Daily Papers

Mechanistic interpretability aims to understand the behavior of neural networks by reverse-engineering their internal computations. However, current methods struggle to find clear interpretations of neural network activations because a decomposition of activations into computational features is missing. Individual neurons or model components do not cleanly correspond to distinct features or functions. We present a novel interpretability method that aims to overcome this limitation by transforming the activations of the network into a new basis - the Local Interaction Basis (LIB). LIB aims to identify computational features by removing irrelevant activations and interactions. Our method drops irrelevant activation directions and aligns the basis with the singular vectors of the Jacobian matrix between adjacent layers. It also scales features based on their importance for downstream computation, producing an interaction graph that shows all computationally-relevant features and interactions in a model. We evaluate the effectiveness of LIB on modular addition and CIFAR-10 models, finding that it identifies more computationally-relevant features that interact more sparsely, compared to principal component analysis. However, LIB does not yield substantial improvements in interpretability or interaction sparsity when applied to language models. We conclude that LIB is a promising theory-driven approach for analyzing neural networks, but in its current form is not applicable to large language models.

Recent advances in large reasoning models (LRMs) have enabled agentic search systems to perform complex multi-step reasoning across multiple sources. However, most studies focus on general information retrieval and rarely explores vertical domains with unique challenges. In this work, we focus on local life services and introduce LocalSearchBench, which encompass diverse and complex business scenarios. Real-world queries in this domain are often ambiguous and require multi-hop reasoning across merchants and products, remaining challenging and not fully addressed. As the first comprehensive benchmark for agentic search in local life services, LocalSearchBench includes over 150,000 high-quality entries from various cities and business types. We construct 300 multi-hop QA tasks based on real user queries, challenging agents to understand questions and retrieve information in multiple steps. We also developed LocalPlayground, a unified environment integrating multiple tools for agent interaction. Experiments show that even state-of-the-art LRMs struggle on LocalSearchBench: the best model (DeepSeek-V3.1) achieves only 34.34% correctness, and most models have issues with completeness (average 77.33%) and faithfulness (average 61.99%). This highlights the need for specialized benchmarks and domain-specific agent training in local life services. Code, Benchmark, and Leaderboard are available at localsearchbench.github.io.

Neural architectures that learn potential energy surfaces from molecular data have undergone fast improvement in recent years. A key driver of this success is the Message Passing Neural Network (MPNN) paradigm. Its favorable scaling with system size partly relies upon a spatial distance limit on messages. While this focus on locality is a useful inductive bias, it also impedes the learning of long-range interactions such as electrostatics and van der Waals forces. To address this drawback, we propose Ewald message passing: a nonlocal Fourier space scheme which limits interactions via a cutoff on frequency instead of distance, and is theoretically well-founded in the Ewald summation method. It can serve as an augmentation on top of existing MPNN architectures as it is computationally inexpensive and agnostic to architectural details. We test the approach with four baseline models and two datasets containing diverse periodic (OC20) and aperiodic structures (OE62). We observe robust improvements in energy mean absolute errors across all models and datasets, averaging 10% on OC20 and 16% on OE62. Our analysis shows an outsize impact of these improvements on structures with high long-range contributions to the ground truth energy.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

As machine learning systems are increasingly deployed in high-stakes domains such as criminal justice, finance, and healthcare, the demand for interpretable and trustworthy models has intensified. Despite the proliferation of local explanation techniques, including SHAP, LIME, and counterfactual methods, there exists no standardized, reproducible framework for their comparative evaluation, particularly in fairness-sensitive settings. We introduce ExplainBench, an open-source benchmarking suite for systematic evaluation of local model explanations across ethically consequential datasets. ExplainBench provides unified wrappers for popular explanation algorithms, integrates end-to-end pipelines for model training and explanation generation, and supports evaluation via fidelity, sparsity, and robustness metrics. The framework includes a Streamlit-based graphical interface for interactive exploration and is packaged as a Python module for seamless integration into research workflows. We demonstrate ExplainBench on datasets commonly used in fairness research, such as COMPAS, UCI Adult Income, and LendingClub, and showcase how different explanation methods behave under a shared experimental protocol. By enabling reproducible, comparative analysis of local explanations, ExplainBench advances the methodological foundations of interpretable machine learning and facilitates accountability in real-world AI systems.

Prediction of protein-ligand (PL) binding affinity remains the key to drug discovery. Popular approaches in recent years involve graph neural networks (GNNs), which are used to learn the topology and geometry of PL complexes. However, GNNs are computationally heavy and have poor scalability to graph sizes. On the other hand, traditional machine learning (ML) approaches, such as gradient-boosted decision trees (GBDTs), are lightweight yet extremely efficient for tabular data. We propose to use PL interaction features along with PL graph-level features in GBDT. We show that this combination outperforms the existing solutions.

Foundation models, or large atomistic models (LAMs), aim to universally represent the ground-state potential energy surface (PES) of atomistic systems as defined by density functional theory (DFT). The scaling law is pivotal in the development of large models, suggesting that their generalizability in downstream tasks consistently improves with increased model size, expanded training datasets, and larger computational budgets. In this study, we present DPA3, a multi-layer graph neural network founded on line graph series (LiGS), designed explicitly for the era of LAMs. We demonstrate that the generalization error of the DPA3 model adheres to the scaling law. The scalability in the number of model parameters is attained by stacking additional layers within DPA3. Additionally, the model employs a dataset encoding mechanism that decouples the scaling of training data size from the model size within its multi-task training framework. When trained as problem-oriented potential energy models, the DPA3 model exhibits superior accuracy in the majority of benchmark cases, encompassing systems with diverse features, including molecules, bulk materials, surface and cluster catalysts, two-dimensional materials, and battery materials. When trained as a LAM on the OpenLAM-v1 dataset, the DPA-3.1-3M model exhibits state-of-the-art performance in the LAMBench benchmark suite for LAMs, demonstrating lowest overall zero-shot generalization error across 17 downstream tasks from a broad spectrum of research domains. This performance suggests superior accuracy as an out-of-the-box potential model, requiring minimal fine-tuning data for downstream scientific applications.

We present the design of a flexible quantum-chemical method development framework, which supports employing any type of basis function. This design has been implemented in the light-weight program package molsturm, yielding a basis-function-independent self-consistent field scheme. Versatile interfaces, making use of open standards like python, mediate the integration of molsturm with existing third-party packages. In this way both rapid extension of the present set of methods for electronic structure calculations as well as adding new basis function types can be readily achieved. This makes molsturm well-suitable for testing novel approaches for discretising the electronic wave function and allows comparing them to existing methods using the same software stack. This is illustrated by two examples, an implementation of coupled-cluster doubles as well as a gradient-free geometry optimisation, where in both cases, an arbitrary basis functions could be used. molsturm is open-source and can be obtained from https://molsturm.org.

Machine learning force fields (MLFFs) have revolutionized molecular simulations by providing quantum mechanical accuracy at the speed of molecular mechanical computations. However, a fundamental reliance of these models on fixed-cutoff architectures limits their applicability to macromolecular systems where long-range interactions dominate. We demonstrate that this locality constraint causes force prediction errors to scale monotonically with system size, revealing a critical architectural bottleneck. To overcome this, we establish the systematically designed MolLR25 ({Mol}ecules with {L}ong-{R}ange effect) benchmark up to 1200 atoms, generated using high-fidelity DFT, and introduce E2Former-LSR, an equivariant transformer that explicitly integrates long-range attention blocks. E2Former-LSR exhibits stable error scaling, achieves superior fidelity in capturing non-covalent decay, and maintains precision on complex protein conformations. Crucially, its efficient design provides up to 30% speedup compared to purely local models. This work validates the necessity of non-local architectures for generalizable MLFFs, enabling high-fidelity molecular dynamics for large-scale chemical and biological systems.

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

LLM-based reasoning models have enabled the development of agentic systems that act as co-scientists, assisting in multi-step scientific analysis. However, evaluating these systems is challenging, as it requires realistic, end-to-end research scenarios that integrate data analysis, interpretation, and the generation of new insights from the experimental data. To address this limitation, we introduce HeurekaBench, a framework to create benchmarks with exploratory, open-ended research questions for experimental datasets. Each such question is grounded in a scientific study and its corresponding code repository, and is created using a semi-automated pipeline that leverages multiple LLMs to extract insights and generate candidate workflows, which are then verified against reported findings. We instantiate the framework in single-cell biology to obtain sc-HeurekaBench benchmark and use it to compare state-of-the-art single-cell agents. We further showcase the benefits of our benchmark for quantitatively analyzing current design choices in agentic systems. We find that the addition of a critic module can improve ill-formed responses for open-source LLM-based agents by up to 22% and close the gap with their closed-source counterparts. Overall, HeurekaBench sets a path toward rigorous, end-to-end evaluation of scientific agents, grounding benchmark construction in real scientific workflows.

ResearchPilot is an open-source, self-hostable multi-agent system for literature-review assistance. Given a natural-language research question, it retrieves papers from Semantic Scholar and arXiv, extracts structured findings from paper abstracts, synthesizes cross-paper patterns, and drafts a citation-aware related-work section. The system combines FastAPI, Next.js, DSPy, SQLite, and Qdrant in a local-first architecture that supports bring-your-own-key model access and remote-or-local embeddings. This paper describes the system design, typed agent interfaces, persistence and history-search mechanisms, and the engineering tradeoffs involved in building a transparent research assistant. Rather than claiming algorithmic novelty, we present ResearchPilot as a systems contribution and evaluate it through automated tests and end-to-end local runs. We discuss limitations including external API rate limits, abstract-only extraction, incomplete corpus coverage, and the lack of citation verification.

Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.

Library learning compresses a given corpus of programs by extracting common structure from the corpus into reusable library functions. Prior work on library learning suffers from two limitations that prevent it from scaling to larger, more complex inputs. First, it explores too many candidate library functions that are not useful for compression. Second, it is not robust to syntactic variation in the input. We propose library learning modulo theory (LLMT), a new library learning algorithm that additionally takes as input an equational theory for a given problem domain. LLMT uses e-graphs and equality saturation to compactly represent the space of programs equivalent modulo the theory, and uses a novel e-graph anti-unification technique to find common patterns in the corpus more directly and efficiently. We implemented LLMT in a tool named BABBLE. Our evaluation shows that BABBLE achieves better compression orders of magnitude faster than the state of the art. We also provide a qualitative evaluation showing that BABBLE learns reusable functions on inputs previously out of reach for library learning.

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development of all-atom foundation models for molecular modeling and generation, existing approaches face challenges in generalization due to the multi-modal nature of atomic data and the lack of comprehensive analysis of training and sampling strategies. To address these limitations, we propose PharMolixFM, a unified framework for constructing all-atom foundation models based on multi-modal generative techniques. Our framework includes three variants using state-of-the-art multi-modal generative models. By formulating molecular tasks as a generalized denoising process with task-specific priors, PharMolixFM achieves robust performance across various structural biology applications. Experimental results demonstrate that PharMolixFM-Diff achieves competitive prediction accuracy in protein-small-molecule docking (83.9% vs. 90.2% RMSD < 2Å, given pocket) with significantly improved inference speed. Moreover, we explore the empirical inference scaling law by introducing more sampling repeats or steps. Our code and model are available at https://github.com/PharMolix/OpenBioMed.

Three-dimensional (3D) point cloud analysis has become central to applications ranging from autonomous driving and robotics to forestry and ecological monitoring. Although numerous deep learning methods have been proposed for point cloud understanding, including supervised backbones, self-supervised pre-training (SSL), and parameter-efficient fine-tuning (PEFT), their implementations are scattered across incompatible codebases with differing data pipelines, evaluation protocols, and configuration formats, making fair comparisons difficult. We introduce , a unified, extensible PyTorch library that integrates over 55 model configurations covering 29 supervised architectures, seven SSL pre-training methods, and five PEFT strategies, all within a single registry-based framework supporting classification, semantic segmentation, part segmentation, and few-shot learning. provides standardised training runners, cross-validation with stratified K-fold splitting, automated LaTeX/CSV table generation, built-in Friedman/Nemenyi statistical testing with critical-difference diagrams for rigorous multi-model comparison, and a comprehensive test suite with 2\,200+ automated tests validating every configuration end-to-end. The code is available at https://github.com/said-ohamouddou/LIDARLearn under the MIT licence.

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. For a pair of input protein structures, PLASMA outputs a clear alignment matrix with an interpretable overall similarity score. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Reproducibility is ensured via our official implementation at https://github.com/ZW471/PLASMA-Protein-Local-Alignment.git.

