Daily Papers

Pre-trained language models are increasingly important components across multiple information retrieval (IR) paradigms. Late interaction, introduced with the ColBERT model and recently refined in ColBERTv2, is a popular paradigm that holds state-of-the-art status across many benchmarks. To dramatically speed up the search latency of late interaction, we introduce the Performance-optimized Late Interaction Driver (PLAID). Without impacting quality, PLAID swiftly eliminates low-scoring passages using a novel centroid interaction mechanism that treats every passage as a lightweight bag of centroids. PLAID uses centroid interaction as well as centroid pruning, a mechanism for sparsifying the bag of centroids, within a highly-optimized engine to reduce late interaction search latency by up to 7times on a GPU and 45times on a CPU against vanilla ColBERTv2, while continuing to deliver state-of-the-art retrieval quality. This allows the PLAID engine with ColBERTv2 to achieve latency of tens of milliseconds on a GPU and tens or just few hundreds of milliseconds on a CPU at large scale, even at the largest scales we evaluate with 140M passages.

Recent progress in Natural Language Understanding (NLU) is driving fast-paced advances in Information Retrieval (IR), largely owed to fine-tuning deep language models (LMs) for document ranking. While remarkably effective, the ranking models based on these LMs increase computational cost by orders of magnitude over prior approaches, particularly as they must feed each query-document pair through a massive neural network to compute a single relevance score. To tackle this, we present ColBERT, a novel ranking model that adapts deep LMs (in particular, BERT) for efficient retrieval. ColBERT introduces a late interaction architecture that independently encodes the query and the document using BERT and then employs a cheap yet powerful interaction step that models their fine-grained similarity. By delaying and yet retaining this fine-granular interaction, ColBERT can leverage the expressiveness of deep LMs while simultaneously gaining the ability to pre-compute document representations offline, considerably speeding up query processing. Beyond reducing the cost of re-ranking the documents retrieved by a traditional model, ColBERT's pruning-friendly interaction mechanism enables leveraging vector-similarity indexes for end-to-end retrieval directly from a large document collection. We extensively evaluate ColBERT using two recent passage search datasets. Results show that ColBERT's effectiveness is competitive with existing BERT-based models (and outperforms every non-BERT baseline), while executing two orders-of-magnitude faster and requiring four orders-of-magnitude fewer FLOPs per query.

The ColBERT model has recently been proposed as an effective BERT based ranker. By adopting a late interaction mechanism, a major advantage of ColBERT is that document representations can be precomputed in advance. However, the big downside of the model is the index size, which scales linearly with the number of tokens in the collection. In this paper, we study various designs for ColBERT models in order to attack this problem. While compression techniques have been explored to reduce the index size, in this paper we study token pruning techniques for ColBERT. We compare simple heuristics, as well as a single layer of attention mechanism to select the tokens to keep at indexing time. Our experiments show that ColBERT indexes can be pruned up to 30\% on the MS MARCO passage collection without a significant drop in performance. Finally, we experiment on MS MARCO documents, which reveal several challenges for such mechanism.

Unsupervised large-scale vision-language pre-training has shown promising advances on various downstream tasks. Existing methods often model the cross-modal interaction either via the similarity of the global feature of each modality which misses sufficient information, or finer-grained interactions using cross/self-attention upon visual and textual tokens. However, cross/self-attention suffers from inferior efficiency in both training and inference. In this paper, we introduce a large-scale Fine-grained Interactive Language-Image Pre-training (FILIP) to achieve finer-level alignment through a cross-modal late interaction mechanism, which uses a token-wise maximum similarity between visual and textual tokens to guide the contrastive objective. FILIP successfully leverages the finer-grained expressiveness between image patches and textual words by modifying only contrastive loss, while simultaneously gaining the ability to pre-compute image and text representations offline at inference, keeping both large-scale training and inference efficient. Furthermore, we construct a new large-scale image-text pair dataset called FILIP300M for pre-training. Experiments show that FILIP achieves state-of-the-art performance on multiple downstream vision-language tasks including zero-shot image classification and image-text retrieval. The visualization on word-patch alignment further shows that FILIP can learn meaningful fine-grained features with promising localization ability.

