Daily Papers

The success of drug discovery and development relies on the precise prediction of molecular activities and properties. While in silico molecular property prediction has shown remarkable potential, its use has been limited so far to assays for which large amounts of data are available. In this study, we use a fine-tuned large language model to integrate biological assays based on their textual information, coupled with Barlow Twins, a Siamese neural network using a novel self-supervised learning approach. This architecture uses both assay information and molecular fingerprints to extract the true molecular information. TwinBooster enables the prediction of properties of unseen bioassays and molecules by providing state-of-the-art zero-shot learning tasks. Remarkably, our artificial intelligence pipeline shows excellent performance on the FS-Mol benchmark. This breakthrough demonstrates the application of deep learning to critical property prediction tasks where data is typically scarce. By accelerating the early identification of active molecules in drug discovery and development, this method has the potential to help streamline the identification of novel therapeutics.

We introduce AInsteinBench, a large-scale benchmark for evaluating whether large language model (LLM) agents can operate as scientific computing development agents within real research software ecosystems. Unlike existing scientific reasoning benchmarks which focus on conceptual knowledge, or software engineering benchmarks that emphasize generic feature implementation and issue resolving, AInsteinBench evaluates models in end-to-end scientific development settings grounded in production-grade scientific repositories. The benchmark consists of tasks derived from maintainer-authored pull requests across six widely used scientific codebases, spanning quantum chemistry, quantum computing, molecular dynamics, numerical relativity, fluid dynamics, and cheminformatics. All benchmark tasks are carefully curated through multi-stage filtering and expert review to ensure scientific challenge, adequate test coverage, and well-calibrated difficulty. By leveraging evaluation in executable environments, scientifically meaningful failure modes, and test-driven verification, AInsteinBench measures a model's ability to move beyond surface-level code generation toward the core competencies required for computational scientific research.

Rigorous performance evaluation is essential for developing robust algorithms for high-throughput computational chemistry. Traditional benchmarking, however, often struggles to account for system-specific variability, making it difficult to form actionable conclusions. We present a Bayesian hierarchical modeling framework that rigorously quantifies performance metrics and their uncertainty, enabling a nuanced comparison of algorithmic strategies. We apply this framework to analyze the Dimer method, comparing Conjugate Gradient (CG) and L-BFGS rotation optimizers, with and without the removal of external rotations, across a benchmark of 500 molecular systems. Our analysis confirms that CG offers higher overall robustness than L-BFGS in this context. While the theoretically-motivated removal of external rotations led to higher computational cost (>40% more energy and force calls) for most systems in this set, our models also reveal a subtle interplay, hinting that this feature may improve the reliability of the L-BFGS optimizer. Rather than identifying a single superior method, our findings support the design of adaptive "chain of methods" workflows. This work showcases how a robust statistical paradigm can move beyond simple performance rankings to inform the intelligent, context-dependent application of computational chemistry methods.

In this paper, we propose Text-based Open Molecule Generation Benchmark (TOMG-Bench), the first benchmark to evaluate the open-domain molecule generation capability of LLMs. TOMG-Bench encompasses a dataset of three major tasks: molecule editing (MolEdit), molecule optimization (MolOpt), and customized molecule generation (MolCustom). Each task further contains three subtasks, with each subtask comprising 5,000 test samples. Given the inherent complexity of open molecule generation, we have also developed an automated evaluation system that helps measure both the quality and the accuracy of the generated molecules. Our comprehensive benchmarking of 25 LLMs reveals the current limitations and potential areas for improvement in text-guided molecule discovery. Furthermore, with the assistance of OpenMolIns, a specialized instruction tuning dataset proposed for solving challenges raised by TOMG-Bench, Llama3.1-8B could outperform all the open-source general LLMs, even surpassing GPT-3.5-turbo by 46.5\% on TOMG-Bench. Our codes and datasets are available through https://github.com/phenixace/TOMG-Bench.

Quantitative chemistry is central to modern chemical research, yet the ability of large language models (LLMs) to perform its rigorous, step-by-step calculations remains underexplored. To fill this blank, we propose QCBench, a Quantitative Chemistry oriented benchmark comprising 350 computational chemistry problems across 7 chemistry subfields, which contains analytical chemistry, bio/organic chemistry, general chemistry, inorganic chemistry, physical chemistry, polymer chemistry and quantum chemistry. To systematically evaluate the mathematical reasoning abilities of large language models (LLMs), they are categorized into three tiers: easy, medium, and difficult. Each problem, rooted in realistic chemical scenarios, is structured to prevent heuristic shortcuts and demand explicit numerical reasoning. QCBench enables fine-grained diagnosis of computational weaknesses, reveals model-specific limitations across difficulty levels, and lays the groundwork for future improvements such as domain-adaptive fine-tuning or multi-modal integration. Evaluations on 24 LLMs demonstrate a consistent performance degradation with increasing task complexity, highlighting the current gap between language fluency and scientific computation accuracy. Code for QCBench is available at https://github.com/jiaqingxie/QCBench.

The efficient exploration of chemical space to design molecules with intended properties enables the accelerated discovery of drugs, materials, and catalysts, and is one of the most important outstanding challenges in chemistry. Encouraged by the recent surge in computer power and artificial intelligence development, many algorithms have been developed to tackle this problem. However, despite the emergence of many new approaches in recent years, comparatively little progress has been made in developing realistic benchmarks that reflect the complexity of molecular design for real-world applications. In this work, we develop a set of practical benchmark tasks relying on physical simulation of molecular systems mimicking real-life molecular design problems for materials, drugs, and chemical reactions. Additionally, we demonstrate the utility and ease of use of our new benchmark set by demonstrating how to compare the performance of several well-established families of algorithms. Surprisingly, we find that model performance can strongly depend on the benchmark domain. We believe that our benchmark suite will help move the field towards more realistic molecular design benchmarks, and move the development of inverse molecular design algorithms closer to designing molecules that solve existing problems in both academia and industry alike.

Large Language Models (LLMs) have shown growing potential in molecular sciences, but they often produce chemically inaccurate descriptions and struggle to recognize or justify potential errors. This raises important concerns about their robustness and reliability in scientific applications. To support more rigorous evaluation of LLMs in chemical reasoning, we present the MolErr2Fix benchmark, designed to assess LLMs on error detection and correction in molecular descriptions. Unlike existing benchmarks focused on molecule-to-text generation or property prediction, MolErr2Fix emphasizes fine-grained chemical understanding. It tasks LLMs with identifying, localizing, explaining, and revising potential structural and semantic errors in molecular descriptions. Specifically, MolErr2Fix consists of 1,193 fine-grained annotated error instances. Each instance contains quadruple annotations, i.e,. (error type, span location, the explanation, and the correction). These tasks are intended to reflect the types of reasoning and verification required in real-world chemical communication. Evaluations of current state-of-the-art LLMs reveal notable performance gaps, underscoring the need for more robust chemical reasoning capabilities. MolErr2Fix provides a focused benchmark for evaluating such capabilities and aims to support progress toward more reliable and chemically informed language models. All annotations and an accompanying evaluation API will be publicly released to facilitate future research.

Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may output the correct molecule, product, or option while its reasoning violates chemical logic. Existing process-level evaluators are hard to scale because LLM judges and human step-level process annotation are costly, inconsistent, and vulnerable to hallucination. We introduce ChemCoTBench-V2, a rule-verifiable diagnostic benchmark for low-cost, auditable evaluation of structured, verifier-addressable chemical reasoning traces. It spans molecular understanding, molecule editing, molecular optimization, and reaction prediction, with 5,620 evaluation samples across 18 reporting tasks. Models must expose key intermediate steps in expert-designed templates, and those steps are checked with deterministic chemistry rules and, for closed-answer tasks, reference traces rather than another LLM judge. Open-ended molecular optimization is evaluated with oracle-verifiable state constraints rather than strict trace matching. The benchmark reports three separate signals: final-answer correctness, template adherence, and step-wise verifier correctness over expert-refined intermediate commitments. Experiments on frontier models reveal a persistent gap between final-answer success and structured-reasoning-state consistency: models often follow the requested format while failing chemical-step checks, or answer correctly with weak supporting reasoning. ChemCoTBench-V2 enables fine-grained model comparison and identifies the concrete step at which the trace first violates the verifier.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Recent progress has expanded the use of large language models (LLMs) in drug discovery, including synthesis planning. However, objective evaluation of retrosynthesis performance remains limited. Existing benchmarks and metrics typically rely on published synthetic procedures and Top-K accuracy based on single ground-truth, which does not capture the open-ended nature of real-world synthesis planning. We propose a new benchmarking framework for single-step retrosynthesis that evaluates both general-purpose and chemistry-specialized LLMs using ChemCensor, a novel metric for chemical plausibility. By emphasizing plausibility over exact match, this approach better aligns with human synthesis planning practices. We also introduce CREED, a novel dataset comprising millions of ChemCensor-validated reaction records for LLM training, and use it to train a model that improves over the LLM baselines under this benchmark.

Machine Learning (ML) has transformed many scientific fields, yet key applications still lack standardized benchmarks. Raman spectroscopy, a widely used technique for non-invasive molecular analysis, is one such field where progress is limited by fragmented datasets, inconsistent evaluation, and models that fail to capture the structure of spectral data. We introduce RamanBench, the first large-scale, fully reproducible benchmark for ML on Raman spectroscopy, consisting of streamlined data access, evaluation protocols and code, as well as a live leaderboard. It unifies 74 datasets (including 16 first released with this benchmark) across four domains, comprising 325,668 spectra and spanning classification and regression tasks under diverse experimental conditions. We benchmark 28 models under a standardized protocol, including classical methods (e.g., PLS), Raman-specific (e.g., RamanNet), Tabular Foundation Model (TFM) (e.g., TabPFN), and time-series approaches (e.g., ROCKET). TFM consistently outperform domain-specific and gradient boosting baselines, while time-series models remain competitive. However, no method generalizes across datasets, revealing a fundamental gap. Therefore, we invite the community to contribute new approaches to our living benchmark, with the potential to accelerate advances in critical applications such as medical diagnostics, biological research, and materials science.

Function calling is a core capability of large language models, essential for AI agents. Existing benchmarks such as the Berkeley Function Calling Leaderboard (BFCL), tau^2-Bench (arXiv:2506.07982), and ACEBench (arXiv:2501.12851) evaluate argument correctness but do not test adherence to format instructions embedded in parameter descriptions, such as enclosing values in double quotes or using ISO date formats. We introduce IFEval-FC, a benchmark inspired by IFEval (arXiv:2311.07911) that assesses precise instruction following in function calling. IFEval-FC encodes verifiable formats directly within JSON schema descriptions, for example specifying that a value must not contain punctuation. It includes 750 test cases, each consisting of a function with an embedded format for one of its input parameters and a corresponding user query. Evaluation is fully algorithmic, ensuring objectivity, reproducibility, and scalability. Our results show that even state-of-the-art proprietary models, including GPT-5 and Claude 4.1 Opus, frequently fail to follow basic formatting rules, highlighting a practical limitation for real-world agent systems. The complete codebase and data are publicly available at https://github.com/Skripkon/IFEval-FC.

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the minimum binding energy - the adsorption energy - for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration, within a 0.1 eV threshold, 86.33% of the time, while achieving a 1331x speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1,000 diverse surfaces and 85,658 unique configurations.

The extraction of molecular structures and reaction data from scientific documents is challenging due to their varied, unstructured chemical formats and complex document layouts. To address this, we introduce MolMole, a vision-based deep learning framework that unifies molecule detection, reaction diagram parsing, and optical chemical structure recognition (OCSR) into a single pipeline for automating the extraction of chemical data directly from page-level documents. Recognizing the lack of a standard page-level benchmark and evaluation metric, we also present a testset of 550 pages annotated with molecule bounding boxes, reaction labels, and MOLfiles, along with a novel evaluation metric. Experimental results demonstrate that MolMole outperforms existing toolkits on both our benchmark and public datasets. The benchmark testset will be publicly available, and the MolMole toolkit will be accessible soon through an interactive demo on the LG AI Research website. For commercial inquiries, please contact us at mailto:contact_ddu@lgresearch.ai{contact\_ddu@lgresearch.ai}.

Current benchmarks for evaluating the chemical reasoning capabilities of Large Language Models (LLMs) are limited by oversimplified tasks, lack of process-level evaluation, and misalignment with expert-level chemistry skills. To address these issues, we introduce SUPERChem, a benchmark of 500 expert-curated reasoning-intensive chemistry problems, covering diverse subfields and provided in both multimodal and text-only formats. Original content and an iterative curation pipeline eliminate flawed items and mitigate data contamination. Each problem is paired with an expert-authored solution path, enabling Reasoning Path Fidelity (RPF) scoring to evaluate reasoning quality beyond final-answer accuracy. Evaluations against a human baseline of 40.3% accuracy show that even the best-performing model, GPT-5 (High), reaches only 38.5%, followed closely by Gemini 2.5 Pro (37.9%) and DeepSeek-V3.1-Think (37.3%). SUPERChem elicits multi-step, multimodal reasoning, reveals model-dependent effects of visual information, and distinguishes high-fidelity reasoners from heuristic ones. By providing a challenging benchmark and a reliable evaluation framework, SUPERChem aims to facilitate the advancement of LLMs toward expert-level chemical intelligence. The dataset of the benchmark is available at https://huggingface.co/datasets/ZehuaZhao/SUPERChem.