Tool-use capability is a fundamental component of LLM agents, enabling them to interact with external systems through structured function calls. However, existing research exhibits inconsistent interaction representations, largely overlooks the structural distribution of tool-use trajectories, and relies on incompatible evaluation benchmarks. We present UniToolCall, a unified framework for tool learning that standardizes the entire pipeline from toolset construction and dataset generation to evaluation. The framework curates a large tool pool of 22k+ tools and constructs a hybrid training corpus of 390k+ instances by combining 10 standardized public datasets with structurally controlled synthetic trajectories. It explicitly models diverse interaction patterns, including single-hop vs. multi-hop and single-turn vs. multi-turn, while capturing both serial and parallel execution structures. To support coherent multi-turn reasoning, we further introduce an Anchor Linkage mechanism that enforces cross-turn dependencies. Furthermore, we convert 7 public benchmarks into a unified Query--Action--Observation--Answer (QAOA) representation with fine-grained evaluation at the function-call, turn, and conversation levels. Experiments show that fine-tuning Qwen3-8B on our dataset substantially improves tool-use performance. Under the distractor-heavy Hybrid-20 setting, achieves 93.0% single-turn Strict Precision, outperforming commercial models including GPT, Gemini, and Claude.

Large Language Models (LLMs) have become the central paradigm in artificial intelligence, yet the core computational primitive of attention has remained structurally unchanged. Local Linear Attention (LLA) is an attention mechanism derived from nonparametric statistics in the test-time regression framework. In contrast to prior research on efficient attention variants, LLA upgrades the local constant estimate in softmax attention to a local linear estimate, yielding provably superior bias-variance tradeoffs for associative memory. However, LLA has not been scaled in LLM pretraining due to computational and numerical stability concerns. We introduce Parallax, a parameterized Local Linear Attention that is scalable for LLMs. Parallax eliminates the numerical solver in LLA and learns an extra query-like projector that probes the KV covariance. We place Parallax within a family of attention mechanisms connected by the bandwidth, the probe construction and the affine structure. We propose a hardware-aware algorithm that increases the arithmetic intensity over FlashAttention, shifting attention into a more compute bound regime. Our prototype decode kernel matches or outperforms FlashAttention 2/3 across diverse batch sizes and context lengths. We pretrain Parallax at 0.6B and 1.7B scales and find consistent perplexity improvements throughout pretraining with gains that transfer to downstream benchmarks. The advantage persists under both parameter-matched and compute-matched controls, demonstrating a Pareto improvement. We perform careful pretraining ablations and identify a novel phenomenon whereby Muon unlocks the capacity of Parallax. To our knowledge, this is the first empirical demonstration of strong architecture-optimizer codesign for attention mechanisms in the architecture research literature.

Accurate modelling of electrostatic interactions and charge transfer is fundamental to computational chemistry, yet most machine learning interatomic potentials (MLIPs) rely on local atomic descriptors that cannot capture long-range electrostatic effects. We present a new electrostatic foundation model for molecular chemistry that extends the MACE architecture with explicit treatment of long-range interactions and electrostatic induction. Our approach combines local many-body geometric features with a non-self-consistent field formalism that updates learnable charge and spin densities through polarisable iterations to model induction, followed by global charge equilibration via learnable Fukui functions to control total charge and total spin. This design enables an accurate and physical description of systems with varying charge and spin states while maintaining computational efficiency. Trained on the OMol25 dataset of 100 million hybrid DFT calculations, our models achieve chemical accuracy across diverse benchmarks, with accuracy competitive with hybrid DFT on thermochemistry, reaction barriers, conformational energies, and transition metal complexes. Notably, we demonstrate that the inclusion of long-range electrostatics leads to a large improvement in the description of non-covalent interactions and supramolecular complexes over non-electrostatic models, including sub-kcal/mol prediction of molecular crystal formation energy in the X23-DMC dataset and a fourfold improvement over short-ranged models on protein-ligand interactions. The model's ability to handle variable charge and spin states, respond to external fields, provide interpretable spin-resolved charge densities, and maintain accuracy from small molecules to protein-ligand complexes positions it as a versatile tool for computational molecular chemistry and drug discovery.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

A persistent challenge in machine learning for scientific applications is jointly achieving prediction and understanding. Statistical models excel on structured data but operate as black boxes, while existing interpretability methods are largely inspective: they answer "which features matter?" but do not articulate how features interact or refine explanations iteratively alongside human understanding. Asking an LLM to predict the target directly forces it to search the entire output space; we instead anchor predictions with a base model and ask the LLM the narrower question of what that model is missing. We introduce Multi-Agent Residual In-Context Learning (MARICL), an agentic framework in which LLM agents analyze where a base-model fails, hypothesize missing structure from high-residual examples provided in context, and produce explicit correction terms refined through multi-turn textual gradient optimization. Across nine benchmarks spanning scientific, biomedical, socioeconomic, and synthetic settings, MARICL improves consistently over its base model on all datasets. To test whether these corrections reflect real structure or batch-specific noise, we freeze formulas learned on one experimental batch of the Cell-Free Protein dataset and apply them (with no retraining and no further LLM calls) to held-out batches. Within the same reagent protocol, the frozen formulas improve predictions in over 92% of cases; across a different protocol, they fail systematically. The success boundary aligns with the biochemistry, not the batch count; direct evidence of mechanistic generalization.

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.

Generative models for structure-based drug design are often limited to a specific modality, restricting their broader applicability. To address this challenge, we introduce FuncBind, a framework based on computer vision to generate target-conditioned, all-atom molecules across atomic systems. FuncBind uses neural fields to represent molecules as continuous atomic densities and employs score-based generative models with modern architectures adapted from the computer vision literature. This modality-agnostic representation allows a single unified model to be trained on diverse atomic systems, from small to large molecules, and handle variable atom/residue counts, including non-canonical amino acids. FuncBind achieves competitive in silico performance in generating small molecules, macrocyclic peptides, and antibody complementarity-determining region loops, conditioned on target structures. FuncBind also generated in vitro novel antibody binders via de novo redesign of the complementarity-determining region H3 loop of two chosen co-crystal structures. As a final contribution, we introduce a new dataset and benchmark for structure-conditioned macrocyclic peptide generation. The code is available at https://github.com/prescient-design/funcbind.

Interventions on model-internal states are fundamental operations in many areas of AI, including model editing, steering, robustness, and interpretability. To facilitate such research, we introduce pyvene, an open-source Python library that supports customizable interventions on a range of different PyTorch modules. pyvene supports complex intervention schemes with an intuitive configuration format, and its interventions can be static or include trainable parameters. We show how pyvene provides a unified and extensible framework for performing interventions on neural models and sharing the intervened upon models with others. We illustrate the power of the library via interpretability analyses using causal abstraction and knowledge localization. We publish our library through Python Package Index (PyPI) and provide code, documentation, and tutorials at https://github.com/stanfordnlp/pyvene.

The enormous scale of state-of-the-art foundation models has limited their accessibility to scientists, because customized experiments at large model sizes require costly hardware and complex engineering that is impractical for most researchers. To alleviate these problems, we introduce NNsight, an open-source Python package with a simple, flexible API that can express interventions on any PyTorch model by building computation graphs. We also introduce NDIF, a collaborative research platform providing researchers access to foundation-scale LLMs via the NNsight API. Code, documentation, and tutorials are available at https://www.nnsight.net.

In this work, we seek new insights into the underlying challenges of the Scene Graph Generation (SGG) task. Quantitative and qualitative analysis of the Visual Genome dataset implies -- 1) Ambiguity: even if inter-object relationship contains the same object (or predicate), they may not be visually or semantically similar, 2) Asymmetry: despite the nature of the relationship that embodied the direction, it was not well addressed in previous studies, and 3) Higher-order contexts: leveraging the identities of certain graph elements can help to generate accurate scene graphs. Motivated by the analysis, we design a novel SGG framework, Local-to-Global Interaction Networks (LOGIN). Locally, interactions extract the essence between three instances of subject, object, and background, while baking direction awareness into the network by explicitly constraining the input order of subject and object. Globally, interactions encode the contexts between every graph component (i.e., nodes and edges). Finally, Attract & Repel loss is utilized to fine-tune the distribution of predicate embeddings. By design, our framework enables predicting the scene graph in a bottom-up manner, leveraging the possible complementariness. To quantify how much LOGIN is aware of relational direction, a new diagnostic task called Bidirectional Relationship Classification (BRC) is also proposed. Experimental results demonstrate that LOGIN can successfully distinguish relational direction than existing methods (in BRC task), while showing state-of-the-art results on the Visual Genome benchmark (in SGG task).

Machine learning (ML) holds great promise for extracting insights from complex quantum many-body data obtained in quantum experiments. This approach can efficiently solve certain quantum problems that are classically intractable, suggesting potential advantages of harnessing quantum data. However, addressing large-scale problems still requires significant amounts of data beyond the limited computational resources of near-term quantum devices. We propose a scalable ML framework called Geometrically Local Quantum Kernel (GLQK), designed to efficiently learn quantum many-body experimental data by leveraging the exponential decay of correlations, a phenomenon prevalent in noncritical systems. In the task of learning an unknown polynomial of quantum expectation values, we rigorously prove that GLQK substantially improves polynomial sample complexity in the number of qubits n, compared to the existing shadow kernel, by constructing a feature space from local quantum information at the correlation length scale. This improvement is particularly notable when each term of the target polynomial involves few local subsystems. Remarkably, for translationally symmetric data, GLQK achieves constant sample complexity, independent of n. We numerically demonstrate its high scalability in two learning tasks on quantum many-body phenomena. These results establish new avenues for utilizing experimental data to advance the understanding of quantum many-body physics.

Tool-augmented LLM agents commonly rely on step-wise atomic tool calls, where each invocation, observation, and value transfer is exposed in the main reasoning trace. This creates an execution-granularity mismatch: locally deterministic tool workflows are unfolded into repeated model-visible decisions, consuming context and forcing the model to manage low-level dataflow in the trace. We introduce HyperTool, a unified executable MCP-style tool interface that changes the model-visible unit of tool execution. A model invokes HyperTool with a code block that can call existing tools through their original schemas, manipulate returned values, and pass intermediate results locally, folding deterministic tool subroutines into a single outer call. To train models to use this interface, we synthesize HyperTool-format trajectories from cross-tool compositional tasks and verify them in real MCP environments. On MCP-Universe, HyperTool improves average accuracy from 15.69\% to 35.29\% on Qwen3-32B and from 9.93\% to 33.33\% on Qwen3-8B, and surpass GPT-OSS and Kimi-k2.5 on average accuracy, showing that our HyperTool can substantially improve multi-step tool use.

Transformer architectures have achieved remarkable success in various domains. While efficient alternatives to Softmax Attention have been widely studied, the search for more expressive mechanisms grounded in theoretical insight-even at greater computational cost-has been relatively underexplored. In this work, we bridge this gap by proposing Local Linear Attention (LLA), a novel attention mechanism derived from nonparametric statistics through the lens of test-time regression. First, we show that LLA offers theoretical advantages over Linear and Softmax Attention for associative memory via a bias-variance trade-off analysis. Next, we address its computational challenges and propose two memory-efficient primitives to tackle the Theta(n^2 d) and Theta(n d^2) complexity. We then introduce FlashLLA, a hardware-efficient, blockwise algorithm that enables scalable and parallel computation on modern accelerators. In addition, we implement and profile a customized inference kernel that significantly reduces memory overheads. Finally, we empirically validate the advantages and limitations of LLA on test-time regression, in-context regression, associative recall and state tracking tasks. Experiment results demonstrate that LLA effectively adapts to non-stationarity, outperforming strong baselines in test-time training and in-context learning, and exhibiting promising evidence for its scalability and applicability in large-scale models. Code is available at https://github.com/Yifei-Zuo/Flash-LLA.

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.

Given the damping factor α and precision tolerance ε, andersen2006local introduced Approximate Personalized PageRank (APPR), the de facto local method for approximating the PPR vector, with runtime bounded by Θ(1/(αε)) independent of the graph size. Recently, fountoulakis2022open asked whether faster local algorithms could be developed using O(1/(sqrtαε)) operations. By noticing that APPR is a local variant of Gauss-Seidel, this paper explores the question of whether standard iterative solvers can be effectively localized. We propose to use the locally evolving set process, a novel framework to characterize the algorithm locality, and demonstrate that many standard solvers can be effectively localized. Let operatorname{vol}{ (S_t)} and overlineγ_{t} be the running average of volume and the residual ratio of active nodes textstyle S_{t} during the process. We show operatorname{vol}{ (S_t)}/overlineγ_{t} leq 1/ε and prove APPR admits a new runtime bound O(operatorname{vol}(S_t)/(αoverlineγ_{t})) mirroring the actual performance. Furthermore, when the geometric mean of residual reduction is Θ(sqrtα), then there exists c in (0,2) such that the local Chebyshev method has runtime O(operatorname{vol}(S_{t})/(sqrtα(2-c))) without the monotonicity assumption. Numerical results confirm the efficiency of this novel framework and show up to a hundredfold speedup over corresponding standard solvers on real-world graphs.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Deep neural networks conventionally employ end-to-end backpropagation for their training process, which lacks biological credibility and triggers a locking dilemma during network parameter updates, leading to significant GPU memory use. Supervised local learning, which segments the network into multiple local blocks updated by independent auxiliary networks. However, these methods cannot replace end-to-end training due to lower accuracy, as gradients only propagate within their local block, creating a lack of information exchange between blocks. To address this issue and establish information transfer across blocks, we propose a Momentum Auxiliary Network (MAN) that establishes a dynamic interaction mechanism. The MAN leverages an exponential moving average (EMA) of the parameters from adjacent local blocks to enhance information flow. This auxiliary network, updated through EMA, helps bridge the informational gap between blocks. Nevertheless, we observe that directly applying EMA parameters has certain limitations due to feature discrepancies among local blocks. To overcome this, we introduce learnable biases, further boosting performance. We have validated our method on four image classification datasets (CIFAR-10, STL-10, SVHN, ImageNet), attaining superior performance and substantial memory savings. Notably, our method can reduce GPU memory usage by more than 45\% on the ImageNet dataset compared to end-to-end training, while achieving higher performance. The Momentum Auxiliary Network thus offers a new perspective for supervised local learning. Our code is available at: https://github.com/JunhaoSu0/MAN.