Documents are visually rich structures that convey information through text, as well as tables, figures, page layouts, or fonts. While modern document retrieval systems exhibit strong performance on query-to-text matching, they struggle to exploit visual cues efficiently, hindering their performance on practical document retrieval applications such as Retrieval Augmented Generation. To benchmark current systems on visually rich document retrieval, we introduce the Visual Document Retrieval Benchmark ViDoRe, composed of various page-level retrieving tasks spanning multiple domains, languages, and settings. The inherent shortcomings of modern systems motivate the introduction of a new retrieval model architecture, ColPali, which leverages the document understanding capabilities of recent Vision Language Models to produce high-quality contextualized embeddings solely from images of document pages. Combined with a late interaction matching mechanism, ColPali largely outperforms modern document retrieval pipelines while being drastically faster and end-to-end trainable.

Neural information retrieval (IR) has greatly advanced search and other knowledge-intensive language tasks. While many neural IR methods encode queries and documents into single-vector representations, late interaction models produce multi-vector representations at the granularity of each token and decompose relevance modeling into scalable token-level computations. This decomposition has been shown to make late interaction more effective, but it inflates the space footprint of these models by an order of magnitude. In this work, we introduce ColBERTv2, a retriever that couples an aggressive residual compression mechanism with a denoised supervision strategy to simultaneously improve the quality and space footprint of late interaction. We evaluate ColBERTv2 across a wide range of benchmarks, establishing state-of-the-art quality within and outside the training domain while reducing the space footprint of late interaction models by 6--10times.

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.

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.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Multitask Gaussian process (MTGP) is powerful for joint learning of multiple tasks with complicated correlation patterns. However, due to the assembling of additive independent latent functions, all current MTGPs including the salient linear model of coregionalization (LMC) and convolution frameworks cannot effectively represent and learn the hierarchical latent interactions between its latent functions. In this paper, we further investigate the interactions in LMC of MTGP and then propose a novel kernel representation of the hierarchical interactions, which ameliorates both the expressiveness and the interpretability of MTGP. Specifically, we express the interaction as a product of function interaction and coefficient interaction. The function interaction is modeled by using cross convolution of latent functions. The coefficient interaction between the LMCs is described as a cross coregionalization term. We validate that considering the interactions can promote knowledge transferring in MTGP and compare our approach with some state-of-the-art MTGPs on both synthetic- and real-world datasets.

Self-supervised training of language models (LMs) has seen great success for protein sequences in learning meaningful representations and for generative drug design. Most protein LMs are based on the Transformer architecture trained on individual proteins with short context lengths. Such protein LMs cannot extrapolate to longer proteins and protein complexes well. They also fail to account for the underlying biological mechanisms carried out by biomolecular interactions and dynamics i.e., proteins often interact with other proteins, molecules, and pathways in complex biological systems. In this work, we propose LC-PLM based on an alternative protein LM architecture, BiMamba-S, built off selective structured state-space models, to learn high-quality universal protein representations at the amino acid token level using masked language modeling. We also introduce its graph-contextual variant, LC-PLM-G, which contextualizes protein-protein interaction (PPI) graphs for a second stage of training. LC-PLM demonstrates favorable neural scaling laws, better length extrapolation capability, and a 7% to 34% improvement on protein downstream tasks than Transformer-based ESM-2. LC-PLM-G further trained within the context of PPI graphs shows promising results on protein structure and function prediction tasks. Our study demonstrates the benefit of increasing the context size with computationally efficient LM architecture (e.g. structured state space models) in learning universal protein representations and incorporating molecular interaction context contained in biological graphs.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

Large Language Models (LLMs) are transforming society and permeating into diverse applications. As a result, LLMs will frequently interact with us and other agents. It is, therefore, of great societal value to understand how LLMs behave in interactive social settings. Here, we propose to use behavioral game theory to study LLM's cooperation and coordination behavior. To do so, we let different LLMs (GPT-3, GPT-3.5, and GPT-4) play finitely repeated games with each other and with other, human-like strategies. Our results show that LLMs generally perform well in such tasks and also uncover persistent behavioral signatures. In a large set of two players-two strategies games, we find that LLMs are particularly good at games where valuing their own self-interest pays off, like the iterated Prisoner's Dilemma family. However, they behave sub-optimally in games that require coordination. We, therefore, further focus on two games from these distinct families. In the canonical iterated Prisoner's Dilemma, we find that GPT-4 acts particularly unforgivingly, always defecting after another agent has defected only once. In the Battle of the Sexes, we find that GPT-4 cannot match the behavior of the simple convention to alternate between options. We verify that these behavioral signatures are stable across robustness checks. Finally, we show how GPT-4's behavior can be modified by providing further information about the other player as well as by asking it to predict the other player's actions before making a choice. These results enrich our understanding of LLM's social behavior and pave the way for a behavioral game theory for machines.