The current irregularities in existing public Fire and Smoke Detection (FSD) datasets have become a bottleneck in the advancement of FSD technology. Upon in-depth analysis, we identify the core issue as the lack of standardized dataset construction, uniform evaluation systems, and clear performance benchmarks. To address this issue and drive innovation in FSD technology, we systematically gather diverse resources from public sources to create a more comprehensive and refined FSD benchmark. Additionally, recognizing the inadequate coverage of existing dataset scenes, we strategically expand scenes, relabel, and standardize existing public FSD datasets to ensure accuracy and consistency. We aim to establish a standardized, realistic, unified, and efficient FSD research platform that mirrors real-life scenes closely. Through our efforts, we aim to provide robust support for the breakthrough and development of FSD technology. The project is available at https://xiaoyihan6.github.io/FSD/{https://xiaoyihan6.github.io/FSD/}.

Recent developments in deep learning have made remarkable progress in speeding up the prediction of quantum chemical (QC) properties by removing the need for expensive electronic structure calculations like density functional theory. However, previous methods learned from 1D SMILES sequences or 2D molecular graphs failed to achieve high accuracy as QC properties primarily depend on the 3D equilibrium conformations optimized by electronic structure methods, far different from the sequence-type and graph-type data. In this paper, we propose a novel approach called Uni-Mol+ to tackle this challenge. Uni-Mol+ first generates a raw 3D molecule conformation from inexpensive methods such as RDKit. Then, the raw conformation is iteratively updated to its target DFT equilibrium conformation using neural networks, and the learned conformation will be used to predict the QC properties. To effectively learn this update process towards the equilibrium conformation, we introduce a two-track Transformer model backbone and train it with the QC property prediction task. We also design a novel approach to guide the model's training process. Our extensive benchmarking results demonstrate that the proposed Uni-Mol+ significantly improves the accuracy of QC property prediction in various datasets. We have made the code and model publicly available at https://github.com/dptech-corp/Uni-Mol.

We present miniF2F, a dataset of formal Olympiad-level mathematics problems statements intended to provide a unified cross-system benchmark for neural theorem proving. The miniF2F benchmark currently targets Metamath, Lean, Isabelle (partially) and HOL Light (partially) and consists of 488 problem statements drawn from the AIME, AMC, and the International Mathematical Olympiad (IMO), as well as material from high-school and undergraduate mathematics courses. We report baseline results using GPT-f, a neural theorem prover based on GPT-3 and provide an analysis of its performance. We intend for miniF2F to be a community-driven effort and hope that our benchmark will help spur advances in neural theorem proving.

We introduce TFRBench, the first benchmark designed to evaluate the reasoning capabilities of forecasting systems. Traditionally, time-series forecasting has been evaluated solely on numerical accuracy, treating foundation models as ``black boxes.'' Unlike existing benchmarks, TFRBench provides a protocol for evaluating the reasoning generated by forecasting systems--specifically their analysis of cross-channel dependencies, trends, and external events. To enable this, we propose a systematic multi-agent framework that utilizes an iterative verification loop to synthesize numerically grounded reasoning traces. Spanning ten datasets across five domains, our evaluation confirms that this reasoning is causally effective; useful for evaluation; and prompting LLMs with our generated traces significantly improves forecasting accuracy compared to direct numerical prediction (e.g., avg. sim40.2%to56.6%), validating the quality of our reasoning. Conversely, benchmarking experiments reveal that off-the-shelf LLMs consistently struggle with both reasoning (lower LLM-as-a-Judge scores) and numerical forecasting, frequently failing to capture domain-specific dynamics. TFRBench thus establishes a new standard for interpretable, reasoning-based evaluation in time-series forecasting. Our benchmark is available at: https://tfrbench.github.io

Foundation Models (FMs) serve as a general class for the development of artificial intelligence systems, offering broad potential for generalization across a spectrum of downstream tasks. Despite extensive research into self-supervised learning as the cornerstone of FMs, several outstanding issues persist in Graph Foundation Models that rely on graph self-supervised learning, namely: 1) Homogenization. The extent of generalization capability on downstream tasks remains unclear. 2) Scalability. It is unknown how effectively these models can scale to large datasets. 3) Efficiency. The training time and memory usage of these models require evaluation. 4) Training Stop Criteria. Determining the optimal stopping strategy for pre-training across multiple tasks to maximize performance on downstream tasks. To address these questions, we have constructed a rigorous benchmark that thoroughly analyzes and studies the generalization and scalability of self-supervised Graph Neural Network (GNN) models. Regarding generalization, we have implemented and compared the performance of various self-supervised GNN models, trained to generate node representations, across tasks such as node classification, link prediction, and node clustering. For scalability, we have compared the performance of various models after training using full-batch and mini-batch strategies. Additionally, we have assessed the training efficiency of these models by conducting experiments to test their GPU memory usage and throughput. Through these experiments, we aim to provide insights to motivate future research. The code for this benchmark is publicly available at https://github.com/NYUSHCS/GraphFM.

We introduce DafnyCOMP, a benchmark for evaluating large language models (LLMs) on compositional specification generation in Dafny. Unlike prior benchmarks that focus on single-function tasks, DafnyCOMP targets programs composed of multiple interacting functions with data dependencies, requiring reasoning across component boundaries. The benchmark consists of 300 automatically synthesized multi-function programs. We evaluate several state-of-the-art LLM families and find that, while they perform well on single-function verification, their performance drops sharply on compositional tasks. Analysis reveals systematic failures in cross-functional reasoning, including fragile specifications, misalignment between implementations and proofs, and unstable reasoning. DafnyCOMP thus provides a diagnostic tool for measuring progress toward reliable, verifiable, and compositional code generation with LLMs.

We present and test the largest benchmark for vericoding, LLM-generation of formally verified code from formal specifications - in contrast to vibe coding, which generates potentially buggy code from a natural language description. Our benchmark contains 12,504 formal specifications, with 3,029 in Dafny, 2,334 in Verus/Rust and 7,141 in Lean. Of these, 6,174 are new unseen problems. We find vericoding success rates of 27% in Lean, 44% in Verus/Rust and 82% in Dafny using off-the-shelf LLMs. Adding natural-language descriptions does not significantly improve performance. We also find that LLM progress has improved progress on pure Dafny verification from 68% to 96% over the past year. The benchmark and vericoding results are shared at https://github.com/Beneficial-AI-Foundation/vericoding-benchmark

Optimizing the performance of large-scale software repositories demands expertise in code reasoning and software engineering (SWE) to reduce runtime while preserving program correctness. However, most benchmarks emphasize what to fix rather than how to fix code. We introduce SWE-fficiency, a benchmark for evaluating repository-level performance optimization on real workloads. Our suite contains 498 tasks across nine widely used data-science, machine-learning, and HPC repositories (e.g., numpy, pandas, scipy): given a complete codebase and a slow workload, an agent must investigate code semantics, localize bottlenecks and relevant tests, and produce a patch that matches or exceeds expert speedup while passing the same unit tests. To enable this how-to-fix evaluation, our automated pipeline scrapes GitHub pull requests for performance-improving edits, combining keyword filtering, static analysis, coverage tooling, and execution validation to both confirm expert speedup baselines and identify relevant repository unit tests. Empirical evaluation of state-of-the-art agents reveals significant underperformance. On average, agents achieve less than 0.15x the expert speedup: agents struggle in localizing optimization opportunities, reasoning about execution across functions, and maintaining correctness in proposed edits. We release the benchmark and accompanying data pipeline to facilitate research on automated performance engineering and long-horizon software reasoning.

Creating a single unified interatomic potential capable of attaining ab initio accuracy across all chemistry remains a long-standing challenge in computational chemistry and materials science. This work introduces a training protocol for foundation machine-learning interatomic potentials (MLIPs) that bridge molecular, surface, and materials chemistry through cross-domain learning. First, we introduce enhancements to the MACE architecture that improve its performance on chemically diverse databases by increasing weight sharing across chemical elements and introducing non-linear factors into the tensor decomposition of the product basis. Second, we develop a multi-head replay post-training methodology that enables efficient knowledge transfer across diverse chemical domains. By fine-tuning on datasets at different levels of electronic structure theory, including inorganic crystals, molecular systems, surface chemistry, and reactive organic chemistry, we demonstrate that a single unified model achieves state-of-the-art performance across several chemical domains. Comprehensive benchmarking reveals superior cross-domain transferability compared with existing specialised and multi-task models, with notable improvements in molecular and surface properties while maintaining state-of-the-art performance in materials-property prediction.

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at https://github.com/Eurekashen/MolSpectLLM{https://github.com/Eurekashen/MolSpectLLM}.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 999 or 2998 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications. Our benchmark is publicly available at https://github.com/divelab/AIRS/tree/main/OpenDFT/QHBench.

We introduce MSC-Bench, a large-scale benchmark for evaluating multi-hop, end-to-end tool orchestration by LLM agents in a hierarchical Model-Context Protocol (MCP) ecosystem. Existing benchmarks often evaluate tools in isolation, ignoring challenges such as functional overlap and cross-server orchestration, leading to overly optimistic assessments. MSC-Bench addresses these gaps by constructing ground truth through 'equal function sets', allowing objective metrics such as F1 score and reducing the dependency on LLM-as-a-judge evaluation. Organized as a five-level curriculum, it systematically tests agent capabilities from single-tool orchestration to complex cross-server planning, and robustness to out-of-scope requests. Experiments reveal that rigid hierarchies can hinder performance without co-designed strategies, and even state-of-the-art agents exhibit systemic weaknesses in robustness. MSC-Bench provides a diagnostic framework to expose these limitations and guide the development of more capable and efficient tool-using agents. The benchmark and resources are publicly available at https://github.com/snooow1029/MSC_Bench.

Materials synthesis is vital for innovations such as energy storage, catalysis, electronics, and biomedical devices. Yet, the process relies heavily on empirical, trial-and-error methods guided by expert intuition. Our work aims to support the materials science community by providing a practical, data-driven resource. We have curated a comprehensive dataset of 17K expert-verified synthesis recipes from open-access literature, which forms the basis of our newly developed benchmark, AlchemyBench. AlchemyBench offers an end-to-end framework that supports research in large language models applied to synthesis prediction. It encompasses key tasks, including raw materials and equipment prediction, synthesis procedure generation, and characterization outcome forecasting. We propose an LLM-as-a-Judge framework that leverages large language models for automated evaluation, demonstrating strong statistical agreement with expert assessments. Overall, our contributions offer a supportive foundation for exploring the capabilities of LLMs in predicting and guiding materials synthesis, ultimately paving the way for more efficient experimental design and accelerated innovation in materials science.

This study presents a novel benchmark for evaluating Large Language Models (LLMs) using challenges derived from the Financial Modeling World Cup (FMWC) Excel competitions. We introduce a methodology for converting 113 existing FMWC challenges into programmatically evaluable JSON formats and use this dataset to compare the performance of several leading LLMs. Our findings demonstrate significant variations in performance across different challenge categories, with models showing specific strengths in pattern recognition tasks but struggling with complex numerical reasoning. The benchmark provides a standardized framework for assessing LLM capabilities in realistic business-oriented tasks rather than abstract academic problems. This research contributes to the growing field of AI benchmarking by establishing proficiency among the 1.5 billion people who daily use Microsoft Excel as a meaningful evaluation metric that bridges the gap between academic AI benchmarks and practical business applications.

Lack of rigorous reproducibility and validation are major hurdles for scientific development across many fields. Materials science in particular encompasses a variety of experimental and theoretical approaches that require careful benchmarking. Leaderboard efforts have been developed previously to mitigate these issues. However, a comprehensive comparison and benchmarking on an integrated platform with multiple data modalities with both perfect and defect materials data is still lacking. This work introduces JARVIS-Leaderboard, an open-source and community-driven platform that facilitates benchmarking and enhances reproducibility. The platform allows users to set up benchmarks with custom tasks and enables contributions in the form of dataset, code, and meta-data submissions. We cover the following materials design categories: Artificial Intelligence (AI), Electronic Structure (ES), Force-fields (FF), Quantum Computation (QC) and Experiments (EXP). For AI, we cover several types of input data, including atomic structures, atomistic images, spectra, and text. For ES, we consider multiple ES approaches, software packages, pseudopotentials, materials, and properties, comparing results to experiment. For FF, we compare multiple approaches for material property predictions. For QC, we benchmark Hamiltonian simulations using various quantum algorithms and circuits. Finally, for experiments, we use the inter-laboratory approach to establish benchmarks. There are 1281 contributions to 274 benchmarks using 152 methods with more than 8 million data-points, and the leaderboard is continuously expanding. The JARVIS-Leaderboard is available at the website: https://pages.nist.gov/jarvis_leaderboard

Vericoding refers to the generation of formally verified code from rigorous specifications. Recent AI models show promise in vericoding, but a unified methodology for cross-paradigm evaluation is lacking. Existing benchmarks test only individual languages/tools (e.g., Dafny, Verus, and Lean) and each covers very different tasks, so the performance numbers are not directly comparable. We address this gap with AlgoVeri, a benchmark that evaluates vericoding of 77 classical algorithms in Dafny, Verus, and Lean. By enforcing identical functional contracts, AlgoVeri reveals critical capability gaps in verification systems. While frontier models achieve tractable success in Dafny (40.3% for Gemini-3 Flash), where high-level abstractions and SMT automation simplify the workflow, performance collapses under the systems-level memory constraints of Verus (24.7%) and the explicit proof construction required by Lean (7.8%). Beyond aggregate metrics, we uncover a sharp divergence in test-time compute dynamics: Gemini-3 effectively utilizes iterative repair to boost performance (e.g., tripling pass rates in Dafny), whereas GPT-OSS saturates early. Finally, our error analysis shows that language design affects the refinement trajectory: while Dafny allows models to focus on logical correctness, Verus and Lean trap models in persistent syntactic and semantic barriers. All data and evaluation code can be found at https://github.com/haoyuzhao123/algoveri.