Diffusion large language models (dLLMs) represent a significant advancement in text generation, offering parallel token decoding capabilities. However, existing open-source implementations suffer from quality-speed trade-offs that impede their practical deployment. Conservative sampling strategies typically decode only the most confident token per step to ensure quality (i.e., greedy decoding), at the cost of inference efficiency due to repeated redundant refinement iterations--a phenomenon we term delayed decoding. Through systematic analysis of dLLM decoding dynamics, we characterize this delayed decoding behavior and propose a training-free adaptive parallel decoding strategy, named LocalLeap, to address these inefficiencies. LocalLeap is built on two fundamental empirical principles: local determinism propagation centered on high-confidence anchors and progressive spatial consistency decay. By applying these principles, LocalLeap identifies anchors and performs localized relaxed parallel decoding within bounded neighborhoods, achieving substantial inference step reduction through early commitment of already-determined tokens without compromising output quality. Comprehensive evaluation on various benchmarks demonstrates that LocalLeap achieves 6.94times throughput improvements and reduces decoding steps to just 14.2\% of the original requirement, achieving these gains with negligible performance impact. The source codes are available at: https://github.com/friedrichor/LocalLeap.

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field.

Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing routines, adapting them for new use cases, sharing and scaling them across collaborators, and stabilizing them with reproducible execution environments. We present Album, an open-source framework for packaging and sharing scientific routines as executable artifacts through two minimal primitives: (i) the solution, a Python-native executable entry point that combines machine-readable metadata, arguments, environment specifications, and lifecycle hooks; and (ii) the catalog, a decentralized, git-native distribution mechanism with indexed search and optional web rendering for discovery, provenance, and governance. Album uses a two-context execution model in which a host controller evaluates manifests and prepares per-solution environments, while lifecycle hooks execute inside isolated solution environments. This design supports reproducible execution, post-environment setup, and the composition of routines with incompatible dependencies. Album can be used in conjunction with LLM agents: solutions can be drafted and revised with LLM assistance, and a MCP interface exposes cataloged solutions as callable tools for tool-grounded discovery and orchestration. We evaluate Album through four realworld imaging deployments spanning interactive visualization of electron microscopy data, integration of multiple segmentation methods, the orchestration of cryo-electron tomography competition workflows, and mineral quantification pipelines. Overall, Album complements package managers, workflow systems, and container runtimes by making scientific routines executable, shareable artifacts. Documentation and examples are available at https://album.solutions.

Machine Learning Interatomic Potentials (MLIP) are a novel in silico approach for molecular property prediction, creating an alternative to disrupt the accuracy/speed trade-off of empirical force fields and density functional theory (DFT). In this white paper, we present our MLIP library which was created with two core aims: (1) provide to industry experts without machine learning background a user-friendly and computationally efficient set of tools to experiment with MLIP models, (2) provide machine learning developers a framework to develop novel approaches fully integrated with molecular dynamics tools. The library includes in this release three model architectures (MACE, NequIP, and ViSNet), and two molecular dynamics (MD) wrappers (ASE, and JAX-MD), along with a set of pre-trained organics models. The seamless integration with JAX-MD, in particular, facilitates highly efficient MD simulations, bringing MLIP models significantly closer to industrial application. The library is available on GitHub and on PyPI under the Apache license 2.0.

Large Language Models (LLMs) can interact with the real world by connecting with versatile external APIs, resulting in better problem-solving and task automation capabilities. Previous research primarily focuses on APIs with limited arguments from a single source or overlooks the complex dependency relationship between different APIs. However, it is essential to utilize multiple APIs collaboratively from various sources (e.g., different Apps in the iPhone), especially for complex user instructions. In this paper, we introduce AppBench, the first benchmark to evaluate LLMs' ability to plan and execute multiple APIs from various sources in order to complete the user's task. Specifically, we consider two significant challenges in multiple APIs: 1) graph structures: some APIs can be executed independently while others need to be executed one by one, resulting in graph-like execution order; and 2) permission constraints: which source is authorized to execute the API call. We have experimental results on 9 distinct LLMs; e.g., GPT-4o achieves only a 2.0\% success rate at the most complex instruction, revealing that the existing state-of-the-art LLMs still cannot perform well in this situation even with the help of in-context learning and finetuning. Our code and data are publicly available at https://github.com/ruleGreen/AppBench.

Information localization within massive repositories is a cornerstone of agentic LLM systems. While synthetic data-driven optimization has proven successful in training LLMs, little attention has been paid to optimizing the agent's working environment (the repository itself) in a data-driven manner. To bridge this gap, we present Libra, a self-evolving framework that introduces mutable "catalogs" (hierarchical Markdown files serving as navigable indices) into the repository. Libra runs an LLM-driven optimization loop where a Prompter generates synthetic queries, a frozen Solver attempts to resolve them by navigating the catalogs, and a Healer rewrites the catalogs in response to the Solver's localization failures. Evaluations across 12 SWE-bench Lite repositories demonstrate that this environmental healing yields continual, logarithmic improvements in code localization accuracy. Furthermore, these environmental improvements transfer zero-shot across different LLMs and problem sets. Although the focus of this paper is to study the general behavior of such a system, we also demonstrate that a minimalist coding agent equipped with Libra-optimized catalogs outperforms state-of-the-art baselines. Code is available at https://github.com/salesforce-misc/Libra and data at https://huggingface.co/datasets/Salesforce/Libra.

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration overhead. We present an agentic end-to-end drug design framework that leverages a Large Language Model (LLM) in conjunction with the Model Context Protocol (MCP) to dynamically coordinate access to biochemical databases, modular toolchains, and task-specific AI models. The system integrates four state-of-the-art components: MaSIF (MaSIF-site and MaSIF-seed-search) for geometric deep learning-based identification of protein-protein interaction (PPI) sites, Rosetta for grafting protein fragments onto protein backbones to form mini proteins, ProteinMPNN for amino acid sequences redesign, and AlphaFold3 for near-experimental accuracy in complex structure prediction. Starting from a target structure, the framework supports de novo binder generation via surface analysis, scaffold grafting and pose construction, sequence optimization, and structure prediction. Additionally, by replacing rigid, script-based workflows with a protocol-driven, LLM-coordinated architecture, the framework improves reproducibility, reduces manual overhead, and ensures extensibility, portability, and auditability across the entire drug design process.

With the availability of various instruction datasets, a pivotal challenge is how to effectively select and integrate these instructions to fine-tune large language models (LLMs). Previous research mainly focuses on selecting individual high-quality instructions. However, these works overlooked the joint interactions and dependencies between different categories of instructions, leading to suboptimal selection strategies. Moreover, the nature of these interaction patterns remains largely unexplored, let alone optimize the instruction set with regard to them. To fill these gaps, in this paper, we: (1) systemically investigate interaction and dependency patterns between different categories of instructions, (2) manage to optimize the instruction set concerning the interaction patterns using a linear programming-based method, and optimize the learning schema of SFT using an instruction dependency taxonomy guided curriculum learning. Experimental results across different LLMs demonstrate improved performance over strong baselines on widely adopted benchmarks.

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.

As deep learning technology advances and more urban spatial-temporal data accumulates, an increasing number of deep learning models are being proposed to solve urban spatial-temporal prediction problems. However, there are limitations in the existing field, including open-source data being in various formats and difficult to use, few papers making their code and data openly available, and open-source models often using different frameworks and platforms, making comparisons challenging. A standardized framework is urgently needed to implement and evaluate these methods. To address these issues, we propose LibCity, an open-source library that offers researchers a credible experimental tool and a convenient development framework. In this library, we have reproduced 65 spatial-temporal prediction models and collected 55 spatial-temporal datasets, allowing researchers to conduct comprehensive experiments conveniently. By enabling fair model comparisons, designing a unified data storage format, and simplifying the process of developing new models, LibCity is poised to make significant contributions to the spatial-temporal prediction field.

Identifying drug-target interactions is essential for developing effective therapeutics. Binding affinity quantifies these interactions, and traditional approaches rely on computationally intensive 3D structural data. In contrast, language models can efficiently process sequential data, offering an alternative approach to molecular representation. In the current study, we introduce BAPULM, an innovative sequence-based framework that leverages the chemical latent representations of proteins via ProtT5-XL-U50 and ligands through MolFormer, eliminating reliance on complex 3D configurations. Our approach was validated extensively on benchmark datasets, achieving scoring power (R) values of 0.925 pm 0.043, 0.914 pm 0.004, and 0.8132 pm 0.001 on benchmark1k2101, Test2016_290, and CSAR-HiQ_36, respectively. These findings indicate the robustness and accuracy of BAPULM across diverse datasets and underscore the potential of sequence-based models in-silico drug discovery, offering a scalable alternative to 3D-centric methods for screening potential ligands.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

LLM agents excel when environments are mostly static and the needed information fits in a model's context window, but they often fail in open-ended investigations where explanations must be constructed by iteratively mining evidence from massive, heterogeneous operational data. These investigations exhibit hidden dependency structure: entities interact, signals co-vary, and the importance of a fact may only become clear after other evidence is discovered. Because the context window is bounded, agents must summarize intermediate findings before their significance is known, increasing the risk of discarding key evidence. ReAct-style agents are especially brittle in this regime. Their retrieve-summarize-reason loop makes conclusions sensitive to exploration order and introduces run-to-run non-determinism, producing a reliability gap where Pass-at-k may be high but Majority-at-k remains low. Simply sampling more rollouts or generating longer reasoning traces does not reliably stabilize results, since hypotheses cannot be autonomously checked as new evidence arrives and there is no explicit mechanism for belief bookkeeping and revision. In addition, ReAct entangles semantic reasoning with controller duties such as tool orchestration and state tracking, so execution errors and plan drift degrade reasoning while consuming scarce context. We address these issues by formulating investigation as abductive reasoning over a dependency graph and proposing EoG (Explanations over Graphs), a disaggregated framework in which an LLM performs bounded local evidence mining and labeling (cause vs symptom) while a deterministic controller manages traversal, state, and belief propagation to compute a minimal explanatory frontier. On a representative ITBench diagnostics task, EoG improves both accuracy and run-to-run consistency over ReAct baselines, including a 7x average gain in Majority-at-k entity F1.

We present VLMEvalKit: an open-source toolkit for evaluating large multi-modality models based on PyTorch. The toolkit aims to provide a user-friendly and comprehensive framework for researchers and developers to evaluate existing multi-modality models and publish reproducible evaluation results. In VLMEvalKit, we implement over 70 different large multi-modality models, including both proprietary APIs and open-source models, as well as more than 20 different multi-modal benchmarks. By implementing a single interface, new models can be easily added to the toolkit, while the toolkit automatically handles the remaining workloads, including data preparation, distributed inference, prediction post-processing, and metric calculation. Although the toolkit is currently mainly used for evaluating large vision-language models, its design is compatible with future updates that incorporate additional modalities, such as audio and video. Based on the evaluation results obtained with the toolkit, we host OpenVLM Leaderboard, a comprehensive leaderboard to track the progress of multi-modality learning research. The toolkit is released at https://github.com/open-compass/VLMEvalKit and is actively maintained.

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.

Achieving a balance between computational speed, prediction accuracy, and universal applicability in molecular simulations has been a persistent challenge. This paper presents substantial advancements in the TorchMD-Net software, a pivotal step forward in the shift from conventional force fields to neural network-based potentials. The evolution of TorchMD-Net into a more comprehensive and versatile framework is highlighted, incorporating cutting-edge architectures such as TensorNet. This transformation is achieved through a modular design approach, encouraging customized applications within the scientific community. The most notable enhancement is a significant improvement in computational efficiency, achieving a very remarkable acceleration in the computation of energy and forces for TensorNet models, with performance gains ranging from 2-fold to 10-fold over previous iterations. Other enhancements include highly optimized neighbor search algorithms that support periodic boundary conditions and the smooth integration with existing molecular dynamics frameworks. Additionally, the updated version introduces the capability to integrate physical priors, further enriching its application spectrum and utility in research. The software is available at https://github.com/torchmd/torchmd-net.