Humans are highly adaptable, swiftly switching between different modes to progressively handle different tasks, situations and contexts. In Human-object interaction (HOI) activities, these modes can be attributed to two mechanisms: (1) the large-scale consistent plan for the whole activity and (2) the small-scale children interactive actions that start and end along the timeline. While neuroscience and cognitive science have confirmed this multi-mechanism nature of human behavior, machine modeling approaches for human motion are trailing behind. While attempted to use gradually morphing structures (e.g., graph attention networks) to model the dynamic HOI patterns, they miss the expeditious and discrete mode-switching nature of the human motion. To bridge that gap, this work proposes to model two concurrent mechanisms that jointly control human motion: the Persistent process that runs continually on the global scale, and the Transient sub-processes that operate intermittently on the local context of the human while interacting with objects. These two mechanisms form an interactive Persistent-Transient Duality that synergistically governs the activity sequences. We model this conceptual duality by a parent-child neural network of Persistent and Transient channels with a dedicated neural module for dynamic mechanism switching. The framework is trialed on HOI motion forecasting. On two rich datasets and a wide variety of settings, the model consistently delivers superior performances, proving its suitability for the challenge.

We present an attention mechanism inspired from definition of screened Coulomb potential. This attention mechanism was used to interpret the Graph Attention (GAT) model layers and training dataset by using a flexible and scalable framework (CoulGAT) developed for this purpose. Using CoulGAT, a forest of plain and resnet models were trained and characterized using this attention mechanism against CHAMPS dataset. The learnable variables of the attention mechanism are used to extract node-node and node-feature interactions to define an empirical standard model for the graph structure and hidden layer. This representation of graph and hidden layers can be used as a tool to compare different models, optimize hidden layers and extract a compact definition of graph structure of the dataset.

Click-through rate prediction is one of the core tasks in commercial recommender systems. It aims to predict the probability of a user clicking a particular item given user and item features. As feature interactions bring in non-linearity, they are widely adopted to improve the performance of CTR prediction models. Therefore, effectively modelling feature interactions has attracted much attention in both the research and industry field. The current approaches can generally be categorized into three classes: (1) na\"ive methods, which do not model feature interactions and only use original features; (2) memorized methods, which memorize feature interactions by explicitly viewing them as new features and assigning trainable embeddings; (3) factorized methods, which learn latent vectors for original features and implicitly model feature interactions through factorization functions. Studies have shown that modelling feature interactions by one of these methods alone are suboptimal due to the unique characteristics of different feature interactions. To address this issue, we first propose a general framework called OptInter which finds the most suitable modelling method for each feature interaction. Different state-of-the-art deep CTR models can be viewed as instances of OptInter. To realize the functionality of OptInter, we also introduce a learning algorithm that automatically searches for the optimal modelling method. We conduct extensive experiments on four large datasets. Our experiments show that OptInter improves the best performed state-of-the-art baseline deep CTR models by up to 2.21%. Compared to the memorized method, which also outperforms baselines, we reduce up to 91% parameters. In addition, we conduct several ablation studies to investigate the influence of different components of OptInter. Finally, we provide interpretable discussions on the results of OptInter.

Large language models (LLMs) provide a compelling foundation for building generally-capable AI agents. These agents may soon be deployed at scale in the real world, representing the interests of individual humans (e.g., AI assistants) or groups of humans (e.g., AI-accelerated corporations). At present, relatively little is known about the dynamics of multiple LLM agents interacting over many generations of iterative deployment. In this paper, we examine whether a "society" of LLM agents can learn mutually beneficial social norms in the face of incentives to defect, a distinctive feature of human sociality that is arguably crucial to the success of civilization. In particular, we study the evolution of indirect reciprocity across generations of LLM agents playing a classic iterated Donor Game in which agents can observe the recent behavior of their peers. We find that the evolution of cooperation differs markedly across base models, with societies of Claude 3.5 Sonnet agents achieving significantly higher average scores than Gemini 1.5 Flash, which, in turn, outperforms GPT-4o. Further, Claude 3.5 Sonnet can make use of an additional mechanism for costly punishment to achieve yet higher scores, while Gemini 1.5 Flash and GPT-4o fail to do so. For each model class, we also observe variation in emergent behavior across random seeds, suggesting an understudied sensitive dependence on initial conditions. We suggest that our evaluation regime could inspire an inexpensive and informative new class of LLM benchmarks, focussed on the implications of LLM agent deployment for the cooperative infrastructure of society.