Existing benchmarks for hardware design primarily evaluate Large Language Models (LLMs) on isolated, component-level tasks such as generating HDL modules from specifications, leaving repository-scale evaluation unaddressed. We introduce HWE-Bench, the first large-scale, repository-level benchmark for evaluating LLM agents on real-world hardware bug repair tasks. HWE-Bench comprises 417 task instances derived from real historical bug-fix pull requests across six major open-source projects spanning both Verilog/SystemVerilog and Chisel, covering RISC-V cores, SoCs, and security roots-of-trust. Each task is grounded in a fully containerized environment where the agent must resolve a real bug report, with correctness validated through the project's native simulation and regression flows. The benchmark is built through a largely automated pipeline that enables efficient expansion to new repositories. We evaluate seven LLMs with four agent frameworks and find that the best agent resolves 70.7% of tasks overall, with performance exceeding 90% on smaller cores but dropping below 65% on complex SoC-level projects. We observe larger performance gaps across models than commonly reported on software benchmarks, and difficulty is driven by project scope and bug-type distribution rather than code size alone. Our failure analysis traces agent failures to three stages of the debugging process: fault localization, hardware-semantic reasoning, and cross-artifact coordination across RTL, configuration, and verification components, providing concrete directions for developing more capable hardware-aware agents.

LLM-based agents struggle to execute complex, multi-step Standard Operating Procedures (SOPs) that are fundamental to industrial automation. Existing benchmarks fail to capture the procedural complexity and tool orchestration demands of real-world workflows. We introduce SOP-Bench, a benchmark of 2,000+ tasks from human expert-authored SOPs across 12 business domains (healthcare, logistics, finance, content moderation, etc.). Using a human-AI collaborative framework, experts crafted authentic SOPs while AI generated artifacts (tools, APIs, datasets), all human-validated, yielding realistic tasks with executable interfaces and ground-truth outputs. SOP-Bench serves as a research enabler for systematically investigating agent architectures, model capabilities, and deployment considerations across diverse procedural tasks. We demonstrate its utility through illustrative experiments with a subset of frontier models across Function-Calling (FC) and ReAct agents, revealing critical insights. For example, (1) newer models do not guarantee better performance - Claude 4 family outperforms Claude 4.5 family on ReAct tasks (Claude 4 Opus: 72.4% vs. Claude 4.5 Sonnet: 63.3% task success rate), demonstrating that production upgrades require validation; (2) no single model-agent combination dominates: best performances range from 57% to 100% depending on domain. These examples illustrate how SOP-Bench enables isolating and studying specific dimensions of agent performance without costly production experiments. Our goal is not to rank model capabilities or build optimal agents, but to provide a rigorous evaluation framework that enables the researchers and practitioners to systematically investigate agent design choices, model selection, and deployment strategies. We release the benchmark at https://github.com/amazon-science/sop-bench.

Automated software engineering has been greatly empowered by the recent advances in Large Language Models (LLMs) for programming. While current benchmarks have shown that LLMs can perform various software engineering tasks like human developers, the majority of their evaluations are limited to short and self-contained algorithmic tasks. Solving challenging and practical programming tasks requires the capability of utilizing diverse function calls as tools to efficiently implement functionalities like data analysis and web development. In addition, using multiple tools to solve a task needs compositional reasoning by accurately understanding complex instructions. Fulfilling both of these characteristics can pose a great challenge for LLMs. To assess how well LLMs can solve challenging and practical programming tasks, we introduce Bench, a benchmark that challenges LLMs to invoke multiple function calls as tools from 139 libraries and 7 domains for 1,140 fine-grained programming tasks. To evaluate LLMs rigorously, each programming task encompasses 5.6 test cases with an average branch coverage of 99%. In addition, we propose a natural-language-oriented variant of Bench, Benchi, that automatically transforms the original docstrings into short instructions only with essential information. Our extensive evaluation of 60 LLMs shows that LLMs are not yet capable of following complex instructions to use function calls precisely, with scores up to 60%, significantly lower than the human performance of 97%. The results underscore the need for further advancements in this area.

Large language models (LLMs) have sparked growing interest in automatic machine learning research agents. Among them, agents capable of autonomously proposing ideas and conducting machine learning experiments are particularly promising, as they maximize research automation and accelerate scientific progress by iteratively refining ideas based on experimental results. However, comprehensively evaluating such agents remains challenging. Existing benchmarks tend to overemphasize engineering aspects while neglecting academic rigor, creating barriers that obscure a clear assessment of an agent's scientific capabilities in machine learning research. They also suffer from limited task diversity, an overemphasis on application-oriented tasks over fundamental research problems, and limited scalability to realistic research settings. To address these limitations, we introduce FML-bench, a benchmark designed to evaluate automatic machine learning research agents on 8 diverse and fundamental machine learning research problems. It reduces coding burden, emphasizes fundamental problems rather than specific use cases, offers high task diversity, and is extensible to real-world machine learning GitHub repositories. Furthermore, we present a unified evaluation framework with five complementary metrics, designed to comprehensively assess agent performance on our benchmark. We evaluate state-of-the-art automatic research agents on FML-bench, and find that agents employing broad research exploration strategies outperform those focusing on narrow but deep exploration. These findings suggest that emphasizing the breadth of exploration may lead to more effective research outcomes than focusing solely on incremental refinement. Our benchmark is available at https://github.com/qrzou/FML-bench.

Universal machine learning force fields (UMLFFs) promise to revolutionize materials science by enabling rapid atomistic simulations across the periodic table. However, their evaluation has been limited to computational benchmarks that may not reflect real-world performance. Here, we present UniFFBench, a comprehensive framework for evaluating UMLFFs against experimental measurements of ~1,500 carefully curated mineral structures spanning diverse chemical environments, bonding types, structural complexity, and elastic properties. Our systematic evaluation of six state-of-the-art UMLFFs reveals a substantial reality gap: models achieving impressive performance on computational benchmarks often fail when confronted with experimental complexity. Even the best-performing models exhibit higher density prediction error than the threshold required for practical applications. Most strikingly, we observe disconnects between simulation stability and mechanical property accuracy, with prediction errors correlating with training data representation rather than the modeling method. These findings demonstrate that while current computational benchmarks provide valuable controlled comparisons, they may overestimate model reliability when extrapolated to experimentally complex chemical spaces. Altogether, UniFFBench establishes essential experimental validation standards and reveals systematic limitations that must be addressed to achieve truly universal force field capabilities.

Large language models (LLMs) have shown promising potential in scientific research, enabling tasks ranging from knowledge retrieval to property prediction. Existing science benchmarks mainly focus on perceptual or knowledge-based tasks, largely ignoring the modelling tasks, a fundamental starting point for any real scientific research. For materials science, constructing and manipulating atomic structures is one of the most creative and least automated steps. In this work, we introduce AtomWorld, a benchmark designed to evaluate the abilities of LLMs on structure modifications. The benchmark includes ten fundamental actions under four widely used modelling categories, enabling verifiable evaluation metrics. We find that Claude Opus 4.6 generally performs the best. While the success rate decreases markedly with increasing modelling complexity, with particularly low success rates (below 12\% for rotation) for operations involving complex spatial relations. Our results suggest that contemporary LLMs are better suited as copilots for materials structure modelling rather than fully unsupervised autonomous scientific agents. Beyond evaluation, AtomWorld also serves as a testbed and playground for developing future structure-aware models, including reinforcement learning and agentic approaches.

Olympiad-level benchmarks in mathematics and physics are crucial testbeds for advanced AI reasoning, but chemistry, with its unique multimodal symbolic language, has remained an open challenge. We introduce ChemO, a new benchmark built from the International Chemistry Olympiad (IChO) 2025. ChemO features two key innovations for automated assessment: Assessment-Equivalent Reformulation (AER), which converts problems requiring visual outputs (e.g., drawing molecules) into computationally tractable formats, and Structured Visual Enhancement (SVE), a diagnostic mechanism to disentangle a model's visual perception capabilities from its core chemical reasoning. To tackle this benchmark, we propose ChemLabs, a hierarchical multi-agent framework that mimics human expert collaboration through specialized agents for problem decomposition, perception, reasoning, and auditing. Experiments on state-of-the-art multimodal models demonstrate that combining SVE with our multi-agent system yields dramatic performance gains. Our top configuration achieves a score of 93.6 out of 100, surpassing an estimated human gold medal threshold and establishing a new state-of-the-art in automated chemical problem-solving. ChemO Dataset: https://huggingface.co/datasets/IDEA-AI4SCI/ChemO

Structure-Based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3%, Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility. Code is available at https://github.com/AlgoMole/MolCRAFT.

We present a vector-based method to balance chemical reactions. The algorithm builds candidates in a deterministic way, removes duplicates, and always prints coefficients in the lowest whole-number form. For redox cases, electrons and protons/hydroxide are treated explicitly, so both mass and charge are balanced. We also outline the basic principles of the vector formulation of stoichiometry, interpreting reactions as integer vectors in composition space, this geometric view supports compact visualizations of reagent-product interactions and helps surface distinct reaction families. The method enumerates valid balances for arbitrary user-specified species lists without special-case balancing rules or symbolic tricks, and it provides a clean foundation for developing new algorithmic variants (e.g., alternative objectives or constraints). On representative examples (neutralization, double displacement, decomposition, classical redox, small multicomponent sets) and a negative control, the method produced correct integer balances. When multiple balances exist, we report a canonical one - minimizing the total coefficient sum with a simple tie-breaker - without claiming global optimality beyond the solutions the search enumerates. The procedure applies per reaction and extends to reaction networks via consistent per-reaction application. We do not report runtimes, broader benchmarking and code/data release are planned.

Large Language Models (LLMs) are increasingly used to automate hardware design tasks, including the generation of Verilog code. While early benchmarks focus primarily on functional correctness, efficient hardware design demands additional optimization for synthesis metrics such as area, delay, and power. Existing benchmarks fall short in evaluating these aspects comprehensively: they often lack optimized baselines or testbenches for verification. To address these gaps, we present Pluto, a benchmark and evaluation framework designed to assess the efficiency of LLM-generated Verilog designs. Pluto presents a comprehensive evaluation set of 114 problems with self-checking testbenches and multiple Pareto-optimal reference implementations. Experimental results show that state-of-the-art LLMs can achieve high functional correctness, reaching 78.3\% at pass@1, but their synthesis efficiency still lags behind expert-crafted implementations, with area efficiency of 63.8\%, delay efficiency of 65.9\%, and power efficiency of 64.0\% at eff@1. This highlights the need for efficiency-aware evaluation frameworks such as Pluto to drive progress in hardware-focused LLM research.

Large language models (LLMs) are increasingly applied to materials science questions, including literature comprehension, property prediction, materials discovery and alloy design. At the same time, a wide range of physics-based computational approaches have been developed in which materials properties can be calculated. Here, we propose a benchmark application to evaluate the proficiency of LLMs to answer materials science questions through the generation and safe execution of codes based on such physics-based computational materials science packages. MatTools is built on two complementary components: a materials simulation tool question-answer (QA) benchmark and a real-world tool-usage benchmark. We designed an automated methodology to efficiently collect real-world materials science tool-use examples. The QA benchmark, derived from the pymatgen (Python Materials Genomics) codebase and documentation, comprises 69,225 QA pairs that assess the ability of an LLM to understand materials science tools. The real-world benchmark contains 49 tasks (138 subtasks) requiring the generation of functional Python code for materials property calculations. Our evaluation of diverse LLMs yields three key insights: (1)Generalists outshine specialists;(2)AI knows AI; and (3)Simpler is better. MatTools provides a standardized framework for assessing and improving LLM capabilities for materials science tool applications, facilitating the development of more effective AI systems for materials science and general scientific research.

The large and chemically diverse GMTKN55 benchmark was used as a training set for parametrizing composite wave function thermochemistry protocols akin to G4(MP2)XK theory (Chan et al, JCTC 2019, 15, 4478-4484). Even after reparametrization, the GMTKN55 WTMAD2 (weighted mean absolute deviation, type 2) for G4(MP2)-XK is actually inferior to that of the best rung-4 DFT functional, wB97M-V. By increasing the basis set for the MP2 part to def2-QZVPPD, we were able to substantially improve performance at modest cost (if an RI-MP2 approximation is made), with WTMAD2 for this G4(MP2)-XK-D method now comparable to the better rung-5 functionals (albeit at greater cost). A three-tier approach with a scaled MP3/def2-TZVPP intermediate step, however, leads to a G4(MP3)-D method that is markedly superior to even the best double hybrids wB97M(2) and revDSD-PBEP86-D4. Evaluating the CCSD(T) component with a triple-zeta, rather than split-valence, basis set yields only a modest further improvement that is incommensurate with the drastic increase in computational cost. G4(MP3)-D and G4(MP2)- XK-D have about 40% better WTMAD2, at similar or lower computational cost, than their counterparts G4 and G4(MP2), respectively: detailed comparison reveals that the difference lies in larger molecules due to basis set incompleteness error. An E2/ {T,Q} extrapolation and a CCSD(T)/def2-TZVP step provided the G4-T method of high accuracy and with just three fitted parameters. Using KS orbitals in MP2 leads to the G4(MP3|KS)-D method, which entirely eliminates the CCSD(T) step and has no steps costlier than scaled MP3; this shows a path forward to further improvements in double-hybrid density functional methods. G4-T-DLPNO, a variant in which post-MP2 corrections are evaluated at the DLPNO- CCSD(T) level, achieves nearly the accuracy of G4-T but is applicable to much larger systems.

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.