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.

Mechanistic Interpretability aims to reverse engineer the algorithms implemented by neural networks by studying their weights and activations. An obstacle to reverse engineering neural networks is that many of the parameters inside a network are not involved in the computation being implemented by the network. These degenerate parameters may obfuscate internal structure. Singular learning theory teaches us that neural network parameterizations are biased towards being more degenerate, and parameterizations with more degeneracy are likely to generalize further. We identify 3 ways that network parameters can be degenerate: linear dependence between activations in a layer; linear dependence between gradients passed back to a layer; ReLUs which fire on the same subset of datapoints. We also present a heuristic argument that modular networks are likely to be more degenerate, and we develop a metric for identifying modules in a network that is based on this argument. We propose that if we can represent a neural network in a way that is invariant to reparameterizations that exploit the degeneracies, then this representation is likely to be more interpretable, and we provide some evidence that such a representation is likely to have sparser interactions. We introduce the Interaction Basis, a tractable technique to obtain a representation that is invariant to degeneracies from linear dependence of activations or Jacobians.

MLMOD is a software package for incorporating machine learning approaches and models into simulations of microscale mechanics and molecular dynamics in LAMMPS. Recent machine learning approaches provide promising data-driven approaches for learning representations for system behaviors from experimental data and high fidelity simulations. The package faciliates learning and using data-driven models for (i) dynamics of the system at larger spatial-temporal scales (ii) interactions between system components, (iii) features yielding coarser degrees of freedom, and (iv) features for new quantities of interest characterizing system behaviors. MLMOD provides hooks in LAMMPS for (i) modeling dynamics and time-step integration, (ii) modeling interactions, and (iii) computing quantities of interest characterizing system states. The package allows for use of machine learning methods with general model classes including Neural Networks, Gaussian Process Regression, Kernel Models, and other approaches. Here we discuss our prototype C++/Python package, aims, and example usage. The package is integrated currently with the mesocale and molecular dynamics simulation package LAMMPS and PyTorch. For related papers, examples, updates, and additional information see https://github.com/atzberg/mlmod and http://atzberger.org/.

Machine-learning interatomic potentials (MLIPs) have advanced rapidly, with many top models relying on strong physics-based inductive biases. However, as models scale to larger systems like biomolecules and electrolytes, they struggle to accurately capture long-range (LR) interactions, leading current approaches to rely on explicit physics-based terms or components. In this work, we propose AllScAIP, a straightforward, attention-based, and energy-conserving MLIP model that scales to O(100 million) training samples. It addresses the long-range challenge using an all-to-all node attention component that is data-driven. Extensive ablations reveal that in low-data/small-model regimes, inductive biases improve sample efficiency. However, as data and model size scale, these benefits diminish or even reverse, while all-to-all attention remains critical for capturing LR interactions. Our model achieves state-of-the-art energy/force accuracy on molecular systems, as well as a number of physics-based evaluations (OMol25), while being competitive on materials (OMat24) and catalysts (OC20). Furthermore, it enables stable, long-timescale MD simulations that accurately recover experimental observables, including density and heat of vaporization predictions.

The Non-Local Network (NLNet) presents a pioneering approach for capturing long-range dependencies, via aggregating query-specific global context to each query position. However, through a rigorous empirical analysis, we have found that the global contexts modeled by non-local network are almost the same for different query positions within an image. In this paper, we take advantage of this finding to create a simplified network based on a query-independent formulation, which maintains the accuracy of NLNet but with significantly less computation. We further observe that this simplified design shares similar structure with Squeeze-Excitation Network (SENet). Hence we unify them into a three-step general framework for global context modeling. Within the general framework, we design a better instantiation, called the global context (GC) block, which is lightweight and can effectively model the global context. The lightweight property allows us to apply it for multiple layers in a backbone network to construct a global context network (GCNet), which generally outperforms both simplified NLNet and SENet on major benchmarks for various recognition tasks. The code and configurations are released at https://github.com/xvjiarui/GCNet.

We present a single-turn agent for graphical user interface (GUI) interaction tasks, using Vision-Language Model Florence-2-Base. The agent's primary task is identifying the screen coordinates of the UI element corresponding to the user's command. It demonstrates strong performance on Screenspot and OmniAct, while maintaining a compact size of 0.27B parameters and minimal latency. Relevant improvement comes from multi-task training and MLLM-based data augmentation. Manually annotated corpora are scarce, but we show that MLLM augmentation might produce better results. On Screenspot and OmniAct, our model outperforms both GUI-specific models (e.g., SeeClick) and MLLMs (e.g., GPT-4V).

Recently, many generative models for de novo protein structure design have emerged. Yet, only few tackle the difficult task of directly generating fully atomistic structures jointly with the underlying amino acid sequence. This is challenging, for instance, because the model must reason over side chains that change in length during generation. We introduce La-Proteina for atomistic protein design based on a novel partially latent protein representation: coarse backbone structure is modeled explicitly, while sequence and atomistic details are captured via per-residue latent variables of fixed dimensionality, thereby effectively side-stepping challenges of explicit side-chain representations. Flow matching in this partially latent space then models the joint distribution over sequences and full-atom structures. La-Proteina achieves state-of-the-art performance on multiple generation benchmarks, including all-atom co-designability, diversity, and structural validity, as confirmed through detailed structural analyses and evaluations. Notably, La-Proteina also surpasses previous models in atomistic motif scaffolding performance, unlocking critical atomistic structure-conditioned protein design tasks. Moreover, La-Proteina is able to generate co-designable proteins of up to 800 residues, a regime where most baselines collapse and fail to produce valid samples, demonstrating La-Proteina's scalability and robustness.

Adapting large-scale image-text pre-training models, e.g., CLIP, to the video domain represents the current state-of-the-art for text-video retrieval. The primary approaches involve transferring text-video pairs to a common embedding space and leveraging cross-modal interactions on specific entities for semantic alignment. Though effective, these paradigms entail prohibitive computational costs, leading to inefficient retrieval. To address this, we propose a simple yet effective method, Global-Local Semantic Consistent Learning (GLSCL), which capitalizes on latent shared semantics across modalities for text-video retrieval. Specifically, we introduce a parameter-free global interaction module to explore coarse-grained alignment. Then, we devise a shared local interaction module that employs several learnable queries to capture latent semantic concepts for learning fine-grained alignment. Furthermore, an Inter-Consistency Loss (ICL) is devised to accomplish the concept alignment between the visual query and corresponding textual query, and an Intra-Diversity Loss (IDL) is developed to repulse the distribution within visual (textual) queries to generate more discriminative concepts. Extensive experiments on five widely used benchmarks (i.e., MSR-VTT, MSVD, DiDeMo, LSMDC, and ActivityNet) substantiate the superior effectiveness and efficiency of the proposed method. Remarkably, our method achieves comparable performance with SOTA as well as being nearly 220 times faster in terms of computational cost. Code is available at: https://github.com/zchoi/GLSCL.

Adapting machine-learned interatomic potential (MLIP) foundation models to specialised tasks through fine-tuning is an increasingly important practice, yet systematic guidance on when and how to fine-tune is currently limited. We evaluate seven fine-tuning strategies -- naive full-parameter updates, two layer-freezing variants, Low-Rank Adaptation (LoRA), multihead replay, pseudolabelled replay, and replay combined with LoRA -- across five chemically diverse benchmarks (aqueous NaCl, ice polymorphs, S_N2 reactions, SPICE biomolecules, and lithium electrolytes), three generations of foundation models, and training sets spanning five orders of magnitude. To support this evaluation we implement three capabilities in the MACE codebase: LoRA adapted for equivariant message-passing architectures, including both scalar and equivariant linear layers; pseudolabelled replay, which decouples the replay data source from the original pretraining corpus; and model-aware atomic reference energy (E0) reestimation for fine-tuning workflows. We find that foundation model quality, correct E0 initialisation, and well-chosen hyperparameters are prerequisites whose impact routinely exceeds that of the fine-tuning strategy itself. Once these prerequisites are met, most strategies achieve strong target-task accuracy, consistently surpassing models trained from scratch. The practical distinction depends on deployment scope: naive fine-tuning offers the best convergence for single-system applications, while multihead replay -- with either original or pseudolabelled data -- is the only approach tested that consistently preserves out-of-distribution robustness, maintaining both pretraining-distribution accuracy for broader deployment and many-body short-range repulsion.

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of the latest docking and structure prediction methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to new proteins); (2) binding multiple (cofactor) ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for generalization to unknown pockets). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL methods for apo-to-holo protein-ligand docking and protein-ligand structure prediction using both primary ligand and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL co-folding methods generally outperform comparable conventional and DL docking baselines, yet popular methods such as AlphaFold 3 are still challenged by prediction targets with novel protein sequences; (2) certain DL co-folding methods are highly sensitive to their input multiple sequence alignments, while others are not; and (3) DL methods struggle to strike a balance between structural accuracy and chemical specificity when predicting novel or multi-ligand protein targets. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences where reproducibility is crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. Here we introduce LLaMP, a multimodal retrieval-augmented generation (RAG) framework of multiple data-aware reasoning-and-acting (ReAct) agents that dynamically interact with computational and experimental data on Materials Project (MP). Without fine-tuning, LLaMP demonstrates an ability to comprehend and integrate various modalities of materials science concepts, fetch relevant data stores on the fly, process higher-order data (such as crystal structures and elastic tensors), and summarize multi-step procedures for solid-state synthesis. We show that LLaMP effectively corrects errors in GPT-3.5's intrinsic knowledge, reducing a 5.21% MAPE on frequently-documented bandgaps and a significant 1103.54% MAPE on formation energies -- errors that GPT-3.5 seems to derive from mixed data sources. Additionally, LLaMP substantially reduces the hallucinated volumetric strain in a diamond cubic silicon structure from 66.3% to 0. The proposed framework offers an intuitive and nearly hallucination-free approach to exploring materials informatics and establishes a pathway for knowledge distillation and fine-tuning other language models. We envision the framework as a valuable component for scientific hypotheses and a foundation for future autonomous laboratories where multiple LLM agents communicate and cooperate with robotics to drive material synthesis and chemical reactions without hard-coded human logic and intervention.

Computer-use agents (CUAs) automate on-screen work, as illustrated by GPT-5.4 and Claude. Yet their reliability on complex, low-frequency interactions is still poor, limiting user trust. Our analysis of failure cases from advanced models suggests a long-tail pattern in GUI operations, where a relatively small fraction of complex and diverse interactions accounts for a disproportionate share of task failures. We hypothesize that this issue largely stems from the scarcity of data for complex interactions. To address this problem, we propose a new benchmark CUActSpot for evaluating models' capabilities on complex interactions across five modalities: GUI, text, table, canvas, and natural image, as well as a variety of actions (click, drag, draw, etc.), covering a broader range of interaction types than prior click-centric benchmarks that focus mainly on GUI widgets. We also design a renderer-based data-synthesis pipeline: scenes are automatically generated for each modality, screenshots and element coordinates are recorded, and an LLM produces matching instructions and action traces. After training on this corpus, our Phi-Ground-Any-4B outperforms open-source models with fewer than 32B parameters. We will release our benchmark, data, code, and models at https://github.com/microsoft/Phi-Ground.git

Molecular dynamics simulation of plasma-surface interactions requires an interatomic potential that is simultaneously accurate, computationally efficient, and able to describe many elements and bonding types in reactive systems. In principle, a foundation model for machine-learned interatomic potential (MLIP) can meet these demands. We explore the use of the Universal Models for Atoms (UMA) model, developed by Meta FAIR, for the interactions of oxygen plasma species on a multilayer of WS_2, a promising 2D material. Starting from the pretrained uma-s-1p1 model under the Open Catalyst 2020 (OC20) task, we apply an iterative fine-tuning loop with maximally diverse configuration sampling using Smooth Overlap of Atomic Positions (SOAP) and Farthest Point Sampling (FPS); DFT labeling at the PBE+D3+U+spin level; and fine-tuning on energy, force, and stress labels. Even in the absence of fine-tuning, the pretrained model reproduces the production-scale observables of interest, namely, chemisorbed S and O coverage under 15eV O^+ and O_2^+ bombardment. These results were obtained without spin polarization and Hubbard U correction. Nonetheless, fine-tuning reduces the energy and force mean absolute error (MAE) to 4.5times10^{-3}eV/atom and 0.076eV/angstrom, respectively.