Model-based reinforcement learning promises to learn an optimal policy from fewer interactions with the environment compared to model-free reinforcement learning by learning an intermediate model of the environment in order to predict future interactions. When predicting a sequence of interactions, the rollout length, which limits the prediction horizon, is a critical hyperparameter as accuracy of the predictions diminishes in the regions that are further away from real experience. As a result, with a longer rollout length, an overall worse policy is learned in the long run. Thus, the hyperparameter provides a trade-off between quality and efficiency. In this work, we frame the problem of tuning the rollout length as a meta-level sequential decision-making problem that optimizes the final policy learned by model-based reinforcement learning given a fixed budget of environment interactions by adapting the hyperparameter dynamically based on feedback from the learning process, such as accuracy of the model and the remaining budget of interactions. We use model-free deep reinforcement learning to solve the meta-level decision problem and demonstrate that our approach outperforms common heuristic baselines on two well-known reinforcement learning environments.

Large language models (LLMs) have demonstrated remarkable capabilities in generating human-like text and exhibiting personality traits similar to those in humans. However, the mechanisms by which LLMs encode and express traits such as agreeableness and impulsiveness remain poorly understood. Drawing on the theory of social determinism, we investigate how long-term background factors, such as family environment and cultural norms, interact with short-term pressures like external instructions, shaping and influencing LLMs' personality traits. By steering the output of LLMs through the utilization of interpretable features within the model, we explore how these background and pressure factors lead to changes in the model's traits without the need for further fine-tuning. Additionally, we suggest the potential impact of these factors on model safety from the perspective of personality.

Autonomous agents powered by large language models (LLMs) have the potential to enhance human capabilities, assisting with digital tasks from sending emails to performing data analysis. The abilities of existing LLMs at such tasks are often hindered by the lack of high-quality agent data from the corresponding environments they interact with. We propose Learn-by-interact, a data-centric framework to adapt LLM agents to any given environments without human annotations. Learn-by-interact synthesizes trajectories of agent-environment interactions based on documentations, and constructs instructions by summarizing or abstracting the interaction histories, a process called backward construction. We assess the quality of our synthetic data by using them in both training-based scenarios and training-free in-context learning (ICL), where we craft innovative retrieval approaches optimized for agents. Extensive experiments on SWE-bench, WebArena, OSWorld and Spider2-V spanning across realistic coding, web, and desktop environments show the effectiveness of Learn-by-interact in various downstream agentic tasks -- baseline results are improved by up to 12.2\% for ICL with Claude-3.5 and 19.5\% for training with Codestral-22B. We further demonstrate the critical role of backward construction, which provides up to 14.0\% improvement for training. Our ablation studies demonstrate the efficiency provided by our synthesized data in ICL and the superiority of our retrieval pipeline over alternative approaches like conventional retrieval-augmented generation (RAG). We expect that Learn-by-interact will serve as a foundation for agent data synthesis as LLMs are increasingly deployed at real-world environments.

Interactions among features are central to understanding the behavior of machine learning models. Recent research has made significant strides in detecting and quantifying feature interactions in single predictive models. However, we argue that the feature interactions extracted from a single pre-specified model may not be trustworthy since: a well-trained predictive model may not preserve the true feature interactions and there exist multiple well-performing predictive models that differ in feature interaction strengths. Thus, we recommend exploring feature interaction strengths in a model class of approximately equally accurate predictive models. In this work, we introduce the feature interaction score (FIS) in the context of a Rashomon set, representing a collection of models that achieve similar accuracy on a given task. We propose a general and practical algorithm to calculate the FIS in the model class. We demonstrate the properties of the FIS via synthetic data and draw connections to other areas of statistics. Additionally, we introduce a Halo plot for visualizing the feature interaction variance in high-dimensional space and a swarm plot for analyzing FIS in a Rashomon set. Experiments with recidivism prediction and image classification illustrate how feature interactions can vary dramatically in importance for similarly accurate predictive models. Our results suggest that the proposed FIS can provide valuable insights into the nature of feature interactions in machine learning models.

The final state interactions (FSI) model in which soft rescattering of low mass intermediate states dominates is suggested. It explains why the strong interaction phases are large in the B_dtopipi channel and are considerably smaller in the B_dtorhorho one. Direct CP asymmetries of B_dtopipi decays which are determined by FSI phases are considered as well.