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

Recent advances in language models have enabled framing molecule generation as sequence modeling. However, existing approaches often rely on single-objective reinforcement learning, limiting their applicability to real-world drug design, where multiple competing properties must be optimized. Traditional multi-objective reinforcement learning (MORL) methods require costly retraining for each new objective combination, making rapid exploration of trade-offs impractical. To overcome these limitations, we introduce Mol-MoE, a mixture-of-experts (MoE) architecture that enables efficient test-time steering of molecule generation without retraining. Central to our approach is a preference-based router training objective that incentivizes the router to combine experts in a way that aligns with user-specified trade-offs. This provides improved flexibility in exploring the chemical property space at test time, facilitating rapid trade-off exploration. Benchmarking against state-of-the-art methods, we show that Mol-MoE achieves superior sample quality and steerability.

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

The application of large language models (LLMs) in the field of coding is evolving rapidly: from code assistants, to autonomous coding agents, and then to generating complete projects through natural language. Early LLM code benchmarks primarily focused on code generation accuracy, but these benchmarks have gradually become saturated. Benchmark saturation weakens their guiding role for LLMs. For example, HumanEval Pass@1 has reached 99.4% and MBPP 94.2%. Among various attempts to address benchmark saturation, approaches based on software engineering have stood out, but the saturation of existing software engineering benchmarks is rapidly increasing. To address this, we propose a new benchmark, Web-Bench, which contains 50 projects, each consisting of 20 tasks with sequential dependencies. The tasks implement project features in sequence, simulating real-world human development workflows. When designing Web-Bench, we aim to cover the foundational elements of Web development: Web Standards and Web Frameworks. Given the scale and complexity of these projects, which were designed by engineers with 5 to 10 years of experience, each presents a significant challenge. On average, a single project takes 4 to 8 hours for a senior engineer to complete. On our given benchmark agent (Web-Agent), SOTA (Claude 3.7 Sonnet) achieves only 25.1% Pass@1, significantly lower (better) than SWE-Bench's Verified (65.4%) and Full (33.8%) scores. Finally, we discuss that in any development field, Standards and Frameworks represent foundational knowledge and efficiency tools, respectively, and LLMs require optimization tailored to them.

Data-driven modeling of fluid dynamics has advanced rapidly with neural PDE solvers, yet a fair and strong benchmark remains fragmented due to the absence of unified PDE datasets and standardized evaluation protocols. Although architectural innovations are abundant, fair assessment is further impeded by the lack of clear disentanglement between spatial, temporal and loss modules. In this paper, we introduce FD-Bench, the first fair, modular, comprehensive and reproducible benchmark for data-driven fluid simulation. FD-Bench systematically evaluates 85 baseline models across 10 representative flow scenarios under a unified experimental setup. It provides four key contributions: (1) a modular design enabling fair comparisons across spatial, temporal, and loss function modules; (2) the first systematic framework for direct comparison with traditional numerical solvers; (3) fine-grained generalization analysis across resolutions, initial conditions, and temporal windows; and (4) a user-friendly, extensible codebase to support future research. Through rigorous empirical studies, FD-Bench establishes the most comprehensive leaderboard to date, resolving long-standing issues in reproducibility and comparability, and laying a foundation for robust evaluation of future data-driven fluid models. The code is open-sourced at https://anonymous.4open.science/r/FD-Bench-15BC.

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

In recent years, large language models (LLMs) have made significant progress in code intelligence, yet systematically evaluating their code understanding and reasoning abilities remains challenging. Mainstream benchmarks such as HumanEval and MBPP primarily assess functional correctness, while reasoning benchmarks like CRUXEVAL are limited to single-function, low-complexity scenarios. As a result, advanced models achieve nearly saturated scores, limiting their discriminative power. To address this, we present STEPWISE-CODEX-Bench (SX-Bench), a novel benchmark designed for complex multi-function understanding and fine-grained execution reasoning. SX-Bench features tasks involving collaboration among multiple sub-functions (e.g., chained calls, nested loops), shifting evaluation towards overall control and data flow modeling. It defines "computation steps" as the minimal execution unit and requires models to predict the total number of steps in reasoning tasks, thereby assessing a model's in-depth understanding of dynamic execution beyond simple I/O matching. Evaluation on over 20 mainstream models (including 14 reasoning-enhanced models) demonstrates that SX-Bench is highly discriminative: even the state-of-the-art OpenAI-O3 achieves only 78.37 percent accuracy on Hard-Reasoning tasks, much lower than its saturated scores on previous benchmarks, thereby revealing bottlenecks in complex and fine-grained reasoning. We also release an automated pipeline combining program synthesis, symbolic execution, and LLM-aided validation for efficient benchmark generation and quality assurance. SX-Bench advances code evaluation from "single-function verification" to "multi-function dynamic reasoning," providing a key tool for the in-depth assessment of advanced code intelligence models.

We present Metal-Sci, a 10-task benchmark of scientific Apple Silicon Metal compute kernels spanning six optimization regimes (stencils, all-pairs in n-body problems, multi-field Boltzmann, neighbor-list molecular dynamics, multi-kernel PDE, FFT). Each task ships a CPU reference, a roofline-anchored fitness function, and a held-out generalization size. We pair the benchmark with a lightweight harness for automatic kernel search that runtime-compiles each candidate, scores it against the roofline across multiple sizes, and feeds structured compile and per-size correctness diagnostics back to a frozen LLM driving a (1{+}1) evolutionary loop. We report matched single-model sweeps of Claude Opus 4.7, Gemini 3.1 Pro, and GPT 5.5 on M1 Pro: in-distribution self-speedups span 1.00times to 10.7times. Beyond raw speedup, our central methodological claim is structural: the held-out gate scoring function Φ_T (evaluated once at end-of-run on a configuration the agent never sees during search) functions as a cheap mechanical oversight primitive on this automatic search loop, catching e.g. an Opus template <uint D> HMC win that returns wrong samples at unseen dimensions, and a GPT FFT3D best that wins in-distribution at 2.95times speedup but collapses to 0.23times on a 256^3 held-out cube, a silent regression that the in-distribution score alone cannot see. Code at https://github.com/vicgalle/metal-sci-kernels

LLM agents have incredible potential for scientific discovery applications. However, the performance of LLM agents on real-world, small molecule drug design (SMDD) tasks across diverse chemistries and targets is unclear. Current evaluation methods are either ad hoc, too simple for real-world discovery, limited in scale, or restricted to single-turn question answering. In effort to standardize the evaluation of LLM agents on small molecule design, we introduce SMDD-Bench, a challenging, multi-turn, long-horizon agentic benchmark consisting of 502 guaranteed-solvable task instances spanning 5 task types: 2D Pharmacophore Identification, Interaction Point Discovery, Scaffold Hopping, Lead Optimization, and Fragment Assembly. SMDD-Bench tasks span a wide region of chemical space and involve 102 unique protein targets. Completely solving the benchmark would require having strong chemical and biological reasoning and 3D intuition, understanding specialized tool use, and displaying planning expertise over a limited number of oracle calls. We benchmark 7 frontier open and closed source LLMs and find even the most performant LLM, GPT5.4, solves only 40.2\% of tasks. We hope SMDD-Bench provides a standardized testbed to invigorate the field towards training and evaluating LLM agents for fully autonomous computational drug design. We host a public leaderboard at smddbench.com .

Recent advancements in language models have started a new era of superior information retrieval and content generation, with embedding models playing an important role in optimizing data representation efficiency and performance. While benchmarks like the Massive Text Embedding Benchmark (MTEB) have standardized the evaluation of general domain embedding models, a gap remains in specialized fields such as chemistry, which require tailored approaches due to domain-specific challenges. This paper introduces a novel benchmark, the Chemical Text Embedding Benchmark (ChemTEB), designed specifically for the chemical sciences. ChemTEB addresses the unique linguistic and semantic complexities of chemical literature and data, offering a comprehensive suite of tasks on chemical domain data. Through the evaluation of 34 open-source and proprietary models using this benchmark, we illuminate the strengths and weaknesses of current methodologies in processing and understanding chemical information. Our work aims to equip the research community with a standardized, domain-specific evaluation framework, promoting the development of more precise and efficient NLP models for chemistry-related applications. Furthermore, it provides insights into the performance of generic models in a domain-specific context. ChemTEB comes with open-source code and data, contributing further to its accessibility and utility.

Large language model (LLM) coding agents increasingly operate at the repository level, motivating benchmarks that evaluate their ability to optimize entire codebases under realistic constraints. Existing code benchmarks largely rely on synthetic tasks, binary correctness signals, or single-objective evaluation, limiting their ability to assess holistic optimization behavior. We introduce FormulaCode, a benchmark for evaluating agentic optimization on large, real-world codebases with fine-grained, multi-objective performance metrics. FormulaCode comprises 957 performance bottlenecks mined from scientific Python repositories on GitHub, each paired with expert-authored patches and, on average, 264.6 community-maintained performance workloads per task, enabling the holistic ability of LLM agents to optimize codebases under realistic correctness and performance constraints. Our evaluations reveal that repository-scale, multi-objective optimization remains a major challenge for frontier LLM agents. Project website at: https://formula-code.github.io

We perform a thorough analysis of the formal and informal statements in the miniF2F benchmark from the perspective of an AI system that is tasked to participate in a math Olympiad consisting of the problems in miniF2F. In such setting, the model has to read and comprehend the problems in natural language, formalize them in Lean language, then proceed with proving the problems, and it will get credit for each problem if the formal proof corresponds to the original informal statement presented to the model. Our evaluation results reveal that the best accuracy of such pipeline can be about 36% using the SoTA models in the literature, considerably lower than the individual SoTA accuracies, 97% and 69% reported in the autoformalization and theorem proving literature. Analyzing the failure modes, we trace back a considerable portion of this drop to discrepancies between the formal and informal statements for more than half of the problems in miniF2F. We proceed with correcting all the errors, discrepancies and simplifications in formal and informal statements, and present the miniF2F-v2 with fully verified formal and informal statements and proofs. Evaluating the full theorem proving pipeline on miniF2F-v2 leads to the best accuracy of 70%, a significant improvement from the 40% on the original miniF2F, yet indicating considerable misalignment between the autoformalization models and theorem provers. Our deep analysis suggests that a higher quality benchmark can help the community better evaluate progress in the field of formal reasoning and also better diagnose the failure and success modes of autoformalization and theorem proving models. Our dataset is available at https://github.com/roozbeh-yz/miniF2F_v2.

Benchmarks are fundamental for evaluating and advancing LLMs and MLLMs by providing standardized and explicit measures of performance. However, their construction is labor-intensive and hard to reuse, raising concerns about sustainability and scalability. Moreover, existing benchmarks often quickly reach performance saturation after their release, resulting in insufficient discrimination among state-of-the-art models. To address these challenges, we introduce Benchmark Agent, a fully autonomous agentic system designed for benchmark building. Our framework orchestrates the complete benchmark construction pipeline, from user query analysis and subtask design to data annotation and quality control. To assess Benchmark Agent, we implement it to produce 15 representative benchmarks, spanning diverse evaluation scenarios, including text understanding, multimodal understanding, and domain-specific reasoning. Extensive experiments, including human evaluation, LLM-as-a-judge assessment, and consistency checks, demonstrate Benchmark Agent can generate high-quality benchmark samples with minimal human involvement. More importantly, through continual evaluation, we observe several insightful findings, including that current models struggle with certain domain-specific reasoning tasks. We believe that rapidly evolving benchmarks can contribute significantly to the research community. The preview and code will be publicly available at the demo page and code repository.

Geo-Foundation Models (GFMs) have been evaluated across diverse Earth observation task including multiple domains and have demonstrated strong potential of producing reliable maps even with sparse labels. However, benchmarking GFMs for Cryosphere applications has remained limited, primarily due to the lack of suitable evaluation datasets. To address this gap, we introduce Cryo-Bench, a benchmark compiled to evaluate GFM performance across key Cryospheric components. Cryo-Bench includes debris-covered glaciers, glacial lakes, sea ice, and calving fronts, spanning multiple sensors and broad geographic regions. We evaluate 14 GFMs alongside UNet and ViT baselines to assess their advantages, limitations, and optimal usage strategies. With a frozen encoder, UNet achieves the highest average mIoU of 66.38, followed by TerraMind at 64.02 across five evluation dataset included in Cryo-Bench. In the few-shot setting (10\% input data), GFMs such as DOFA and TerraMind outperform UNet, achieving mIoU scores of 59.53, 56.62, and 56.60, respectively, comapred to U-Net's 56.60. When fully finetuning GFMs, we observe inconsistent performance across datasets and models. However, tuning learning rate along with finetuning substantially improves GFM performance. For example, evaluation on two representative datasets (GLID and CaFFe) shows an average relative improvement of 12.77\%. Despite having minimal Cryosphere representation in their pretraining data, GFMs exhibit notable domain adaptation capabilities and produce meaningful results across tasks. Based on our findings, We recommend encoder fine-tuning with hyperparameter optimization optimization to achieve the best possible performance, while using frozen encoders when users need quick results without extensive experimentation.(https://github.com/Sk-2103/Cryo-Bench{GitHub}).

Multi-lingual competence in large language models is often evaluated via static data benchmarks such as Belebele, M-MMLU and M-GSM. However, these evaluations often fail to provide an adequate understanding of the practical performance and robustness of models across multi-lingual settings. In response, we create multi-lingual functional benchmarks -- Cross-Lingual Grade School Math Symbolic (CL-GSM Symbolic) and Cross-Lingual Instruction-Following Eval (CL-IFEval)-- by translating existing functional benchmark templates from English to five additional languages that span the range of resources available for NLP: French, Spanish, Hindi, Arabic and Yoruba. Our results reveal that some static multi-lingual benchmarks capture functional performance much more closely than others (i.e. across models, there is a 24%, 17% and 18% decrease in performance between M-GSM and CL-GSM Symbolic in English, French and Spanish respectively; similarly there's a 15 - 24% performance drop across languages between Belebele and CL-IFEval, and only a 0.5% to 3% performance drop between M-MMLU and CL-IFEval). Similarly, we find that model robustness across languages varies significantly, with certain languages (eg. Arabic, English) being the most consistently well performing across evaluation iterations.