Virtual screening of small molecules against protein targets can accelerate drug discovery and development by predicting drug-target interactions (DTIs). However, structure-based methods like molecular docking are too slow to allow for broad proteome-scale screens, limiting their application in screening for off-target effects or new molecular mechanisms. Recently, vector-based methods using protein language models (PLMs) have emerged as a complementary approach that bypasses explicit 3D structure modeling. Here, we develop SPRINT, a vector-based approach for screening entire chemical libraries against whole proteomes for DTIs and novel mechanisms of action. SPRINT improves on prior work by using a self-attention based architecture and structure-aware PLMs to learn drug-target co-embeddings for binder prediction, search, and retrieval. SPRINT achieves SOTA enrichment factors in virtual screening on LIT-PCBA, DTI classification benchmarks, and binding affinity prediction benchmarks, while providing interpretability in the form of residue-level attention maps. In addition to being both accurate and interpretable, SPRINT is ultra-fast: querying the whole human proteome against the ENAMINE Real Database (6.7B drugs) for the 100 most likely binders per protein takes 16 minutes. SPRINT promises to enable virtual screening at an unprecedented scale, opening up new opportunities for in silico drug repurposing and development. SPRINT is available on the web as ColabScreen: https://bit.ly/colab-screen

We introduce the FCHL19 representation for atomic environments in molecules or condensed-phase systems. Machine learning models based on FCHL19 are able to yield predictions of atomic forces and energies of query compounds with chemical accuracy on the scale of milliseconds. FCHL19 is a revision of our previous work [Faber et al. 2018] where the representation is discretized and the individual features are rigorously optimized using Monte Carlo optimization. Combined with a Gaussian kernel function that incorporates elemental screening, chemical accuracy is reached for energy learning on the QM7b and QM9 datasets after training for minutes and hours, respectively. The model also shows good performance for non-bonded interactions in the condensed phase for a set of water clusters with an MAE binding energy error of less than 0.1 kcal/mol/molecule after training on 3,200 samples. For force learning on the MD17 dataset, our optimized model similarly displays state-of-the-art accuracy with a regressor based on Gaussian process regression. When the revised FCHL19 representation is combined with the operator quantum machine learning regressor, forces and energies can be predicted in only a few milliseconds per atom. The model presented herein is fast and lightweight enough for use in general chemistry problems as well as molecular dynamics simulations.

Large language models (LLMs) have become an essential tool to support developers using traditional text-based programming languages, but the graphical notation of the block-based Scratch programming environment inhibits the use of LLMs. To overcome this limitation, we propose the LitterBox+ framework that extends the Scratch static code analysis tool LitterBox with the generative abilities of LLMs. By converting block-based code to a textual representation suitable for LLMs, LitterBox+ allows users to query LLMs about their programs, about quality issues reported by LitterBox, and it allows generating code fixes. Besides offering a programmatic API for these functionalities, LitterBox+ also extends the Scratch user interface to make these functionalities available directly in the environment familiar to learners. The framework is designed to be easily extensible with other prompts, LLM providers, and new features combining the program analysis capabilities of LitterBox with the generative features of LLMs. We provide a screencast demonstrating the tool at https://youtu.be/RZ6E0xgrIgQ.

LLM agent systems are built by stacking scaffolding components (planning, tools, memory, self-reflection, retrieval) assuming more is better. We study cross-component interference (CCI): degradation when components interact destructively. We run a full factorial experiment over all 2^5=32 subsets of five components on HotpotQA and GSM8K with Llama-3.1-8B/70B (96 conditions, up to 10 seeds). The All-In system is consistently suboptimal: on HotpotQA, a single-tool agent surpasses All-In by 32% (F1 0.233 vs 0.177, p=0.023); on GSM8K, a 3-component subset beats All-In by 79% (0.43 vs 0.24, p=0.010). Optimal component count is task-dependent (k*=1-4) and scale-sensitive: at 70B, combinations that hurt at 8B provide gains, though All-In still trails the best subset. We fit a main-effects regression (R^2=0.916, adj-R^2=0.899, LOOCV=0.872), compute exact Shapley values, and find 183/325 submodularity violations (56.3%), showing greedy selection is unreliable. A three-body synergy among Tool Use, Self-Reflection, and Retrieval (INT_3=+0.175, 95% CI [+0.003,+0.351]) is reported as exploratory. CCI replicates across model families (Qwen2.5) and is robust to prompt paraphrasing. Our findings suggest maximally-equipped agent defaults should be replaced by task-specific subset selection via interaction-aware analysis.

Human-object interaction (HOI) detection aims to comprehend the intricate relationships between humans and objects, predicting <human, action, object> triplets, and serving as the foundation for numerous computer vision tasks. The complexity and diversity of human-object interactions in the real world, however, pose significant challenges for both annotation and recognition, particularly in recognizing interactions within an open world context. This study explores the universal interaction recognition in an open-world setting through the use of Vision-Language (VL) foundation models and large language models (LLMs). The proposed method is dubbed as \textbf{UniHOI}. We conduct a deep analysis of the three hierarchical features inherent in visual HOI detectors and propose a method for high-level relation extraction aimed at VL foundation models, which we call HO prompt-based learning. Our design includes an HO Prompt-guided Decoder (HOPD), facilitates the association of high-level relation representations in the foundation model with various HO pairs within the image. Furthermore, we utilize a LLM (i.e. GPT) for interaction interpretation, generating a richer linguistic understanding for complex HOIs. For open-category interaction recognition, our method supports either of two input types: interaction phrase or interpretive sentence. Our efficient architecture design and learning methods effectively unleash the potential of the VL foundation models and LLMs, allowing UniHOI to surpass all existing methods with a substantial margin, under both supervised and zero-shot settings. The code and pre-trained weights are available at: https://github.com/Caoyichao/UniHOI.

All-atom molecular simulation serves as a quintessential ``computational microscope'' for understanding the machinery of life, yet it remains fundamentally limited by the trade-off between quantum-mechanical (QM) accuracy and biological scale. We present UBio-MolFM, a universal foundation model framework specifically engineered to bridge this gap. UBio-MolFM introduces three synergistic innovations: (1) UBio-Mol26, a large bio-specific dataset constructed via a multi-fidelity ``Two-Pronged Strategy'' that combines systematic bottom-up enumeration with top-down sampling of native protein environments (up to 1,200 atoms); (2) E2Former-V2, a linear-scaling equivariant transformer that integrates Equivariant Axis-Aligned Sparsification (EAAS) and Long-Short Range (LSR) modeling to capture non-local physics with up to ~4x higher inference throughput in our large-system benchmarks; and (3) a Three-Stage Curriculum Learning protocol that transitions from energy initialization to energy-force consistency, with force-focused supervision to mitigate energy offsets. Rigorous benchmarking across microscopic forces and macroscopic observables -- including liquid water structure, ionic solvation, and peptide folding -- demonstrates that UBio-MolFM achieves ab initio-level fidelity on large, out-of-distribution biomolecular systems (up to ~1,500 atoms) and realistic MD observables. By reconciling scalability with quantum precision, UBio-MolFM provides a robust, ready-to-use tool for the next generation of computational biology.

Recent surge in Large Language Model (LLM) availability has opened exciting avenues for research. However, efficiently interacting with these models presents a significant hurdle since LLMs often reside on proprietary or self-hosted API endpoints, each requiring custom code for interaction. Conducting comparative studies between different models can therefore be time-consuming and necessitate significant engineering effort, hindering research efficiency and reproducibility. To address these challenges, we present prompto, an open source Python library which facilitates asynchronous querying of LLM endpoints enabling researchers to interact with multiple LLMs concurrently, while maximising efficiency and utilising individual rate limits. Our library empowers researchers and developers to interact with LLMs more effectively and enabling faster experimentation and evaluation. prompto is released with an introductory video (https://youtu.be/-eZAmlV4ypk) under MIT License and is available via GitHub (https://github.com/alan-turing-institute/prompto).

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

Simulating atomic-scale processes, such as protein dynamics and catalytic reactions, is crucial for advancements in biology, chemistry, and materials science. Machine learning force fields (MLFFs) have emerged as powerful tools that achieve near quantum mechanical accuracy, with promising generalization capabilities. However, their practical use is often limited by long inference times compared to classical force fields, especially when running extensive molecular dynamics (MD) simulations required for many biological applications. In this study, we introduce BoostMD, a surrogate model architecture designed to accelerate MD simulations. BoostMD leverages node features computed at previous time steps to predict energies and forces based on positional changes. This approach reduces the complexity of the learning task, allowing BoostMD to be both smaller and significantly faster than conventional MLFFs. During simulations, the computationally intensive reference MLFF is evaluated only every N steps, while the lightweight BoostMD model handles the intermediate steps at a fraction of the computational cost. Our experiments demonstrate that BoostMD achieves an eight-fold speedup compared to the reference model and generalizes to unseen dipeptides. Furthermore, we find that BoostMD accurately samples the ground-truth Boltzmann distribution when running molecular dynamics. By combining efficient feature reuse with a streamlined architecture, BoostMD offers a robust solution for conducting large-scale, long-timescale molecular simulations, making high-accuracy ML-driven modeling more accessible and practical.

Neural networks are widely regarded as black-box models, creating significant challenges in understanding their inner workings, especially in natural language processing (NLP) applications. To address this opacity, model explanation techniques like Local Interpretable Model-Agnostic Explanations (LIME) have emerged as essential tools for providing insights into the behavior of these complex systems. This study leverages LIME to interpret a multi-layer perceptron (MLP) neural network trained on a text classification task. By analyzing the contribution of individual features to model predictions, the LIME approach enhances interpretability and supports informed decision-making. Despite its effectiveness in offering localized explanations, LIME has limitations in capturing global patterns and feature interactions. This research highlights the strengths and shortcomings of LIME and proposes directions for future work to achieve more comprehensive interpretability in neural NLP models.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

Consistency and reliability are crucial for conducting AI research. Many famous research fields, such as object detection, have been compared and validated with solid benchmark frameworks. After AlphaFold2, the protein folding task has entered a new phase, and many methods are proposed based on the component of AlphaFold2. The importance of a unified research framework in protein folding contains implementations and benchmarks to consistently and fairly compare various approaches. To achieve this, we present Solvent, an protein folding framework that supports significant components of state-of-th-arts models in the manner of off-the-shelf interface Solvent contains different models implemented in a unified codebase and supports training and evaluation for defined models on the same dataset. We benchmark well-known algorithms and their components and provide experiments that give helpful insights into the protein structure modeling field. We hope that Solvent will increase the reliability and consistency of proposed models and gives efficiency in both speed and costs, resulting in acceleration on protein folding modeling research. The code is available at https://github.com/kakaobrain/solvent, and the project will continue to be developed.

Machine learning interatomic potentials (MLIPs) have revolutionized molecular and materials modeling, but existing benchmarks suffer from data leakage, limited transferability, and an over-reliance on error-based metrics tied to specific density functional theory (DFT) references. We introduce MLIP Arena, a benchmark platform that evaluates force field performance based on physics awareness, chemical reactivity, stability under extreme conditions, and predictive capabilities for thermodynamic properties and physical phenomena. By moving beyond static DFT references and revealing the important failure modes of current foundation MLIPs in real-world settings, MLIP Arena provides a reproducible framework to guide the next-generation MLIP development toward improved predictive accuracy and runtime efficiency while maintaining physical consistency. The Python package and online leaderboard are available at https://github.com/atomind-ai/mlip-arena.

General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.

Understanding the interplay between intra-modality dependencies (the contribution of an individual modality to a target task) and inter-modality dependencies (the relationships between modalities and the target task) is fundamental to advancing multi-modal learning. However, the nature of and interaction between these dependencies within current benchmark evaluations remains poorly characterized. In this work, we present a large-scale empirical study to quantify these dependencies across 23 visual question-answering benchmarks using multi-modal large language models (MLLMs) covering domains such as general and expert knowledge reasoning, optical character recognition, and document understanding. Our findings show that the reliance on vision, question (text), and their interaction varies significantly, both across and within benchmarks. We discover that numerous benchmarks intended to mitigate text-only biases have inadvertently amplified image-only dependencies. This characterization persists across model sizes and types, with models often obtaining high performance by using each modality independently and showing limited dependence on their interaction. We provide a quantitative characterization of multi-modal datasets, enabling a principled approach to multi-modal benchmark design and evaluation.

Local Friendliness (LF) inequalities follow from seemingly reasonable assumptions about reality: (i) ``absoluteness of observed events'' (e.g., every observed event happens for all observers) and (ii) ``local agency'' (e.g., free choices can be made uncorrelated with other events outside their future light cone). Extended Wigner's Friend Scenario (EWFS) thought experiments show that textbook quantum mechanics violates these inequalities. Thus, experimental evidence of these violations would make these two assumptions incompatible. In [Nature Physics 16, 1199 (2020)], the authors experimentally implemented an EWFS, using a photonic qubit to play the role of each of the ``friends'' and measured violations of LF. One may question whether a photonic qubit is a physical system that counts as an ``observer'' and thereby question whether the experiment's outcome is significant. Intending to measure increasingly meaningful violations, we propose using a statistical measure called the ``branch factor'' to quantify the ``observerness'' of the system. We then encode the EWFS as a quantum circuit such that the components of the circuit that define the friend are quantum systems of increasing branch factor. We run this circuit on quantum simulators and hardware devices, observing LF violations as the system sizes scale. As errors in quantum computers reduce the significance of the violations, better quantum computers can produce better violations. Our results extend the state of the art in proof-of-concept experimental violations from branch factor 0.0 to branch factor 16.0. This is an initial result in an experimental program for measuring LF violations at increasingly meaningful branch factors using increasingly more powerful quantum processors and networks. We introduce this program as a fundamental science application for near-term and developing quantum technology.