Temporal Point Processes (TPP) are probabilistic generative frameworks. They model discrete event sequences localized in continuous time. Generally, real-life events reveal descriptive information, known as marks. Marked TPPs model time and marks of the event together for practical relevance. Conditioned on past events, marked TPPs aim to learn the joint distribution of the time and the mark of the next event. For simplicity, conditionally independent TPP models assume time and marks are independent given event history. They factorize the conditional joint distribution of time and mark into the product of individual conditional distributions. This structural limitation in the design of TPP models hurt the predictive performance on entangled time and mark interactions. In this work, we model the conditional inter-dependence of time and mark to overcome the limitations of conditionally independent models. We construct a multivariate TPP conditioning the time distribution on the current event mark in addition to past events. Besides the conventional intensity-based models for conditional joint distribution, we also draw on flexible intensity-free TPP models from the literature. The proposed TPP models outperform conditionally independent and dependent models in standard prediction tasks. Our experimentation on various datasets with multiple evaluation metrics highlights the merit of the proposed approach.

We describe the accurate prediction of ligand-protein interaction (LPI) affinities, also known as drug-target interactions (DTI), with instruction fine-tuned pretrained generative small language models (SLMs). We achieved accurate predictions for a range of affinity values associated with ligand-protein interactions on out-of-sample data in a zero-shot setting. Only the SMILES string of the ligand and the amino acid sequence of the protein were used as the model inputs. Our results demonstrate a clear improvement over machine learning (ML) and free-energy perturbation (FEP+) based methods in accurately predicting a range of ligand-protein interaction affinities, which can be leveraged to further accelerate drug discovery campaigns against challenging therapeutic targets.

Drug-target interaction (DTI) prediction is crucial for identifying new therapeutics and detecting mechanisms of action. While structure-based methods accurately model physical interactions between a drug and its protein target, cell-based assays such as Cell Painting can better capture complex DTI interactions. This paper introduces MOTIVE, a Morphological cOmpound Target Interaction Graph dataset that comprises Cell Painting features for 11,000 genes and 3,600 compounds along with their relationships extracted from seven publicly available databases. We provide random, cold-source (new drugs), and cold-target (new genes) data splits to enable rigorous evaluation under realistic use cases. Our benchmark results show that graph neural networks that use Cell Painting features consistently outperform those that learn from graph structure alone, feature-based models, and topological heuristics. MOTIVE accelerates both graph ML research and drug discovery by promoting the development of more reliable DTI prediction models. MOTIVE resources are available at https://github.com/carpenter-singh-lab/motive.

Training recurrent neural networks (RNNs) is a high-dimensional process that requires updating numerous parameters. Therefore, it is often difficult to pinpoint the underlying learning mechanisms. To address this challenge, we propose to gain mechanistic insights into the phenomenon of abrupt learning by studying RNNs trained to perform diverse short-term memory tasks. In these tasks, RNN training begins with an initial search phase. Following a long period of plateau in accuracy, the values of the loss function suddenly drop, indicating abrupt learning. Analyzing the neural computation performed by these RNNs reveals geometric restructuring (GR) in their phase spaces prior to the drop. To promote these GR events, we introduce a temporal consistency regularization that accelerates (bioplausible) training, facilitates attractor formation, and enables efficient learning in strongly connected networks. Our findings offer testable predictions for neuroscientists and emphasize the need for goal-agnostic secondary mechanisms to facilitate learning in biological and artificial networks.

Large language models (LLMs) have demonstrated impressive performance in understanding language and executing complex reasoning tasks. However, LLMs with long context windows have been notorious for their expensive training costs and high inference latency. Even the most advanced models such as GPT-4 and Claude2 often make mistakes when processing inputs of over 100k tokens, a phenomenon also known as lost in the middle. In this paper, we propose LongAgent, a method based on multi-agent collaboration, which scales LLMs (e.g., LLaMA) to a context of 128K and demonstrates potential superiority in long-text processing compared to GPT-4. In LongAgent, a leader is responsible for understanding user intent and directing team members to acquire information from documents. Due to members' hallucinations, it is non-trivial for a leader to obtain accurate information from the responses of dozens to hundreds of members. To address this, we develop an inter-member communication mechanism to resolve response conflicts caused by hallucinations through information sharing. Our experimental results indicate that LongAgent offers a promising alternative for long-text processing. The agent team instantiated with LLaMA-7B achieves significant improvements in tasks such as 128k-long text retrieval, multi-hop question answering, compared to GPT-4.