Transition state (TS) structures define the critical geometries and energy barriers underlying chemical reactivity, yet their fleeting nature renders them experimentally elusive and drives the reliance on costly, high-throughput density functional theory (DFT) calculations. Here, we introduce TS-GEN, a conditional flow-matching generative model that maps samples from a simple Gaussian prior directly to transition-state saddle-point geometries in a single, deterministic pass. By embedding both reactant and product conformations as conditioning information, TS-GEN learns to transport latent noise to true TS structures via an optimal-transport path, effectively replacing the iterative optimization common in nudged-elastic band or string-method algorithms. TS-GEN delivers unprecedented accuracy, achieving a root-mean-square deviation of 0.004 mathring{A} (vs. 0.103 mathring{A} for prior state-of-the-art) and a mean barrier-height error of 1.019 {rm kcal/mol} (vs. 2.864 {rm kcal/mol}), while requiring only 0.06 {rm s} GPU time per inference. Over 87% of generated TSs meet chemical-accuracy criteria (<1.58 {rm kcal/mol} error), substantially outpacing existing methods. TS-GEN also exhibits strong transferability to out-of-distribution reactions from a larger database. By uniting sub-angstrom precision, sub-second speed, and broad applicability, TS-GEN will be highly useful for high-throughput exploration of complex reaction networks, paving the way to the exploration of novel chemical reaction mechanisms.

We introduce ISO-Bench, a benchmark for coding agents to test their capabilities on real-world inference optimization tasks. These tasks were taken from vLLM and SGLang, two of the most popular LLM serving frameworks. Each task provides an agent with a codebase and bottleneck description, whereby the agent must produce an optimization patch evaluated against expert human solutions. We curated 54 tasks from merged pull requests with measurable performance improvements. While existing benchmarks heavily use runtime-based metrics, such approaches can be gamed to pass tests without capturing the actual intent of the code changes. Therefore, we combine both hard (execution-based) and soft (LLM-based) metrics to show that both are necessary for complete evaluation. While evaluating both closed and open-source coding agents, we find no single agent dominates across codebases. Surprisingly, agents often identify correct bottlenecks but fail to execute working solutions. We also show that agents with identical underlying models differ substantially, suggesting scaffolding is as important as the model.

Autonomous agents powered by large language models (LLMs) promise to accelerate scientific discovery end-to-end, but rigorously evaluating their capacity for verifiable discovery remains a central challenge. Existing benchmarks face a trade-off: they either heavily rely on LLM-as-judge evaluations of automatically generated research outputs or optimize convenient yet isolated performance metrics that provide coarse proxies for scientific insight. To address this gap, we introduce FIRE-Bench (Full-cycle Insight Rediscovery Evaluation), a benchmark that evaluates agents through the rediscovery of established findings from recent, high-impact machine learning research. Agents are given only a high-level research question extracted from a published, verified study and must autonomously explore ideas, design experiments, implement code, execute their plans, and derive conclusions supported by empirical evidence. We evaluate a range of state-of-the-art agents with frontier LLMs backbones like gpt-5 on FIRE-Bench. Our results show that full-cycle scientific research remains challenging for current agent systems: even the strongest agents achieve limited rediscovery success (<50 F1), exhibit high variance across runs, and display recurring failure modes in experimental design, execution, and evidence-based reasoning. FIRE-Bench provides a rigorous and diagnostic framework for measuring progress toward reliable agent-driven scientific discovery.

In light of the rapid adoption of AI coding assistants, LLM-assisted development has become increasingly prevalent, creating an urgent need for robust evaluation of generated code quality. Existing benchmarks often require extensive manual effort to create static datasets, rely on indirect or insufficiently challenging tasks, depend on non-scalable ground truth, or neglect critical low-level security evaluations, particularly memory-safety issues. In this work, we introduce OSS-Bench, a benchmark generator that automatically constructs large-scale, live evaluation tasks from real-world open-source software. OSS-Bench replaces functions with LLM-generated code and evaluates them using three natural metrics: compilability, functional correctness, and memory safety, leveraging robust signals like compilation failures, test-suite violations, and sanitizer alerts as ground truth. In our evaluation, the benchmark, instantiated as OSS-Bench(php) and OSS-Bench(sql), profiles 17 diverse LLMs, revealing insights such as intra-family behavioral patterns and inconsistencies between model size and performance. Our results demonstrate that OSS-Bench mitigates overfitting by leveraging the evolving complexity of OSS and highlights LLMs' limited understanding of low-level code security via extended fuzzing experiments. Overall, OSS-Bench offers a practical and scalable framework for benchmarking the real-world coding capabilities of LLMs.

We present a new approach for benchmarking Large Language Model (LLM) capabilities on research-level mathematics. Existing benchmarks largely rely on static, hand-curated sets of contest or textbook-style problems as proxies for mathematical research. Instead, we establish an updatable benchmark evaluating models directly on the latest research results in mathematics. This consists of an automatic pipeline that extracts lemmas from arXiv and rewrites them into self-contained statements by making all assumptions and required definitions explicit. It results in a benchmark that can be updated regularly with new problems taken directly from human mathematical research, while previous instances can be used for training without compromising future evaluations. We benchmark current state-of-the-art LLMs, which obtain around 10-15% accuracy in theorem proving (pass@1) depending on the model, showing that there is currently a large margin of progression for LLMs to reach human-level proving capabilities in a research context.

Code Agent development is an extremely active research area, where a reliable performance metric is critical for tracking progress and guiding new developments. This demand is underscored by the meteoric rise in popularity of SWE-Bench. This benchmark challenges code agents to generate patches addressing GitHub issues given the full repository as context. The correctness of generated patches is then evaluated by executing a human-written test suite extracted from the repository after the issue's resolution. However, constructing benchmarks like SWE-Bench requires substantial manual effort to set up historically accurate execution environments for testing. Crucially, this severely limits the number of considered repositories, e.g., just 12 for SWE-Bench. Considering so few repositories, selected for their popularity runs the risk of leading to a distributional mismatch, i.e., the measured performance may not be representative of real-world scenarios potentially misguiding development efforts. In this work, we address this challenge and introduce SetUpAgent, a fully automated system capable of historically accurate dependency setup, test execution, and result parsing. Using SetUpAgent, we generate two new datasets: (i) SWEE-Bench an extended version of SWE-Bench encompassing hundreds of repositories, and (ii) SWA-Bench a benchmark focusing on applications rather than libraries. Comparing these datasets to SWE-Bench with respect to their characteristics and code agent performance, we find significant distributional differences, including lower issue description quality and detail level, higher fix complexity, and most importantly up to 40% lower agent success rates.

Generative models for materials, especially inorganic crystals, hold potential to transform the theoretical prediction of novel compounds and structures. Advancement in this field depends critically on robust benchmarks and minimal, information-rich datasets that enable meaningful model evaluation. This paper critically examines common datasets and reported metrics for a crystal structure prediction taskx2014generating the most likely structures given the chemical composition of a material. We focus on three key issues: First, materials datasets should contain unique crystal structures; for example, we show that the widely-utilized carbon-24 dataset only contains approx40% unique structures. Second, materials datasets should not be split randomly if polymorphs of many different compositions are numerous, which we find to be the case for the perov-5 dataset. Third, benchmarks can mislead if used uncritically, e.g., reporting a match rate metric without considering the structural variety exhibited by identical building blocks. To address these oft-overlooked issues, we introduce several fixes. We provide revised versions of the carbon-24 dataset: one with duplicates removed, one deduplicated and split by number of atoms N, and two containing only identical structures but with different unit cells. We also propose a new split for the perov-5 dataset which ensures polymorphs are grouped within each split subset, setting a more sensible standard for benchmarking model performance. Finally, we present METRe and cRMSE, new model evaluation metrics that can correct existing issues with the match rate metric.

Language-model agents are increasingly used as persistent coworkers that assist users across multiple working days. During such workflows, the surrounding environment may change independently of the agent: new emails arrive, calendar entries shift, knowledge-base records are updated, and evidence appears across images, scanned PDFs, audio, video, and spreadsheets. Existing benchmarks do not adequately evaluate this setting because they typically run within a single static episode and remain largely text-centric. We introduce , a benchmark for coworker agents built around multi-turn multi-day tasks, a stateful sandboxed service environment whose state evolves between turns, and rule-based verification. The current release contains 100 tasks across 13 professional scenarios, executed against five stateful sandboxed services (filesystem, email, calendar, knowledge base, spreadsheet) and scored by 1537 deterministic Python checkers over post-execution service state; no LLM-as-judge is invoked during scoring. We benchmark seven frontier agent systems. The strongest model reaches 75.8 weighted score, but the best strict Task Success is only 20.0\%, indicating that partial progress is common while complete end-to-end workflow completion remains rare. Turn-level analysis shows that performance drops after the first exogenous environment update, highlighting adaptation to changing state as a key open challenge. We release the benchmark, evaluation harness, and construction pipeline to support reproducible coworker-agent evaluation.

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular properties. However, algorithmic progress has been limited due to the lack of a standard benchmark to compare the efficacy of proposed methods; most new algorithms are benchmarked on different datasets making it challenging to gauge the quality of proposed methods. This work introduces MoleculeNet, a large scale benchmark for molecular machine learning. MoleculeNet curates multiple public datasets, establishes metrics for evaluation, and offers high quality open-source implementations of multiple previously proposed molecular featurization and learning algorithms (released as part of the DeepChem open source library). MoleculeNet benchmarks demonstrate that learnable representations are powerful tools for molecular machine learning and broadly offer the best performance. However, this result comes with caveats. Learnable representations still struggle to deal with complex tasks under data scarcity and highly imbalanced classification. For quantum mechanical and biophysical datasets, the use of physics-aware featurizations can be more important than choice of particular learning algorithm.

Machine learning has promised to change the landscape of laboratory chemistry, with impressive results in molecular property prediction and reaction retro-synthesis. However, chemical datasets are often inaccessible to the machine learning community as they tend to require cleaning, thorough understanding of the chemistry, or are simply not available. In this paper, we introduce a novel dataset for yield prediction, providing the first-ever transient flow dataset for machine learning benchmarking, covering over 1200 process conditions. While previous datasets focus on discrete parameters, our experimental set-up allow us to sample a large number of continuous process conditions, generating new challenges for machine learning models. We focus on solvent selection, a task that is particularly difficult to model theoretically and therefore ripe for machine learning applications. We showcase benchmarking for regression algorithms, transfer-learning approaches, feature engineering, and active learning, with important applications towards solvent replacement and sustainable manufacturing.

Precise recognition, editing, and generation of molecules are essential prerequisites for both chemists and AI systems tackling various chemical tasks. We present MolLangBench, a comprehensive benchmark designed to evaluate fundamental molecule-language interface tasks: language-prompted molecular structure recognition, editing, and generation. To ensure high-quality, unambiguous, and deterministic outputs, we construct the recognition tasks using automated cheminformatics tools, and curate editing and generation tasks through rigorous expert annotation and validation. MolLangBench supports the evaluation of models that interface language with different molecular representations, including linear strings, molecular images, and molecular graphs. Evaluations of state-of-the-art models reveal significant limitations: the strongest model (o3) achieves 79.2% and 78.5% accuracy on recognition and editing tasks, which are intuitively simple for humans, and performs even worse on the generation task, reaching only 29.0% accuracy. These results highlight the shortcomings of current AI systems in handling even preliminary molecular recognition and manipulation tasks. We hope MolLangBench will catalyze further research toward more effective and reliable AI systems for chemical applications.

Existing evaluation benchmarks of language models of code (code LMs) focus almost exclusively on whether the LMs can generate functionally-correct code. In real-world software engineering, developers think beyond functional correctness. They have requirements on "how" a functionality should be implemented to meet overall system design objectives like efficiency, security, and maintainability. They would also trust the code LMs more if the LMs demonstrate robust understanding of requirements and code semantics. We propose a new benchmark NoFunEval to evaluate code LMs on non-functional requirements and simple classification instances for both functional and non-functional requirements. We propose a prompting method, Coding Concepts (CoCo), as a way for a developer to communicate the domain knowledge to the LMs. We conduct an extensive evaluation of twenty-two code LMs. Our finding is that they generally falter when tested on our benchmark, hinting at fundamental blindspots in their training setups. Surprisingly, even the classification accuracy on functional-correctness instances derived from the popular HumanEval benchmark is low, calling in question the depth of their comprehension and the source of their success in generating functionally-correct code in the first place. We will release our benchmark and evaluation scripts publicly at https://aka.ms/NoFunEval.