Graph Neural Networks (GNNs), especially message-passing neural networks (MPNNs), have emerged as powerful architectures for learning on graphs in diverse applications. However, MPNNs face challenges when modeling non-local interactions in graphs such as large conjugated molecules, and social networks due to oversmoothing and oversquashing. Although Spectral GNNs and traditional neural networks such as recurrent neural networks and transformers mitigate these challenges, they often lack generalizability, or fail to capture detailed structural relationships or symmetries in the data. To address these concerns, we introduce Matrix Function Neural Networks (MFNs), a novel architecture that parameterizes non-local interactions through analytic matrix equivariant functions. Employing resolvent expansions offers a straightforward implementation and the potential for linear scaling with system size. The MFN architecture achieves stateof-the-art performance in standard graph benchmarks, such as the ZINC and TU datasets, and is able to capture intricate non-local interactions in quantum systems, paving the way to new state-of-the-art force fields.

We introduce IntFold, a controllable foundation model for both general and specialized biomolecular structure prediction. IntFold demonstrates predictive accuracy comparable to the state-of-the-art AlphaFold3, while utilizing a superior customized attention kernel. Beyond standard structure prediction, IntFold can be adapted to predict allosteric states, constrained structures, and binding affinity through the use of individual adapters. Furthermore, we introduce a novel confidence head to estimate docking quality, offering a more nuanced assessment for challenging targets such as antibody-antigen complexes. Finally, we share insights gained during the training process of this computationally intensive model.

Bioassay activity prediction is often data-limited because drug-discovery datasets rely on time-consuming and expensive wet-lab experiments for data generation and evaluation. This challenge has inspired recent research into molecular foundation models (MFMs), which aim to encode general-purpose chemical knowledge into molecular representations that generalize well in data-constrained scenarios. This paper presents Monroe, a new MFM with several innovations over the existing state of the art: increased scale allowing pre-training on over 81 million molecules from the PM6 quantum chemistry dataset; improved graph representation of stereochemistry; improved training losses including conformer denoising and embedding decorrelation; improved multi-task learning; and the use of a prior-data-fitted model (TabPFN) for downstream in-context prediction. Our evaluations use a principled pairwise comparison framework that measures statistically significant performance differences. Across established Polaris benchmarks, Monroe matches or exceeds existing MFMs, while on activity cliff benchmarks, designed to assess utility for molecular discovery, it achieves significant improvements over prior methods. Finally, ablation and transfer experiments show that PFN-based downstream predictors also substantially improve two leading existing models, MiniMol and CheMeleon, yielding new state-of-the-art variants we call MiniMol_PFN and CheMeleon_PFN, suggesting that our downstream adaptation strategy generalizes beyond Monroe. Source code is at github.com/blazejba/monroe.

We build a team of specialized large language-model agents and present an agent-driven workflow for research-level formalization in theoretical physics, with the autoformalization of the fundamental theorem of matrix-product states as a demonstration. The agents, coordinated through a structured mathematical blueprint and periodic human review, orchestrated and executed the full formalization autonomously. For some statements, the agents were able to explore new proof routes that are not part of the standard literature. Along the way the agents produced extensive tensor-network and quantum-information libraries not previously available in Mathlib, Lean's mathematical library. As a physical application, the formalization also extends towards symmetry-protected topological phases in one dimension. We find that the main bottleneck in large-scale autoformalization is enforcing mathematical intent and we provide a detailed study of the full process and various subtleties involved. We release the codebase as the library https://github.com/LionSR/TNLean{TNLean}, together with a -chapter https://lionsr.github.io/TNLean/blueprint/{blueprint} of the formalization effort.

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}.

Effectively configuring scalable large language model (LLM) experiments, spanning architecture design, hyperparameter tuning, and beyond, is crucial for advancing LLM research, as poor configuration choices can waste substantial computational resources and prevent models from realizing their full potential. Prior automated methods are designed for low-cost settings where repeated trial and error is feasible, but scalable LLM experiments are too expensive for such extensive iteration. To our knowledge, no work has addressed the automation of high-cost LLM experiment configurations, leaving this problem labor-intensive and dependent on expert intuition. Motivated by this gap, we propose AutoLLMResearch, an agentic framework that mimics how human researchers learn generalizable principles from low-fidelity experiments and extrapolate to efficiently identify promising configurations in expensive LLM settings. The core challenge is how to enable an agent to learn, through interaction with a multi-fidelity experimental environment that captures the structure of the LLM configuration landscape. To achieve this, we propose a systematic framework with two key components: 1) LLMConfig-Gym, a multi-fidelity environment encompassing four critical LLM experiment tasks, supported by over one million GPU hours of verifiable experiment outcomes; 2) A structured training pipeline that formulates configuration research as a long-horizon Markov Decision Process and accordingly incentivizes cross-fidelity extrapolation reasoning. Extensive evaluation against diverse strong baselines on held-out experiments demonstrates the effectiveness, generalization, and interpretability of our framework, supporting its potential as a practical and general solution for scalable real-world LLM experiment automation.

Automated theorem proving (ATP) benchmarks largely consist of problems formalized in MathLib, so current ATP training and evaluation are heavily biased toward MathLib's definitional framework. However, frontier mathematics is often exploratory and prototype-heavy, relying on bespoke constructions that deviate from standard libraries. In this work, we evaluate the robustness of current ATP systems when applied to a novel definitional framework, specifically examining the performance gap between standard library problems and bespoke mathematical constructions. We introduce TaoBench, an undergraduate-level benchmark derived from Terence Tao's Analysis I, which formalizes analysis by constructing core mathematical concepts from scratch, without relying on standard Mathlib definitions, as well as by mixing from-scratch and MathLib constructions. For fair evaluation, we build an agentic pipeline that automatically extracts a compilable, self-contained local environment for each problem. To isolate the effect of definitional frameworks, we additionally translate every problem into a mathematically equivalent Mathlib formulation, yielding paired TaoBench-Mathlib statements for direct comparison. While state-of-the-art ATP models perform capably within the MathLib framework, performance drops by an average of roughly 26% on the definitionally equivalent Tao formulation. This indicates that the main bottleneck is limited generalization across definitional frameworks rather than task difficulty. TaoBench thus highlights a gap between benchmark performance and applicability, and provides a concrete foundation for developing and testing provers better aligned with research mathematics.

Structure-based drug design (SBDD) leverages the 3D structure of protein targets, often complemented by other spatial constraints, to generate candidate binding molecules. While diffusion models have dominated as a leading paradigm for high-quality 3D molecule generation, LLM-based methods are rapidly emerging in molecular design and have shown competitive performance in pocket-conditioned molecular generation. However, their ability to reason about physics and 3D spatial environments is largely underexplored. In this work, we systematically analyze whether current general-purpose LLMs are capable of navigating complex 3D constraints compared to established baselines such as specialized diffusion models. We consider 3D ligand generation conditioned on protein pockets together with ligand- and interaction-derived spatial constraints, including anchor fragments, pharmacophore points, and mandatory pocket-ligand interactions. To enable this evaluation, we introduce 3D-Fit - a token-efficient benchmarking strategy for assessing LLM performance on multi-conditioned spatial molecule generation. Our findings reveal a clear pattern in LLM spatial capabilities: while they still lag behind state-of-the-art approaches, they are promising and can handle multiple spatial constraints simultaneously, enabling scaling to heterogeneous setups.

Demonstrating the practical utility of Noisy Intermediate-Scale Quantum (NISQ) hardware for recurrent tasks in Computer-Aided Drug Discovery is of paramount importance. We tackle this challenge by performing three-dimensional protein pockets hydration-site prediction on a quantum computer. Formulating the water placement problem as a Quadratic Unconstrained Binary Optimization (QUBO), we use a hybrid approach coupling a classical three-dimensional reference-interaction site model (3D-RISM) to an efficient quantum optimization solver, to run various hardware experiments up to 123 qubits. Matching the precision of classical approaches, our results reproduced experimental predictions on real-life protein-ligand complexes. Furthermore, through a detailed resource estimation analysis, we show that accuracy can be systematically improved with increasing number of qubits, indicating that full quantum utility is in reach. Finally, we provide evidence that advantageous situations could be found for systems where classical optimization struggles to provide optimal solutions. The method has potential for assisting simulations of protein-ligand complexes for drug lead optimization and setup of docking calculations.

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.

Multimodal Large Language Models (MLLMs) have demonstrated remarkable performance on the design-to-code task, i.e., generating UI code from UI mock-ups. However, existing benchmarks only contain static web pages for evaluation and ignore the dynamic interaction, limiting the practicality, usability and user engagement of the generated webpages. To bridge these gaps, we present the first systematic investigation of MLLMs in generating interactive webpages. Specifically, we formulate the Interaction-to-Code task and establish the Interaction2Code benchmark, encompassing 127 unique webpages and 374 distinct interactions across 15 webpage types and 31 interaction categories. Through comprehensive experiments utilizing state-of-the-art (SOTA) MLLMs, evaluated via both automatic metrics and human assessments, we identify four critical limitations of MLLM on Interaction-to-Code task: (1) inadequate generation of interaction compared with full page, (2) prone to ten types of failure, (3) poor performance on visually subtle interactions, and (4) insufficient undestanding on interaction when limited to single-modality visual descriptions. To address these limitations, we propose four enhancement strategies: Interactive Element Highlighting, Failureaware Prompting (FAP), Visual Saliency Enhancement, and Visual-Textual Descriptions Combination, all aiming at improving MLLMs' performance on the Interaction-toCode task. The Interaction2Code benchmark and code are available in https://github. com/WebPAI/Interaction2Code.

Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, as well as software ecosystems that are very well developed in their own merit, but do not share many commonalities. To address these issues and facilitate the adoption of ML in atomistic simulations, we introduce two dedicated software libraries. The first one, metatensor, provides multi-platform and multi-language storage and manipulation of arrays with many potentially sparse indices, designed from the ground up for atomistic ML applications. By combining the actual values with metadata that describes their nature and that facilitates the handling of geometric information and gradients with respect to the atomic positions, metatensor provides a common framework to enable data sharing between ML software -- typically written in Python -- and established atomistic modeling tools -- typically written in Fortran, C or C++. The second library, metatomic, provides an interface to store an atomistic ML model and metadata about this model in a portable way, facilitating the implementation, training and distribution of models, and their use across different simulation packages. We showcase a growing ecosystem of tools, from low-level libraries, training utilities, to interfaces with existing software packages that demonstrate the effectiveness of metatensor and metatomic in bridging the gap between traditional simulation software and modern ML frameworks.

Accurate protein-ligand binding affinity prediction is central to computational drug discovery, yet modern docking engines frequently disagree without indicating which prediction to trust. Consensus scoring and ensemble methods improve mean accuracy but treat all predictions identically without interpretable confidence measures or uncertainty decomposition, ignoring the chemical context of each protein-ligand pair. To address this limitation, we introduce RELIABLE-BA (RELIABiLity-aware Evidential fusion for Binding Affinity), an evidential framework for multi-engine binding affinity prediction. Our model comprises three steps: (1) modeling each engine as an evidential expert via Normal-Inverse-Gamma distributions, (2) scaling epistemic uncertainty through learned reliability from molecular context while preserving each expert's predictive mean, and (3) fusing experts through closed-form aggregation that captures both individual uncertainty and inter-engine disagreement. Experiments on the PDBBind and BDB2020+ benchmarks demonstrate competitive point prediction with substantially improved uncertainty calibration, and additional validation on the SARS-CoV-2 Mpro dataset and 5HT2A receptor demonstrates applicability to clinically relevant drug targets. Crucially, these uncertainty estimates enable reliable filtering of protein-ligand pairs, reducing prediction error by up to 25% when retaining only high-confidence pairs. To our knowledge, RELIABLE-BA is the first multi-engine binding affinity prediction framework to combine evidential fusion with context-dependent reliability, offering a principled path toward trustworthy AI-guided drug discovery. Our code is publicly available at https://github.com/yongchand/RELIABLE-BA.