Recurrent neural networks (RNNs) in the brain and in silico excel at solving tasks with intricate temporal dependencies. Long timescales required for solving such tasks can arise from properties of individual neurons (single-neuron timescale, tau, e.g., membrane time constant in biological neurons) or recurrent interactions among them (network-mediated timescale). However, the contribution of each mechanism for optimally solving memory-dependent tasks remains poorly understood. Here, we train RNNs to solve N-parity and N-delayed match-to-sample tasks with increasing memory requirements controlled by N by simultaneously optimizing recurrent weights and taus. We find that for both tasks RNNs develop longer timescales with increasing N, but depending on the learning objective, they use different mechanisms. Two distinct curricula define learning objectives: sequential learning of a single-N (single-head) or simultaneous learning of multiple Ns (multi-head). Single-head networks increase their tau with N and are able to solve tasks for large N, but they suffer from catastrophic forgetting. However, multi-head networks, which are explicitly required to hold multiple concurrent memories, keep tau constant and develop longer timescales through recurrent connectivity. Moreover, we show that the multi-head curriculum increases training speed and network stability to ablations and perturbations, and allows RNNs to generalize better to tasks beyond their training regime. This curriculum also significantly improves training GRUs and LSTMs for large-N tasks. Our results suggest that adapting timescales to task requirements via recurrent interactions allows learning more complex objectives and improves the RNN's performance.

The study of social emergence has long been a central focus in social science. Traditional modeling approaches, such as rule-based Agent-Based Models (ABMs), struggle to capture the diversity and complexity of human behavior, particularly the irrational factors emphasized in behavioral economics. Recently, large language model (LLM) agents have gained traction as simulation tools for modeling human behavior in social science and role-playing applications. Studies suggest that LLMs can account for cognitive biases, emotional fluctuations, and other non-rational influences, enabling more realistic simulations of socio-economic dynamics. In this work, we introduce TwinMarket, a novel multi-agent framework that leverages LLMs to simulate socio-economic systems. Specifically, we examine how individual behaviors, through interactions and feedback mechanisms, give rise to collective dynamics and emergent phenomena. Through experiments in a simulated stock market environment, we demonstrate how individual actions can trigger group behaviors, leading to emergent outcomes such as financial bubbles and recessions. Our approach provides valuable insights into the complex interplay between individual decision-making and collective socio-economic patterns.

Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and the expanded availability of experimental 3D protein structures have accelerated structure prediction, the dynamic nature of protein structures has received limited attention. This study introduces an innovative 4D diffusion model incorporating molecular dynamics (MD) simulation data to learn dynamic protein structures. Our approach is distinguished by the following components: (1) a unified diffusion model capable of generating dynamic protein structures, including both the backbone and side chains, utilizing atomic grouping and side-chain dihedral angle predictions; (2) a reference network that enhances structural consistency by integrating the latent embeddings of the initial 3D protein structures; and (3) a motion alignment module aimed at improving temporal structural coherence across multiple time steps. To our knowledge, this is the first diffusion-based model aimed at predicting protein trajectories across multiple time steps simultaneously. Validation on benchmark datasets demonstrates that our model exhibits high accuracy in predicting dynamic 3D structures of proteins containing up to 256 amino acids over 32 time steps, effectively capturing both local flexibility in stable states and significant conformational changes.

The temporal credit assignment problem is a central challenge in Reinforcement Learning (RL), concerned with attributing the appropriate influence to each actions in a trajectory for their ability to achieve a goal. However, when feedback is delayed and sparse, the learning signal is poor, and action evaluation becomes harder. Canonical solutions, such as reward shaping and options, require extensive domain knowledge and manual intervention, limiting their scalability and applicability. In this work, we lay the foundations for Credit Assignment with Language Models (CALM), a novel approach that leverages Large Language Models (LLMs) to automate credit assignment via reward shaping and options discovery. CALM uses LLMs to decompose a task into elementary subgoals and assess the achievement of these subgoals in state-action transitions. Every time an option terminates, a subgoal is achieved, and CALM provides an auxiliary reward. This additional reward signal can enhance the learning process when the task reward is sparse and delayed without the need for human-designed rewards. We provide a preliminary evaluation of CALM using a dataset of human-annotated demonstrations from MiniHack, suggesting that LLMs can be effective in assigning credit in zero-shot settings, without examples or LLM fine-tuning. Our preliminary results indicate that the knowledge of LLMs is a promising prior for credit assignment in RL, facilitating the transfer of human knowledge into value functions.

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