Equation discovery from data is a core challenge in machine learning for science, requiring the recovery of concise symbolic expressions that govern complex physical and geometric phenomena. Recent approaches with large language models (LLMs) show promise in symbolic regression, but their success often hinges on memorized formulas or overly simplified functional forms. Existing benchmarks exacerbate this limitation: they focus on scalar functions, ignore domain grounding, and rely on brittle string-matching based metrics that fail to capture scientific equivalence. We introduce SurfaceBench, first comprehensive benchmark for symbolic surface discovery. SurfaceBench comprises 183 tasks across 15 categories of symbolic complexity, spanning explicit, implicit, and parametric equation representation forms. Each task includes ground-truth equations, variable semantics, and synthetically sampled three dimensional data. Unlike prior SR datasets, our tasks reflect surface-level structure, resist LLM memorization through novel symbolic compositions, and are grounded in scientific domains such as fluid dynamics, robotics, electromagnetics, and geometry. To evaluate equation discovery quality, we pair symbolic checks with geometry-aware metrics such as Chamfer and Hausdorff distances, capturing both algebraic fidelity and spatial reconstruction accuracy. Our experiments reveal that state-of-the-art frameworks, while occasionally successful on specific families, struggle to generalize across representation types and surface complexities. SurfaceBench thus establishes a challenging and diagnostic testbed that bridges symbolic reasoning with geometric reconstruction, enabling principled benchmarking of progress in compositional generalization, data-driven scientific induction, and geometry-aware reasoning with LLMs. We release the code here: https://github.com/Sanchit-404/surfacebench

We introduce the Formally Verified Automated Programming Progress Standards, or FVAPPS, a benchmark of 4715 samples for writing programs and proving their correctness, the largest formal verification benchmark, including 1083 curated and quality controlled samples. Previously, APPS provided a benchmark and dataset for programming puzzles to be completed in Python and checked against unit tests, of the kind seen in technical assessments in the software engineering industry. Building upon recent approaches for benchmarks in interactive theorem proving, we generalize the unit tests to Lean 4 theorems given without proof (i.e., using Lean's "sorry" keyword). On the 406 theorems of 100 randomly selected samples, Sonnet correctly proves 30% and Gemini correctly proves 18%. We challenge the machine learning and program synthesis communities to solve both each general purpose programming problem and its associated correctness specifications. The benchmark is available at https://huggingface.co/datasets/quinn-dougherty/fvapps.

Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule. Generative models such as OXtal dramatically reduce this cost by sampling stable organic crystal structures directly. However, OXtal forgoes explicit lattice parametrization in favour of modelling large crops of the bulk material with expensive triangle layers, which can incur a computational cost of minutes per molecule. In this paper, we reduce this to seconds with Clari, a large-scale flow matching model that generates redundancy-free unit cells and replaces triangle layers with pure pair-bias attention. Clari requires only atom types and bonds as input and does not need an RDKit-sanitizable input molecule, which expands its applicability to challenging chemistries such as fullerenes, metal complexes, and atom clusters. We further ablate key design choices such as auxiliary losses, timestep distributions, noise priors, and self-conditioning. On OXtal's test sets, we surpass OXtal's solve rate while obtaining a speedup of 15-30times. Because Clari also models explicit hydrogens, it supports inference-time scaling via direct energy ranking, without any decoration or relaxation step. When generating 150 crystals and selecting the top-30 by energy, we further improve solve rate while maintaining a speedup of 5-8times. We also introduce the CSD Teaching Subset as a new test split of diverse and complex molecules for future benchmarking. Our contributions enable CSP within seconds, making large-scale virtual screening of organic solids practical. Code is available at https://github.com/aspuru-guzik-group/clari.

Developing high-performance software is a complex task that requires specialized expertise. We introduce GSO, a benchmark for evaluating language models' capabilities in developing high-performance software. We develop an automated pipeline that generates and executes performance tests to analyze repository commit histories to identify 102 challenging optimization tasks across 10 codebases, spanning diverse domains and programming languages. An agent is provided with a codebase and performance test as a precise specification, and tasked to improve the runtime efficiency, which is measured against the expert developer optimization. Our quantitative evaluation reveals that leading SWE-Agents struggle significantly, achieving less than 5% success rate, with limited improvements even with inference-time scaling. Our qualitative analysis identifies key failure modes, including difficulties with low-level languages, practicing lazy optimization strategies, and challenges in accurately localizing bottlenecks. We release the code and artifacts of our benchmark along with agent trajectories to enable future research.

De novo design seeks to generate molecules with required property profiles by virtual design-make-test cycles. With the emergence of deep learning and neural generative models in many application areas, models for molecular design based on neural networks appeared recently and show promising results. However, the new models have not been profiled on consistent tasks, and comparative studies to well-established algorithms have only seldom been performed. To standardize the assessment of both classical and neural models for de novo molecular design, we propose an evaluation framework, GuacaMol, based on a suite of standardized benchmarks. The benchmark tasks encompass measuring the fidelity of the models to reproduce the property distribution of the training sets, the ability to generate novel molecules, the exploration and exploitation of chemical space, and a variety of single and multi-objective optimization tasks. The benchmarking open-source Python code, and a leaderboard can be found on https://benevolent.ai/guacamol

We introduce GraphNet, a dataset of 2.7K real-world deep learning computational graphs with rich metadata, spanning six major task categories across multiple deep learning frameworks. To evaluate tensor compiler performance on these samples, we propose the benchmark metric Speedup Score S(t), which jointly considers runtime speedup and execution correctness under tunable tolerance levels, offering a reliable measure of general optimization capability. Furthermore, we extend S(t) to the Error-aware Speedup Score ES(t), which incorporates error information and helps compiler developers identify key performance bottlenecks. In this report, we benchmark the default tensor compilers, CINN for PaddlePaddle and TorchInductor for PyTorch, on computer vision (CV) and natural language processing (NLP) samples to demonstrate the practicality of GraphNet. The full construction pipeline with graph extraction and compiler evaluation tools is available at https://github.com/PaddlePaddle/GraphNet .

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

Neurosymbolic approaches leveraging Large Language Models (LLMs) with formal methods have recently achieved strong results on mathematics-oriented theorem-proving benchmarks. However, success on competition-style mathematics does not by itself demonstrate the ability to construct proofs about real-world implementations. We address this gap with a benchmark derived from an industrial cryptographic library whose assembly routines are already verified in HOL Light. s2n-bignum is a library used at AWS for providing fast assembly routines for cryptography, and its correctness is established by formal verification. The task of formally verifying this library has been a significant achievement for the Automated Reasoning Group. It involved two tasks: (1) precisely specifying the correct behavior of a program as a mathematical proposition, and (2) proving that the proposition is correct. In the case of s2n-bignum, both tasks were carried out by human experts. In s2n-bignum-bench, we provide the formal specification and ask the LLM to generate a proof script that is accepted by HOL Light within a fixed proof-check timeout. To our knowledge, s2n-bignum-bench is the first public benchmark focused on machine-checkable proof synthesis for industrial low-level cryptographic assembly routines in HOL Light. This benchmark provides a challenging and practically relevant testbed for evaluating LLM-based theorem proving beyond competition mathematics. The code to set up and use the benchmark is available here: https://github.com/kings-crown/s2n-bignum-bench{s2n-bignum-bench}.

We propose a framework for robust evaluation of reasoning capabilities of language models, using functional variants of benchmarks. Models that solve a reasoning test should exhibit no difference in performance over the static version of a problem compared to a snapshot of the functional variant. We have rewritten the relevant fragment of the MATH benchmark into its functional variant MATH(), with functionalization of other benchmarks to follow. When evaluating current state-of-the-art models over snapshots of MATH(), we find a reasoning gap -- the percentage difference between the static and functional accuracies. We find reasoning gaps from 58.35% to 80.31% among the state-of-the-art closed and open weights models that perform well on static benchmarks, with the caveat that the gaps are likely to be smaller with more sophisticated prompting strategies. Here we show that models which anecdotally have good reasoning performance over real-world tasks, have quantifiable lower gaps, motivating the open problem of building "gap 0" models. Code for evaluation and new evaluation datasets, three MATH() snapshots, are publicly available at https://github.com/consequentai/fneval/.

Despite advancements in evaluating Large Language Models (LLMs) for code synthesis, benchmarks have predominantly focused on functional correctness, overlooking the importance of code efficiency. We present Mercury, the first benchmark designated for assessing the code efficiency of LLM code synthesis tasks. Mercury consists of 1,889 programming tasks covering diverse difficulty levels alongside test case generators generating unlimited cases for comprehensive evaluation. Unlike existing benchmarks, Mercury integrates a novel metric Beyond@K to measure normalized code efficiency based on historical submissions, leading to a new evaluation indicator for code synthesis, which encourages generating functionally correct and computationally efficient code, mirroring the real-world software development standard. Our findings reveal that while LLMs demonstrate the remarkable capability to generate functionally correct code, there still exists a substantial gap in their efficiency output, underscoring a new frontier for LLM research and development.

Organic reaction mechanisms are the stepwise elementary reactions by which reactants form intermediates and products, and are fundamental to understanding chemical reactivity and designing new molecules and reactions. Although large language models (LLMs) have shown promise in understanding chemical tasks such as synthesis design, it is unclear to what extent this reflects genuine chemical reasoning capabilities, i.e., the ability to generate valid intermediates, maintain chemical consistency, and follow logically coherent multi-step pathways. We address this by introducing oMeBench, the first large-scale, expert-curated benchmark for organic mechanism reasoning in organic chemistry. It comprises over 10,000 annotated mechanistic steps with intermediates, type labels, and difficulty ratings. Furthermore, to evaluate LLM capability more precisely and enable fine-grained scoring, we propose oMeS, a dynamic evaluation framework that combines step-level logic and chemical similarity. We analyze the performance of state-of-the-art LLMs, and our results show that although current models display promising chemical intuition, they struggle with correct and consistent multi-step reasoning. Notably, we find that using prompting strategy and fine-tuning a specialist model on our proposed dataset increases performance by 50% over the leading closed-source model. We hope that oMeBench will serve as a rigorous foundation for advancing AI systems toward genuine chemical reasoning.

In this paper, we propose a real-world benchmark for studying robotic learning in the context of functional manipulation: a robot needs to accomplish complex long-horizon behaviors by composing individual manipulation skills in functionally relevant ways. The core design principles of our Functional Manipulation Benchmark (FMB) emphasize a harmonious balance between complexity and accessibility. Tasks are deliberately scoped to be narrow, ensuring that models and datasets of manageable scale can be utilized effectively to track progress. Simultaneously, they are diverse enough to pose a significant generalization challenge. Furthermore, the benchmark is designed to be easily replicable, encompassing all essential hardware and software components. To achieve this goal, FMB consists of a variety of 3D-printed objects designed for easy and accurate replication by other researchers. The objects are procedurally generated, providing a principled framework to study generalization in a controlled fashion. We focus on fundamental manipulation skills, including grasping, repositioning, and a range of assembly behaviors. The FMB can be used to evaluate methods for acquiring individual skills, as well as methods for combining and ordering such skills to solve complex, multi-stage manipulation tasks. We also offer an imitation learning framework that includes a suite of policies trained to solve the proposed tasks. This enables researchers to utilize our tasks as a versatile toolkit for examining various parts of the pipeline. For example, researchers could propose a better design for a grasping controller and evaluate it in combination with our baseline reorientation and assembly policies as part of a pipeline for solving multi-stage tasks. Our dataset, object CAD files, code, and evaluation videos can be found on our project website: https://functional-manipulation-benchmark.github.io

Large Language Models (LLMs) have made notable progress in automated theorem proving, yet existing formal benchmarks remain limited in both mathematical coverage and difficulty. Most are concentrated in areas that are easier to formalize, such as algebra and elementary number theory, and provide limited coverage of subfields that require deeper reasoning, including mathematical analysis. To address this gap, we introduce MA-ProofBench, to the best of our knowledge, the first formal theorem-proving benchmark dedicated to Mathematical Analysis. The benchmark contains 200 formalized theorems covering 6 core topics and 27 subcategories, including measure and integration theory, complex analysis, and functional analysis. The problems are divided into two difficulty levels, an undergraduate level (Level I, 100 problems) and a Ph.D. qualifying level (Level II, 100 problems), to evaluate how well LLMs perform formal reasoning at different mathematical depths. Each problem is constructed through a human-led, LLM-assisted formalization pipeline followed by independent expert review, ensuring that the formal statements remain faithful to the original mathematics. We evaluate a range of recent general-purpose reasoning models and formal theorem provers on MA-ProofBench. However, most models perform poorly: even the best-performing model, GPT-5.5, achieves only 16% Pass@8 on Level I and 5% on Level II, while most models stay close to 0% on Level II. Further analysis identifies Mathlib hallucinations and incomplete proofs as the two dominant failure modes, while an evaluation on the natural-language version of the benchmark exposes a clear gap between informal and formal reasoning. MA-ProofBench is intended to serve as a reliable reference for tracking progress in formal mathematical reasoning in advanced domains.

General-purpose agents such as OpenClaw are increasingly used as autonomous tool users, but their coding ability is difficult to measure under SWE-bench: a generic agent does not by itself satisfy the clean Docker workspace, patch, and prediction contract required for scoring. We introduce Claw-SWE-Bench, a multilingual SWE-bench-style benchmark and adapter protocol that makes heterogeneous agent harnesses, or claws, comparable under fair settings including a fixed prompt, runtime budget, workspace contract, patch extraction procedure, and evaluator. The full benchmark contains 350 GitHub issue-resolution instances across 8 languages and 43 repositories, drawn from SWE-bench-Multilingual and SWE-bench-Verified-Mini after future-commit cleanup. We also release Claw-SWE-Bench Lite for faster validation, which is an 80-instance subset selected by a cost-aware, rank-aware procedure over 17 calibration columns. On the full benchmark, OpenClaw with a minimal direct-diff adapter scores only 19.1% Pass@1, whereas the full adapter reaches 73.4% with the same GLM 5.1 backbone, showing that adapter design is essential for enabling OpenClaw-style harnesses to perform coding tasks effectively. Across an OpenClaw times nine-model sweep and a five-claw times two-model sweep, model choice changes Pass@1 by 29.4 pp and harness choice by 27.4 pp under fixed models; systems with similar accuracy can differ substantially in total API cost. Claw-SWE-Bench therefore treats harness and cost accounting as first-class axes of SWE-style coding-agent evaluation, providing both a full benchmark and a low-cost reference set for reproducible comparison. The data is available at https://github.com/opensquilla/claw-swe-bench and https://huggingface.co/datasets/TokenRhythm/Claw-SWE-Bench.