Protein biology focuses on the intricate relationships among sequences, structures, and functions. Deciphering protein functions is crucial for understanding biological processes, advancing drug discovery, and enabling synthetic biology applications. Since protein sequences determine tertiary structures, which in turn govern functions, integrating sequence and structure information is essential for accurate prediction of protein functions. Traditional protein language models (pLMs) have advanced protein-related tasks by learning representations from large-scale sequence and structure data. However, pLMs are limited in integrating broader contextual knowledge, particularly regarding functional modalities that are fundamental to protein biology. In contrast, large language models (LLMs) have exhibited outstanding performance in contextual understanding, reasoning, and generation across diverse domains. Leveraging these capabilities, STELLA is proposed as a multimodal LLM integrating protein sequence-structure representations with general knowledge to address protein function prediction. Through multimodal instruction tuning (MMIT) using the proposed OPI-Struc dataset, STELLA achieves state-of-the-art performance in two function-related tasks-functional description prediction (FP) and enzyme-catalyzed reaction prediction (EP). This study highlights the potential of multimodal LLMs as an alternative paradigm to pLMs to advance protein biology research.

Systems of interacting objects often evolve under the influence of field effects that govern their dynamics, yet previous works have abstracted away from such effects, and assume that systems evolve in a vacuum. In this work, we focus on discovering these fields, and infer them from the observed dynamics alone, without directly observing them. We theorize the presence of latent force fields, and propose neural fields to learn them. Since the observed dynamics constitute the net effect of local object interactions and global field effects, recently popularized equivariant networks are inapplicable, as they fail to capture global information. To address this, we propose to disentangle local object interactions -- which are SE(n) equivariant and depend on relative states -- from external global field effects -- which depend on absolute states. We model interactions with equivariant graph networks, and combine them with neural fields in a novel graph network that integrates field forces. Our experiments show that we can accurately discover the underlying fields in charged particles settings, traffic scenes, and gravitational n-body problems, and effectively use them to learn the system and forecast future trajectories.

Though LLMs are capable of generating plausible programs, it's challenging to interact with the LLMs further to revise the program, especially if the user's specific requirements are different from the initial proposal. In this paper, we introduce ANPL, an interactive programming system that ensures users can always refine the generated code towards their specific programmatic intents via structured decompositions. Borrowing the paradigm of sketching from program synthesis, an ANPL program consists of a set of input-outputs that it must satisfy, a ``sketch'' -- control/data flow expressed in precise code (e.g. Python), and ``holes'' -- sub-modules to be implemented by the LLM specified with natural language. The user revises an ANPL program by either modifying the sketch, changing the language used to describe the holes, or providing additional input-outputs to a particular hole, turning it into a sub-ANPL program that can be solved recursively. This workflow allows the users to offload programming burdens to the LLM as much as possible while retaining the ability to pinpoint and resolve bugs locally, without exposing the rest of the program to the LLM. We deploy ANPL on the Abstraction and Reasoning Corpus (ARC), a set of unique tasks that are challenging for state-of-the-art AI systems, showing it outperforms baseline programming systems that (a) without the ability to decompose tasks interactively and (b) without the guarantee that the modules can be correctly composed together. Additional evaluations on APPS, HumanEval, and real-world programming tasks have validated that the ANPL framework is applicable to multiple programming domains. We release the ANPL solutions to the ARC tasks as a dataset, providing insights into how humans decompose novel tasks programmatically. See our code at https://iprc-dip.github.io/ANPL/.

The LLM Agent, equipped with a code interpreter, is capable of automatically solving real-world coding tasks, such as data analysis and image editing. However, existing benchmarks primarily focus on either simplistic tasks, such as completing a few lines of code, or on extremely complex and specific tasks at the repository level, neither of which are representative of various daily coding tasks. To address this gap, we introduce PyBench, a benchmark encompassing five main categories of real-world tasks, covering more than 10 types of files. Given a high-level user query and related files, the LLM Agent needs to reason and execute Python code via a code interpreter for a few turns before making a formal response to fulfill the user's requirements. Successfully addressing tasks in PyBench demands a robust understanding of various Python packages, superior reasoning capabilities, and the ability to incorporate feedback from executed code. Our evaluations indicate that current open-source LLMs are struggling with these tasks. Hence, we conduct analysis and experiments on four kinds of datasets proving that comprehensive abilities are needed for PyBench. Our fine-tuned 8B size model: PyLlama3 achieves an exciting performance on PyBench which surpasses many 33B and 70B size models. Our Benchmark, Training Dataset, and Model are available at: https://github.com/Mercury7353/PyBench{https://github.com/Mercury7353/PyBench}

Machine Learning Force Fields (MLFFs) are a promising alternative to expensive ab initio quantum mechanical molecular simulations. Given the diversity of chemical spaces that are of interest and the cost of generating new data, it is important to understand how MLFFs generalize beyond their training distributions. In order to characterize and better understand distribution shifts in MLFFs, we conduct diagnostic experiments on chemical datasets, revealing common shifts that pose significant challenges, even for large foundation models trained on extensive data. Based on these observations, we hypothesize that current supervised training methods inadequately regularize MLFFs, resulting in overfitting and learning poor representations of out-of-distribution systems. We then propose two new methods as initial steps for mitigating distribution shifts for MLFFs. Our methods focus on test-time refinement strategies that incur minimal computational cost and do not use expensive ab initio reference labels. The first strategy, based on spectral graph theory, modifies the edges of test graphs to align with graph structures seen during training. Our second strategy improves representations for out-of-distribution systems at test-time by taking gradient steps using an auxiliary objective, such as a cheap physical prior. Our test-time refinement strategies significantly reduce errors on out-of-distribution systems, suggesting that MLFFs are capable of and can move towards modeling diverse chemical spaces, but are not being effectively trained to do so. Our experiments establish clear benchmarks for evaluating the generalization capabilities of the next generation of MLFFs. Our code is available at https://tkreiman.github.io/projects/mlff_distribution_shifts/.

The recent development and success of Large Language Models (LLMs) necessitate an evaluation of their performance across diverse NLP tasks in different languages. Although several frameworks have been developed and made publicly available, their customization capabilities for specific tasks and datasets are often complex for different users. In this study, we introduce the LLMeBench framework. Initially developed to evaluate Arabic NLP tasks using OpenAI's GPT and BLOOM models; it can be seamlessly customized for any NLP task and model, regardless of language. The framework also features zero- and few-shot learning settings. A new custom dataset can be added in less than 10 minutes, and users can use their own model API keys to evaluate the task at hand. The developed framework has been already tested on 31 unique NLP tasks using 53 publicly available datasets within 90 experimental setups, involving approximately 296K data points. We plan to open-source the framework for the community (https://github.com/qcri/LLMeBench/). A video demonstrating the framework is available online (https://youtu.be/FkQn4UjYA0s).

Parameterized tight-binding models fit to first principles calculations can provide an efficient and accurate quantum mechanical method for predicting properties of molecules and solids. However, well-tested parameter sets are generally only available for a limited number of atom combinations, making routine use of this method difficult. Furthermore, most previous models consider only simple two-body interactions, which limits accuracy. To tackle these challenges, we develop a density functional theory database of nearly one million materials, which we use to fit a universal set of tight-binding parameters for 65 elements and their binary combinations. We include both two-body and three-body effective interaction terms in our model, plus self-consistent charge transfer, enabling our model to work for metallic, covalent, and ionic bonds with the same parameter set. To ensure predictive power, we adopt a learning framework where we repeatedly test the model on new low energy crystal structures and then add them to the fitting dataset, iterating until predictions improve. We distribute the materials database and tools developed in this work publicly.

Large Language Models (LLMs) are increasingly integrated into software systems, giving rise to a new class of systems referred to as LLMware. Beyond traditional source-code components, LLMware embeds or interacts with LLMs that depend on other models and datasets, forming complex supply chains across open-source software (OSS), models, and datasets. However, licensing issues emerging from these intertwined dependencies remain largely unexplored. Leveraging GitHub and Hugging Face, we curate a large-scale dataset capturing LLMware supply chains, including 12,180 OSS repositories, 3,988 LLMs, and 708 datasets. Our analysis reveals that license distributions in LLMware differ substantially from traditional OSS ecosystems. We further examine license-related discussions and find that license selection and maintenance are the dominant concerns, accounting for 84% of cases. To understand incompatibility risks, we analyze license conflicts along supply chains and evaluate state-of-the-art detection approaches, which achieve only 58% and 76% F1 scores in this setting. Motivated by these limitations, we propose LiAgent, an LLM-based agent framework for ecosystem-level license compatibility analysis. LiAgent achieves an F1 score of 87%, improving performance by 14 percentage points over prior methods. We reported 60 incompatibility issues detected by LiAgent, 11 of which have been confirmed by developers. Notably, two conflicted LLMs have over 107 million and 5 million downloads on Hugging Face, respectively, indicating potentially widespread downstream impact. We conclude with implications and recommendations to support the sustainable growth of the LLMware ecosystem.

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities -- continuous 3D positions and discrete 2D topologies -- which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9% on CrossDock, more than 10% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Large language models (LLMs) have gained significant attention in chemistry. However, most existing datasets center on molecular-level property prediction and overlook the role of fine-grained functional group (FG) information. Incorporating FG-level data can provide valuable prior knowledge that links molecular structures with textual descriptions, which can be used to build more interpretable, structure-aware LLMs for reasoning on molecule-related tasks. Moreover, LLMs can learn from such fine-grained information to uncover hidden relationships between specific functional groups and molecular properties, thereby advancing molecular design and drug discovery. Here, we introduce FGBench, a dataset comprising 625K molecular property reasoning problems with functional group information. Functional groups are precisely annotated and localized within the molecule, which ensures the dataset's interoperability thereby facilitating further multimodal applications. FGBench includes both regression and classification tasks on 245 different functional groups across three categories for molecular property reasoning: (1) single functional group impacts, (2) multiple functional group interactions, and (3) direct molecular comparisons. In the benchmark of state-of-the-art LLMs on 7K curated data, the results indicate that current LLMs struggle with FG-level property reasoning, highlighting the need to enhance reasoning capabilities in LLMs for chemistry tasks. We anticipate that the methodology employed in FGBench to construct datasets with functional group-level information will serve as a foundational framework for generating new question-answer pairs, enabling LLMs to better understand fine-grained molecular structure-property relationships. The dataset and evaluation code are available at https://github.com/xuanliugit/FGBench.

The evaluation and comparison of Learned Image Compression (LIC) systems is complicated by heterogeneous software stacks, varying training conditions, and divergent evaluation methodologies. To address these challenges, we introduce UI-LIC, an open-source software framework for evaluating LIC models. We integrate six high-performance LIC models, and provide a centralized controller for performing training, inference, and analysis with shared configuration parameters. Our GUI program offers a streamlined interface to evaluate these models alongside traditional video intra-frame encoders, equalizing the compressed bitrates and calculating quality metrics such as PSNR, SSIM, VMAF, and LPIPS. Finally, we provide an interactive image analyzer with configurable quality heatmap overlays. Our framework lowers barriers to further LIC research, unlocking comparative metrics and subjective analysis with a single setup command. The open-source software is released under the MIT license and is available at github.com/BaylorMultimediaLab/UI-LIC.

Deep sparse networks are widely investigated as a neural network architecture for prediction tasks with high-dimensional sparse features, with which feature interaction selection is a critical component. While previous methods primarily focus on how to search feature interaction in a coarse-grained space, less attention has been given to a finer granularity. In this work, we introduce a hybrid-grained feature interaction selection approach that targets both feature field and feature value for deep sparse networks. To explore such expansive space, we propose a decomposed space which is calculated on the fly. We then develop a selection algorithm called OptFeature, which efficiently selects the feature interaction from both the feature field and the feature value simultaneously. Results from experiments on three large real-world benchmark datasets demonstrate that OptFeature performs well in terms of accuracy and efficiency. Additional studies support the feasibility of our method.

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing F_{max} from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets improve model accuracy and generalization but are computationally expensive to produce and train on, while smaller datasets risk discarding rare but important atomic environments and compromising MLIP accuracy/reliability. Here, we develop an information-theoretical framework to quantify the efficiency of dataset compression methods and propose an algorithm that maximizes this efficiency. By framing atomistic dataset compression as an instance of the minimum set cover (MSC) problem over atom-centered environments, our method identifies the smallest subset of structures that contains as much information as possible from the original dataset while pruning redundant information. The approach is extensively demonstrated on the GAP-20 and TM23 datasets, and validated on 64 varied datasets from the ColabFit repository. Across all cases, MSC consistently retains outliers, preserves dataset diversity, and reproduces the long-tail distributions of forces even at high compression rates, outperforming other subsampling methods. Furthermore, MLIPs trained on MSC-compressed datasets exhibit reduced error for out-of-distribution data even in low-data regimes. We explain these results using an outlier analysis and show that such quantitative conclusions could not be achieved with conventional dimensionality reduction methods. The algorithm is implemented in the open-source QUESTS package and can be used for several tasks in atomistic modeling, from data subsampling, outlier detection, and training improved MLIPs at a lower cost.

