sequences from source code snippets has a variety of applications such as code summarization, documentation, and retrieval. Sequence-to-sequence (seq2seq) models, adopted from neural machine translation (NMT), have achieved state-of-the-art performance on these tasks by treating source code as a sequence of tokens. We present {scriptsize CODE2SEQ}: an alternative approach that leverages the syntactic structure of programming languages to better encode source code. Our model represents a code snippet as the set of compositional paths in its abstract syntax tree (AST) and uses attention to select the relevant paths while decoding. We demonstrate the effectiveness of our approach for two tasks, two programming languages, and four datasets of up to 16M examples. Our model significantly outperforms previous models that were specifically designed for programming languages, as well as state-of-the-art NMT models. An interactive online demo of our model is available at http://code2seq.org. Our code, data and trained models are available at http://github.com/tech-srl/code2seq.

Weakly-Supervised Scene Graph Generation (WSSGG) research has recently emerged as an alternative to the fully-supervised approach that heavily relies on costly annotations. In this regard, studies on WSSGG have utilized image captions to obtain unlocalized triplets while primarily focusing on grounding the unlocalized triplets over image regions. However, they have overlooked the two issues involved in the triplet formation process from the captions: 1) Semantic over-simplification issue arises when extracting triplets from captions, where fine-grained predicates in captions are undesirably converted into coarse-grained predicates, resulting in a long-tailed predicate distribution, and 2) Low-density scene graph issue arises when aligning the triplets in the caption with entity/predicate classes of interest, where many triplets are discarded and not used in training, leading to insufficient supervision. To tackle the two issues, we propose a new approach, i.e., Large Language Model for weakly-supervised SGG (LLM4SGG), where we mitigate the two issues by leveraging the LLM's in-depth understanding of language and reasoning ability during the extraction of triplets from captions and alignment of entity/predicate classes with target data. To further engage the LLM in these processes, we adopt the idea of Chain-of-Thought and the in-context few-shot learning strategy. To validate the effectiveness of LLM4SGG, we conduct extensive experiments on Visual Genome and GQA datasets, showing significant improvements in both Recall@K and mean Recall@K compared to the state-of-the-art WSSGG methods. A further appeal is that LLM4SGG is data-efficient, enabling effective model training with a small amount of training images.

Although we have witnessed impressive progress in Semantic Role Labeling (SRL), most of the research in the area is carried out assuming that the majority of predicates are verbs. Conversely, predicates can also be expressed using other parts of speech, e.g., nouns and adjectives. However, non-verbal predicates appear in the benchmarks we commonly use to measure progress in SRL less frequently than in some real-world settings -- newspaper headlines, dialogues, and tweets, among others. In this paper, we put forward a new PropBank dataset which boasts wide coverage of multiple predicate types. Thanks to it, we demonstrate empirically that standard benchmarks do not provide an accurate picture of the current situation in SRL and that state-of-the-art systems are still incapable of transferring knowledge across different predicate types. Having observed these issues, we also present a novel, manually-annotated challenge set designed to give equal importance to verbal, nominal, and adjectival predicate-argument structures. We use such dataset to investigate whether we can leverage different linguistic resources to promote knowledge transfer. In conclusion, we claim that SRL is far from "solved", and its integration with other semantic tasks might enable significant improvements in the future, especially for the long tail of non-verbal predicates, thereby facilitating further research on SRL for non-verbal predicates.

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.