Large language model (LLM) agents are increasingly deployed to automate productivity tasks (e.g., email, scheduling, document management), but evaluating them on live services is risky due to potentially irreversible changes. Existing benchmarks rely on simplified environments and fail to capture realistic, stateful, multi-service workflows. We introduce ClawsBench, a benchmark for evaluating and improving LLM agents in realistic productivity settings. It includes five high-fidelity mock services (Gmail, Slack, Google Calendar, Google Docs, Google Drive) with full state management and deterministic snapshot/restore, along with 44 structured tasks covering single-service, cross-service, and safety-critical scenarios. We decompose agent scaffolding into two independent levers (domain skills that inject API knowledge via progressive disclosure, and a meta prompt that coordinates behavior across services) and vary both to measure their separate and combined effects. Experiments across 6 models, 4 agent harnesses, and 33 conditions show that with full scaffolding, agents achieve task success rates of 39-64% but exhibit unsafe action rates of 7-33%. On OpenClaw, the top five models fall within a 10 percentage-point band on task success (53-63%), with unsafe action rates from 7% to 23% and no consistent ordering between the two metrics. We identify eight recurring patterns of unsafe behavior, including multi-step sandbox escalation and silent contract modification.

The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is the leading technique for high-throughput elucidation of molecular structures. However, decoding a molecular structure from its mass spectrum is exceptionally challenging, even when performed by human experts. As a result, the vast majority of acquired MS/MS spectra remain uninterpreted, thereby limiting our understanding of the underlying (bio)chemical processes. Despite decades of progress in machine learning applications for predicting molecular structures from MS/MS spectra, the development of new methods is severely hindered by the lack of standard datasets and evaluation protocols. To address this problem, we propose MassSpecGym -- the first comprehensive benchmark for the discovery and identification of molecules from MS/MS data. Our benchmark comprises the largest publicly available collection of high-quality labeled MS/MS spectra and defines three MS/MS annotation challenges: de novo molecular structure generation, molecule retrieval, and spectrum simulation. It includes new evaluation metrics and a generalization-demanding data split, therefore standardizing the MS/MS annotation tasks and rendering the problem accessible to the broad machine learning community. MassSpecGym is publicly available at https://github.com/pluskal-lab/MassSpecGym.

Large language models (LLMs) exhibit advancing capabilities in complex tasks, such as reasoning and graduate-level question answering, yet their resilience against misuse, particularly involving scientifically sophisticated risks, remains underexplored. Existing safety benchmarks typically focus either on instructions requiring minimal knowledge comprehension (e.g., ``tell me how to build a bomb") or utilize prompts that are relatively low-risk (e.g., multiple-choice or classification tasks about hazardous content). Consequently, they fail to adequately assess model safety when handling knowledge-intensive, hazardous scenarios. To address this critical gap, we introduce SOSBench, a regulation-grounded, hazard-focused benchmark encompassing six high-risk scientific domains: chemistry, biology, medicine, pharmacology, physics, and psychology. The benchmark comprises 3,000 prompts derived from real-world regulations and laws, systematically expanded via an LLM-assisted evolutionary pipeline that introduces diverse, realistic misuse scenarios (e.g., detailed explosive synthesis instructions involving advanced chemical formulas). We evaluate frontier models within a unified evaluation framework using our SOSBench. Despite their alignment claims, advanced models consistently disclose policy-violating content across all domains, demonstrating alarmingly high rates of harmful responses (e.g., 79.1% for Deepseek-R1 and 47.3% for GPT-4.1). These results highlight significant safety alignment deficiencies and underscore urgent concerns regarding the responsible deployment of powerful LLMs.

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

Traditional AI methods often rely on task-specific model designs and training, which constrain both the scalability of model size and generalization across different tasks. Here, we introduce ChemFM, a large foundation model specifically developed for chemicals. By conducting a series of scaling experiments, we identify UniChem as the informative molecular database for pre-training the foundation model. ChemFM comprises 3 billion parameters and is pre-trained on 178 million molecules using self-supervised causal language modeling to extract generalizable molecular representations. This model can be adapted to diverse downstream chemical applications using either full-parameter or parameter-efficient fine-tuning methods. ChemFM consistently outperforms state-of-the-art task-specific AI models across all tested tasks. Notably, it achieves up to 67.48% performance improvement across 34 property prediction benchmarks, up to 33.80% reduction in mean average deviation between conditioned and actual properties of generated molecules in conditional molecular generation tasks, and up to 3.7% top-1 accuracy improvement across 4 reaction prediction datasets. Moreover, ChemFM demonstrates its superior performance in predicting antibiotic activity and cytotoxicity, highlighting its potential to advance the discovery of novel antibiotics. Furthermore, we demonstrate that, as a foundation model, ChemFM exhibits strong data efficiency, requiring significantly fewer labeled training samples to achieve state-of-the-art performance. We anticipate that ChemFM will significantly advance chemistry research by providing a foundation model capable of effectively generalizing across a broad range of tasks with minimal additional training.

While large language models (LLMs) have shown considerable promise in code generation, real-world software development demands advanced repository-level reasoning. This includes understanding dependencies, project structures, and managing multi-file changes. However, the ability of LLMs to effectively comprehend and handle complex code repositories has yet to be fully explored. To address challenges, we introduce a hierarchical benchmark designed to evaluate repository dependency understanding (DependEval). Benchmark is based on 15,576 repositories collected from real-world websites. It evaluates models on three core tasks: Dependency Recognition, Repository Construction, and Multi-file Editing, across 8 programming languages from actual code repositories. Our evaluation of over 25 LLMs reveals substantial performance gaps and provides valuable insights into repository-level code understanding.

Existing code generation benchmarks primarily evaluate functional correctness, with limited focus on code efficiency and often restricted to a single language like Python. To address this gap, we introduce EffiBench-X, the first multi-language benchmark designed to measure the efficiency of LLM-generated code. EffiBench-X supports Python, C++, Java, JavaScript, Ruby, and Golang. It comprises competitive programming tasks with human-expert solutions as efficiency baselines. Evaluating state-of-the-art LLMs on EffiBench-X reveals that while models generate functionally correct code, they consistently underperform human experts in efficiency. Even the most efficient LLM-generated solutions (Qwen3-32B) achieve only around 62\% of human efficiency on average, with significant language-specific variations. LLMs show better efficiency in Python, Ruby, and JavaScript than in Java, C++, and Golang. For instance, DeepSeek-R1's Python code is significantly more efficient than its Java code. These results highlight the critical need for research into LLM optimization techniques to improve code efficiency across diverse languages. The dataset and evaluation infrastructure are submitted and available at https://github.com/EffiBench/EffiBench-X.git and https://huggingface.co/datasets/EffiBench/effibench-x.

Recent advances in large language models (LLMs) have led to models that tackle diverse molecular tasks, such as chemical reaction prediction and molecular property prediction. Large-scale molecular instruction-tuning datasets have enabled sequence-only (e.g., SMILES or SELFIES) generalist molecular LLMs, and researchers are now exploring multimodal approaches that incorporate molecular structural information for further gains. However, a genuinely multimodal, generalist LLM that covers a broad spectrum of molecular tasks has yet to be fully investigated. We observe that naive next token prediction training ignores graph-structural information, limiting an LLM's ability to exploit molecular graphs. To address this, we propose (i) Molecular structure Preference Optimization (MolPO), which facilitates graph usage by optimizing preferences between pairs of correct and perturbed molecular structures, and (ii) an advanced graph encoder with a tailored pre-training strategy to improve the effect of graph utilization by MolPO. Building on these contributions, we introduce Mol-LLM, the first multimodal generalist model that (a) handles a broad spectrum of molecular tasks among molecular LLMs, (b) explicitly leverages molecular-structure information, and (c) takes advantage of extensive instruction tuning. Mol-LLM attains state-of-the-art or comparable results across the most comprehensive molecular-LLM benchmark-even on out-of-distribution datasets for reaction and property prediction, where it surpasses prior generalist molecular LLMs by a large margin.

Chemical reasoning inherently integrates visual, textual, and symbolic modalities, yet existing benchmarks rarely capture this complexity, often relying on simple image-text pairs with limited chemical semantics. As a result, the actual ability of Multimodal Large Language Models (MLLMs) to process and integrate chemically meaningful information across modalities remains unclear. We introduce ChemVTS-Bench, a domain-authentic benchmark designed to systematically evaluate the Visual-Textual-Symbolic (VTS) reasoning abilities of MLLMs. ChemVTS-Bench contains diverse and challenging chemical problems spanning organic molecules, inorganic materials, and 3D crystal structures, with each task presented in three complementary input modes: (1) visual-only, (2) visual-text hybrid, and (3) SMILES-based symbolic input. This design enables fine-grained analysis of modality-dependent reasoning behaviors and cross-modal integration. To ensure rigorous and reproducible evaluation, we further develop an automated agent-based workflow that standardizes inference, verifies answers, and diagnoses failure modes. Extensive experiments on state-of-the-art MLLMs reveal that visual-only inputs remain challenging, structural chemistry is the hardest domain, and multimodal fusion mitigates but does not eliminate visual, knowledge-based, or logical errors, highlighting ChemVTS-Bench as a rigorous, domain-faithful testbed for advancing multimodal chemical reasoning. All data and code will be released to support future research.

In recent years, pretraining models have made significant advancements in the fields of natural language processing (NLP), computer vision (CV), and life sciences. The significant advancements in NLP and CV are predominantly driven by the expansion of model parameters and data size, a phenomenon now recognized as the scaling laws. However, research exploring scaling law in molecular pretraining models remains unexplored. In this work, we present Uni-Mol2 , an innovative molecular pretraining model that leverages a two-track transformer to effectively integrate features at the atomic level, graph level, and geometry structure level. Along with this, we systematically investigate the scaling law within molecular pretraining models, characterizing the power-law correlations between validation loss and model size, dataset size, and computational resources. Consequently, we successfully scale Uni-Mol2 to 1.1 billion parameters through pretraining on 800 million conformations, making it the largest molecular pretraining model to date. Extensive experiments show consistent improvement in the downstream tasks as the model size grows. The Uni-Mol2 with 1.1B parameters also outperforms existing methods, achieving an average 27% improvement on the QM9 and 14% on COMPAS-1D dataset.

Accurate determination of transition states is central to an understanding of reaction kinetics. Double-endpoint methods where both initial and final states are specified, such as the climbing image nudged elastic band (CI-NEB), identify the minimum energy path between the two and thereby the saddle point on the energy surface that is relevant for the given transition, thus providing an estimate of the transition state within the harmonic approximation of transition state theory. Such calculations can, however, incur high computational costs and may suffer stagnation on exceptionally flat or rough energy surfaces. Conversely, methods that only require specification of an initial set of atomic coordinates, such as the minimum mode following (MMF) method, offer efficiency but can converge on saddle points that are not relevant for transition of interest. Here, we present an adaptive hybrid algorithm that integrates the CI-NEB with the MMF method so as to get faster convergence to the relevant saddle point. The method is benchmarked for the Baker-Chan (BC) saddle point test set using the PET-MAD machine-learned potential as well as 59 transitions of a heptamer island on Pt(111) from the OptBench benchmark set. A Bayesian analysis of the performance shows a reduction in energy and force calculations of 57% [95% CrI: -64%, -50%] relative to CI-NEB for the BC set, while a 31% mean reduction is found for the transitions of the heptamer island. These results establish this hybrid method as a highly effective tool for high-throughput automated chemical discovery of atomic rearrangements.

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.

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}

Finding new drugs is getting harder and harder. One of the hopes of drug discovery is to use machine learning models to predict molecular properties. That is why models for molecular property prediction are being developed and tested on benchmarks such as MoleculeNet. However, existing benchmarks are unrealistic and are too different from applying the models in practice. We have created a new practical Lo-Hi benchmark consisting of two tasks: Lead Optimization (Lo) and Hit Identification (Hi), corresponding to the real drug discovery process. For the Hi task, we designed a novel molecular splitting algorithm that solves the Balanced Vertex Minimum k-Cut problem. We tested state-of-the-art and classic ML models, revealing which works better under practical settings. We analyzed modern benchmarks and showed that they are unrealistic and overoptimistic. Review: https://openreview.net/forum?id=H2Yb28qGLV Lo-Hi benchmark: https://github.com/SteshinSS/lohi_neurips2023 Lo-Hi splitter library: https://github.com/SteshinSS/lohi_splitter

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 17 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.

The release of ChatGPT in November 2022 sparked an explosion of interest in post-training and an avalanche of new preference optimization (PO) methods. These methods claim superior alignment by virtue of better correspondence with human pairwise preferences, often measured by LLM judges. In this work, we attempt to answer the following question -- do LLM-judge preferences translate to progress on other, more concrete metrics for alignment, and if not, why not? We define a concrete metric for alignment, and introduce SOS-Bench, the largest standardized, reproducible LLM meta-benchmark to date. We find that (1) LLM-judgments do not correlate with concrete measures of safety, world knowledge, and instruction following; (2) LLM judges have powerful implicit biases, prioritizing style over factuality and safety; and (3) the supervised fine-tuning (SFT) stage of post-training, and not the PO stage, has the greatest impact on alignment, with data scaling and prompt diversity as the driving factors. Our codebase and complete results can be found at https://github.com/penfever/sos-bench.

Scientific equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorized forms, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy. These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.