LLM-integrated software, which embeds or interacts with large language models (LLMs) as functional components, exhibits probabilistic and context-dependent behaviors that fundamentally differ from those of traditional software. This shift introduces a new category of integration defects that arise not only from code errors but also from misaligned interactions among LLM-specific artifacts, including prompts, API calls, configurations, and model outputs. However, existing defect localization techniques are ineffective at identifying these LLM-specific integration defects because they fail to capture cross-layer dependencies across heterogeneous artifacts, cannot exploit incomplete or misleading error traces, and lack semantic reasoning capabilities for identifying root causes. To address these challenges, we propose LIDL, a multi-agent framework for defect localization in LLM-integrated software. LIDL (1) constructs a code knowledge graph enriched with LLM-aware annotations that represent interaction boundaries across source code, prompts, and configuration files, (2) fuses three complementary sources of error evidence inferred by LLMs to surface candidate defect locations, and (3) applies context-aware validation that uses counterfactual reasoning to distinguish true root causes from propagated symptoms. We evaluate LIDL on 146 real-world defect instances collected from 105 GitHub repositories and 16 agent-based systems. The results show that LIDL significantly outperforms five state-of-the-art baselines across all metrics, achieving a Top-3 accuracy of 0.64 and a MAP of 0.48, which represents a 64.1% improvement over the best-performing baseline. Notably, LIDL achieves these gains while reducing cost by 92.5%, demonstrating both high accuracy and cost efficiency.

We demonstrate CEDAR, an application for automating data science (DS) tasks with an agentic setup. Solving DS problems with LLMs is an underexplored area that has immense market value. The challenges are manifold: task complexities, data sizes, computational limitations, and context restrictions. We show that these can be alleviated via effective context engineering. We first impose structure into the initial prompt with DS-specific input fields, that serve as instructions for the agentic system. The solution is then materialized as an enumerated sequence of interleaved plan and code blocks generated by separate LLM agents, providing a readable structure to the context at any step of the workflow. Function calls for generating these intermediate texts, and for corresponding Python code, ensure that data stays local, and only aggregate statistics and associated instructions are injected into LLM prompts. Fault tolerance and context management are introduced via iterative code generation and smart history rendering. The viability of our agentic data scientist is demonstrated using canonical Kaggle challenges.

Human-Scene Interaction (HSI) is a vital component of fields like embodied AI and virtual reality. Despite advancements in motion quality and physical plausibility, two pivotal factors, versatile interaction control and the development of a user-friendly interface, require further exploration before the practical application of HSI. This paper presents a unified HSI framework, UniHSI, which supports unified control of diverse interactions through language commands. This framework is built upon the definition of interaction as Chain of Contacts (CoC): steps of human joint-object part pairs, which is inspired by the strong correlation between interaction types and human-object contact regions. Based on the definition, UniHSI constitutes a Large Language Model (LLM) Planner to translate language prompts into task plans in the form of CoC, and a Unified Controller that turns CoC into uniform task execution. To facilitate training and evaluation, we collect a new dataset named ScenePlan that encompasses thousands of task plans generated by LLMs based on diverse scenarios. Comprehensive experiments demonstrate the effectiveness of our framework in versatile task execution and generalizability to real scanned scenes. The project page is at https://github.com/OpenRobotLab/UniHSI .

In this paper, we introduce a mesh-free two-level hybrid Tucker tensor format for approximation of multivariate functions, which combines the product Chebyshev interpolation with the ALS-based Tucker decomposition of the tensor of Chebyshev coefficients. It allows to avoid the expenses of the rank-structured approximation of function-related tensors defined on large spacial grids, while benefiting from the Tucker decomposition of the rather small core tensor of Chebyshev coefficients. This leads to nearly optimal Tucker rank parameters which are close to the results for well established Tucker-ALS algorithm applied to the large grid-based tensors. These rank parameters inherited from the Tucker-ALS decomposition of the coefficient tensor can be much less than the polynomial degrees of the initial Chebyshev interpolant via function independent basis set. Furthermore, the tensor product Chebyshev polynomials discretized on a tensor grid leads to a low-rank two-level orthogonal algebraic Tucker tensor that approximates the initial function with controllable accuracy. It is shown that our techniques could be gainfully applied to the long-range part of the electrostatic potential of multi-particle systems approximated in the range-separated tensor format. Error and complexity estimates of the proposed methods are presented. We demonstrate the efficiency of the suggested method numerically on examples of the long-range components of multi-particle interaction potentials generated by 3D Newton kernel for large bio-molecule systems and lattice-type compounds.

AI tools and agents are reshaping how researchers work, from proving theorems to training neural networks. Yet for many, it remains unclear how these tools fit into everyday research practice. This paper is a practical guide to AI-assisted research in mathematics and machine learning: We discuss how researchers can use modern AI systems productively, where these systems help most, and what kinds of guardrails are needed to use them responsibly. It is organized into three parts: (I) a five-level taxonomy of AI integration, (II) an open-source framework that, through a set of methodological rules formulated as agent prompts, turns CLI coding agents (e.g., Claude Code, Codex CLI, OpenCode) into autonomous research assistants, and (III) case studies from deep learning and mathematics. The framework runs inside a sandboxed container, works with any frontier LLM through existing CLI agents, is simple enough to install and use within minutes, and scales from personal-laptop prototyping to multi-node, multi-GPU experimentation across compute clusters. In practice, our longest autonomous session ran for over 20 hours, dispatching independent experiments across multiple nodes without human intervention. We stress that our framework is not intended to replace the researcher in the loop, but to augment them. Our code is publicly available at https://github.com/ZIB-IOL/The-Agentic-Researcher.

Large language model (LLM) agents are evolving from request-response assistants into long-running software actors: they maintain state across model calls, fork subtasks, wait for external events, request human authority, generate tools, and perform side effects that must be resumed and audited. This paper presents Agent libOS, a library-OS-inspired runtime substrate for LLM agents. Agent libOS runs above a conventional host operating system; it does not implement hardware drivers, kernel-mode isolation, or a POSIX-compatible operating system. Instead, it treats an agent as an AgentProcess: a schedulable execution subject with process identity, parent-child lineage, lifecycle state, a tool table derived from an AgentImage, typed Object Memory, explicit capabilities, human queues, checkpoints, events, and audit records. Its central design rule is tools are libc-like wrappers; runtime primitives are the authority boundary. Filesystem access, object access, sleeps, human approval, JIT tool registration, and external side effects are checked at primitive boundaries under explicit capabilities and policy. We describe the design, threat model, Python prototype, and safety-oriented evaluation. The current prototype implements async scheduling, namespace-local Object Memory, runtime-integrated human approval, one-shot permission grants, per-process working directories, shell and image-registration primitives, Deno/TypeScript JIT tools over a libOS syscall broker, filesystem/object bridge tools, an injectable Resource Provider Substrate, deterministic demos, real-model smoke scripts, and 123 regression tests at the time of writing. Rather than improving planner accuracy, Agent libOS demonstrates a runtime substrate in which long-running LLM agents can be scheduled, authorized, resumed, and audited without treating tool dispatch as the trust boundary.

Large language models (LLMs) now play a central role in code generation, yet they continue to hallucinate, frequently inventing non-existent libraries. Such library hallucinations are not just benign errors: they can mislead developers, break builds, and expose systems to supply chain threats such as slopsquatting. Despite growing awareness of these risks, there is limited understanding of how library hallucinations manifest under realistic usage conditions. To fill this gap, we present the first systematic study of how user-level prompt variations influence library hallucinations in LLM-generated code. Across seven diverse LLMs, we analyse library name hallucinations (invalid imports) and library member hallucinations (invalid calls from valid libraries), examining the effects of realistic developer language and controlled user mistakes, including misspellings and fabricated libraries or members. Our findings expose systemic vulnerabilities: one-character misspellings trigger hallucinations in up to 26% of tasks; fabricated library names are accepted in up to 99%; and time-based prompts induce hallucinations in up to 85%. Grounded in the highest-risk prompts identified in our study, we introduce LibHalluBench, a benchmark that enables a systematic and reproducible evaluation of these library hallucinations. Our findings underscore the fragility of LLMs to natural prompt variation and highlight the urgent need for safeguards against library-related hallucinations and their downstream risks.

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA

In contrast to their remarkable performance on general knowledge QA, the true abilities of Large Language Models (LLMs) in tasks demanding deep, specialized reasoning, such as in protein biology, have yet to be thoroughly investigated. Current benchmarks suffer from critical deficiencies, such as data contamination due to outdated test sets, insufficient focus on essential protein-specific tasks, and a neglect of multimodal assessments. To resolve these issues, we introduce LiveProteinBench, a contamination-free, multimodal benchmark of 12 tasks for evaluating LLM performance on protein property and function prediction. Its central innovation lies in a test set composed exclusively of proteins validated after the start of 2025, guaranteeing that the data is novel to all tested models. We benchmarked a suite of prominent general-purpose LLMs and specialized biological LLMs using both unimodal and multimodal input schemes. Our results show that: 1) General-purpose proprietary large models demonstrate superior zero-shot performance when encountering new protein data, outperforming their open-source and domain-specific counterparts by over 20\% accuracy. 2) The effective use of multi-view structural information remains a significant challenge, as the inclusion of structural images often fails to provide a consistent benefit and can even degrade performance. This highlights the limitations of current models in effectively fusing information across different modalities. 3) Models' performance scales more directly with the computational cost during inference than with its parameter count, underscoring the critical role of Chain-of-Thought reasoning capabilities for protein-specific tasks. LiveProteinBench delineates the current performance frontiers for LLMs in bioinformatics and presents new challenges for the development of future multimodal foundation models for biology

Scientific discovery is a closed-loop process in which hypotheses guide data acquisition and observations refine the hypothesis space. Yet most approaches reduce discovery to supervised learning over fixed datasets, where limited observations can support multiple plausible mechanisms that fit locally but fail to generalize. Thus, the key challenge is selecting informative observations to resolve uncertainty, shifting the focus from static inference to adaptive data acquisition. To address this, we propose LLM-AutoSciLab, a closed-loop framework that couples hypothesis generation with hypothesis-conditioned experiment selection and mechanism refinement. Rather than fitting models to passively collected data, LLM-AutoSciLab iteratively proposes plausible hypotheses, selects informative experiments to distinguish or refine them, and updates its state using the resulting evidence. To evaluate dynamic, closed-loop scientific discovery with active data acquisition, we introduce ActiveSciBench, comprising two datasets: ActiveSciBench-Chem with 57 enzyme-kinetics tasks and ActiveSciBench-GRN with 45 gene-regulatory-network tasks. These datasets model discovery as a budget-constrained process requiring adaptive experiment design, variable selection, and recovery of true mechanisms. Across NewtonBench, ActiveSciBench-Chem, and ActiveSciBench-GRN, LLM-AutoSciLab outperforms prior methods, achieving 67.6% and 35.1% symbolic accuracy on NewtonBench and ActiveSciBench-Chem, respectively, and 31.1% exact graph recovery on ActiveSciBench-GRN. Moreover, hypothesis-guided experimentation is 2-5x more sample-efficient than the strongest competing baselines. Code and data are available at: https://github.com/scientific-discovery/LLM-AutoSciLab

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor generalization due to limited supervised data. In this paper, we propose to learn protein-ligand binding representation in a self-supervised learning manner. Different from existing pre-training approaches which treat proteins and ligands individually, we emphasize to discern the intricate binding patterns from fine-grained interactions. Specifically, this self-supervised learning problem is formulated as a prediction of the conclusive binding complex structure given a pocket and ligand with a Transformer based interaction module, which naturally emulates the binding process. To ensure the representation of rich binding information, we introduce two pre-training tasks, i.e.~atomic pairwise distance map prediction and mask ligand reconstruction, which comprehensively model the fine-grained interactions from both structure and feature space. Extensive experiments have demonstrated the superiority of our method across various binding tasks, including protein-ligand affinity prediction, virtual screening and protein-ligand docking.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Recent advancements in large language models (LLMs) have been remarkable. Users face a choice between using cloud-based LLMs for generation quality and deploying local-based LLMs for lower computational cost. The former option is typically costly and inefficient, while the latter usually fails to deliver satisfactory performance for reasoning steps requiring deliberate thought processes. In this work, we propose a novel LLM utilization paradigm that facilitates the collaborative operation of large cloud-based LLMs and smaller local-deployed LLMs. Our framework comprises two primary modules: the local agent instantiated with a relatively smaller LLM, handling less complex reasoning steps, and the cloud agent equipped with a larger LLM, managing more intricate reasoning steps. This collaborative processing is enabled through an adaptive mechanism where the local agent introspectively identifies errors and proactively seeks assistance from the cloud agent, thereby effectively integrating the strengths of both locally-deployed and cloud-based LLMs, resulting in significant enhancements in task completion performance and efficiency. We evaluate AdaSwitch across 7 benchmarks, ranging from mathematical reasoning and complex question answering, using various types of LLMs to instantiate the local and cloud agents. The empirical results show that AdaSwitch effectively improves the performance of the local agent, and sometimes achieves competitive results compared to the cloud agent while utilizing much less computational overhead.