Computational high-throughput virtual screening is essential for identifying redox-active molecules for sustainable applications such as electrochemical carbon capture. A primary challenge in this approach is the high computational cost associated with accurate quantum chemistry calculations. Machine learning foundation potentials (FPs) trained on extensive density functional theory (DFT) calculations offer a computationally efficient alternative. Here, we benchmark the MACE-OMol-0 and UMA FPs against a hierarchy of DFT functionals for predicting experimental molecular redox potentials for both electron transfer (ET) and proton-coupled electron transfer (PCET) reactions. We find that these FPs achieve exceptional accuracy for PCET processes, rivaling their target DFT method. However, the performance is diminished for ET reactions, particularly for multi-electron transfers involving reactive ions that are underrepresented in the OMol25 training data, revealing a key out-of-distribution limitation. To overcome this, we propose an optimal hybrid workflow that uses the FPs for efficient geometry optimization and thermochemical analysis, followed by a crucial single-point DFT energy refinement and an implicit solvation correction. This pragmatic approach provides a robust and scalable strategy for accelerating high-throughput virtual screening in sustainable chemistry.

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

We present CRUXEval (Code Reasoning, Understanding, and eXecution Evaluation), a benchmark consisting of 800 Python functions (3-13 lines). Each function comes with an input-output pair, leading to two natural tasks: input prediction and output prediction. First, we propose a generic recipe for generating our execution benchmark which can be used to create future variation of the benchmark. Second, we evaluate twenty code models on our benchmark and discover that many recent high-scoring models on HumanEval do not show the same improvements on our benchmark. Third, we show that simple CoT and fine-tuning schemes can improve performance on our benchmark but remain far from solving it. The best setup, GPT-4 with chain of thought (CoT), achieves a pass@1 of 75% and 81% on input and output prediction, respectively. In contrast, Code Llama 34B achieves a pass@1 of 50% and 46% on input and output prediction, highlighting the gap between open and closed source models. As no model is close to acing CRUXEval, we provide examples of consistent GPT-4 failures on simple programs as a lens into its code reasoning capabilities and areas for improvement.

With the growing reliance on automated code completion tools in software development, the need for robust evaluation benchmarks has become critical. However, existing benchmarks focus more on code generation tasks in function and class level and provide rich text description to prompt the model. By contrast, such descriptive prompt is commonly unavailable in real development and code completion can occur in wider range of situations such as in the middle of a function or a code block. These limitations makes the evaluation poorly align with the practical scenarios of code completion tools. In this paper, we propose RepoMasterEval, a novel benchmark for evaluating code completion models constructed from real-world Python and TypeScript repositories. Each benchmark datum is generated by masking a code snippet (ground truth) from one source code file with existing test suites. To improve test accuracy of model generated code, we employ mutation testing to measure the effectiveness of the test cases and we manually crafted new test cases for those test suites with low mutation score. Our empirical evaluation on 6 state-of-the-art models shows that test argumentation is critical in improving the accuracy of the benchmark and RepoMasterEval is able to report difference in model performance in real-world scenarios. The deployment of RepoMasterEval in a collaborated company for one month also revealed that the benchmark is useful to give accurate feedback during model training and the score is in high correlation with the model's performance in practice. Based on our findings, we call for the software engineering community to build more LLM benchmarks tailored for code generation tools taking the practical and complex development environment into consideration.

The emergence of large language models (LLMs) has significantly pushed the frontiers of program synthesis. Advancement of LLM-based program synthesis calls for a thorough evaluation of LLM-generated code. Most evaluation frameworks focus on the (functional) correctness of generated code; efficiency, as an important measure of code quality, has been overlooked in existing evaluations. In this work, we develop ENAMEL (EfficeNcy AutoMatic EvaLuator), a rigorous and high-standard benchmark for evaluating the capability of LLMs in generating efficient code. Firstly, we propose a new efficiency metric called eff@k, which generalizes the pass@k metric from correctness to efficiency and appropriately handles right-censored execution time. Furthermore, we derive an unbiased and variance-reduced estimator of eff@k via Rao--Blackwellization; we also provide a numerically stable implementation for the new estimator. Secondly, to set a high-standard for efficiency evaluation, we employ a human expert to design best algorithms and implementations as our reference solutions of efficiency, many of which are much more efficient than existing canonical solutions in HumanEval and HumanEval+. Moreover, to ensure a rigorous evaluation, we employ a human expert to curate strong test case generators to filter out wrong code and differentiate suboptimal algorithms. An extensive study across 30 popular LLMs using our benchmark ENAMEL shows that LLMs still fall short of generating expert-level efficient code. Using two subsets of our problem set, we demonstrate that such deficiency is because current LLMs struggle in designing advanced algorithms and are barely aware of implementation optimization. Our benchmark is publicly available at https://github.com/q-rz/enamel .

We introduce featom, an open source code that implements a high-order finite element solver for the radial Schr\"odinger, Dirac, and Kohn-Sham equations. The formulation accommodates various mesh types, such as uniform or exponential, and the convergence can be systematically controlled by increasing the number and/or polynomial order of the finite element basis functions. The Dirac equation is solved using a squared Hamiltonian approach to eliminate spurious states. To address the slow convergence of the kappa=pm1 states due to divergent derivatives at the origin, we incorporate known asymptotic forms into the solutions. We achieve a high level of accuracy (10^{-8} Hartree) for total energies and eigenvalues of heavy atoms such as uranium in both Schr\"odinger and Dirac Kohn-Sham solutions. We provide detailed convergence studies and computational parameters required to attain commonly required accuracies. Finally, we compare our results with known analytic results as well as the results of other methods. In particular, we calculate benchmark results for atomic numbers (Z) from 1 to 92, verifying current benchmarks. We demonstrate significant speedup compared to the state-of-the-art shooting solver dftatom. An efficient, modular Fortran 2008 implementation, is provided under an open source, permissive license, including examples and tests, wherein particular emphasis is placed on the independence (no global variables), reusability, and generality of the individual routines.

The issue-resolving task, where a model generates patches to fix real-world bugs, has emerged as a critical benchmark for evaluating the capabilities of large language models (LLMs). While SWE-bench and its variants have become standard in this domain, they suffer from key limitations: they have not been updated since their initial releases, cover a narrow set of repositories, and depend heavily on manual effort for instance construction and environment setup. These factors hinder scalability and introduce risks of overfitting and data contamination. In this work, we present SWE-bench-Live, a live-updatable benchmark designed to overcome these challenges. Our initial release consists of 1,319 tasks derived from real GitHub issues created since 2024, spanning 93 repositories. Each task is accompanied by a dedicated Docker image to ensure reproducible execution. Central to our benchmark is \method, an automated curation pipeline that streamlines the entire process from instance creation to environment setup, removing manual bottlenecks and enabling scalability and continuous updates. We evaluate a range of state-of-the-art agent frameworks and LLMs on SWE-bench-Live, revealing a substantial performance gap compared to static benchmarks like SWE-bench, even under controlled evaluation conditions. To better understand this discrepancy, we perform detailed analyses across repository origin, issue recency, and task difficulty. By providing a fresh, diverse, and executable benchmark grounded in live repository activity, SWE-bench-Live facilitates rigorous, contamination-resistant evaluation of LLMs and agents in dynamic, real-world software development settings.

Modern Lean theorem provers achieve strong performance only with substantial training and inference compute, driven in part by scarce verified proof data and the long reasoning traces of formal proof search, making both supervised fine-tuning (SFT) and sampling expensive. We introduce Pythagoras-Prover, a compute-efficient open-source family of Lean theorem provers built for practical compute budgets. The family spans two generation paradigms: autoregressive models at 4B and 32B parameters, and a first proof-of-concept diffusion-based prover (4B) that iteratively refines Lean proofs at inference time. For training efficiency, we build a Lean-verified corpus stratified into easy, medium, and hard problems for curriculum SFT, so models acquire proof skills progressively from shorter, simpler proofs to longer, harder ones. During SFT, a dynamic proof-reasoning filtering scheme preserves informative proof traces while keeping each instance within an 8k-token context budget. We also introduce Augmented Lean Formalisation (ALF), which expands scarce verified corpora into variants of formal statements, populated via self-distillation for extra training signal without formally verifying every mutated instance. By perturbing known problems while preserving their formal character, ALF reduces reliance on any statement's surface form. Empirically, Pythagoras-Prover-4B surpasses DeepSeek-Prover-V2-671B at pass@32 on MiniF2F-Test (86.1% vs 82.4%) with ~167x fewer parameters, while Pythagoras-Prover-32B sets the open-source state of the art at 93.0% on MiniF2F-Test and solves 93 of 672 PutnamBench problems. We release MiniF2F-ALF, an ALF-mutated contamination-sensitive benchmark on which every evaluated model loses accuracy; here our 32B remains strongest and our 4B matches the prior state of the art, Goedel-Prover-V2-32B.

Large language models (LLMs) are powerful tools capable of handling diverse tasks. Comparing and selecting appropriate LLMs for specific tasks requires systematic evaluation methods, as models exhibit varying capabilities across different domains. However, finding suitable benchmarks is difficult given the many available options. This complexity not only increases the risk of benchmark misuse and misinterpretation but also demands substantial effort from LLM users, seeking the most suitable benchmarks for their specific needs. To address these issues, we introduce BenchmarkCards, an intuitive and validated documentation framework that standardizes critical benchmark attributes such as objectives, methodologies, data sources, and limitations. Through user studies involving benchmark creators and users, we show that BenchmarkCards can simplify benchmark selection and enhance transparency, facilitating informed decision-making in evaluating LLMs. Data & Code: https://github.com/SokolAnn/BenchmarkCards

Deep research is emerging as a representative long-horizon task for large language model (LLM) agents. However, long trajectories in deep research often exceed model context limits, compressing token budgets for both evidence collection and report writing, and preventing effective test-time scaling. We introduce FS-Researcher, a file-system-based, dual-agent framework that scales deep research beyond the context window via a persistent workspace. Specifically, a Context Builder agent acts as a librarian which browses the internet, writes structured notes, and archives raw sources into a hierarchical knowledge base that can grow far beyond context length. A Report Writer agent then composes the final report section by section, treating the knowledge base as the source of facts. In this framework, the file system serves as a durable external memory and a shared coordination medium across agents and sessions, enabling iterative refinement beyond the context window. Experiments on two open-ended benchmarks (DeepResearch Bench and DeepConsult) show that FS-Researcher achieves state-of-the-art report quality across different backbone models. Further analyses demonstrate a positive correlation between final report quality and the computation allocated to the Context Builder, validating effective test-time scaling under the file-system paradigm. The code and data are anonymously open-sourced at https://github.com/Ignoramus0817/FS-Researcher.

Foundation models have shown remarkable success across scientific domains, yet their impact in chemistry remains limited due to the absence of diverse, large-scale, high-quality datasets that reflect the field's multifaceted nature. We present the ChemPile, an open dataset containing over 75 billion tokens of curated chemical data, specifically built for training and evaluating general-purpose models in the chemical sciences. The dataset mirrors the human learning journey through chemistry -- from educational foundations to specialized expertise -- spanning multiple modalities and content types including structured data in diverse chemical representations (SMILES, SELFIES, IUPAC names, InChI, molecular renderings), scientific and educational text, executable code, and chemical images. ChemPile integrates foundational knowledge (textbooks, lecture notes), specialized expertise (scientific articles and language-interfaced data), visual understanding (molecular structures, diagrams), and advanced reasoning (problem-solving traces and code) -- mirroring how human chemists develop expertise through diverse learning materials and experiences. Constructed through hundreds of hours of expert curation, the ChemPile captures both foundational concepts and domain-specific complexity. We provide standardized training, validation, and test splits, enabling robust benchmarking. ChemPile is openly released via HuggingFace with a consistent API, permissive license, and detailed documentation. We hope the ChemPile will serve as a catalyst for chemical AI, enabling the development of the next generation of chemical foundation models.

Large language model (LLM)-powered agents have demonstrated strong capabilities in automating software engineering tasks such as static bug fixing, as evidenced by benchmarks like SWE-bench. However, in the real world, the development of mature software is typically predicated on complex requirement changes and long-term feature iterations -- a process that static, one-shot repair paradigms fail to capture. To bridge this gap, we propose SWE-CI, the first repository-level benchmark built upon the Continuous Integration loop, aiming to shift the evaluation paradigm for code generation from static, short-term functional correctness toward dynamic, long-term maintainability. The benchmark comprises 100 tasks, each corresponding on average to an evolution history spanning 233 days and 71 consecutive commits in a real-world code repository. SWE-CI requires agents to systematically resolve these tasks through dozens of rounds of analysis and coding iterations. SWE-CI provides valuable insights into how well agents can sustain code quality throughout long-term evolution.

The development of machine learning models for electrocatalysts requires a broad set of training data to enable their use across a wide variety of materials. One class of materials that currently lacks sufficient training data is oxides, which are critical for the development of OER catalysts. To address this, we developed the OC22 dataset, consisting of 62,331 DFT relaxations (~9,854,504 single point calculations) across a range of oxide materials, coverages, and adsorbates. We define generalized total energy tasks that enable property prediction beyond adsorption energies; we test baseline performance of several graph neural networks; and we provide pre-defined dataset splits to establish clear benchmarks for future efforts. In the most general task, GemNet-OC sees a ~36% improvement in energy predictions when combining the chemically dissimilar OC20 and OC22 datasets via fine-tuning. Similarly, we achieved a ~19% improvement in total energy predictions on OC20 and a ~9% improvement in force predictions in OC22 when using joint training. We demonstrate the practical utility of a top performing model by capturing literature adsorption energies and important OER scaling relationships. We expect OC22 to provide an important benchmark for models seeking to incorporate intricate long-range electrostatic and magnetic interactions in oxide surfaces. Dataset and baseline models are open sourced, and a public leaderboard is available to encourage continued community developments on the total energy tasks and data.

The discovery of next-generation photoinitiators for two-photon polymerization (TPP) is hindered by the absence of large, open datasets containing the quantum-chemical and photophysical properties required to model photodissociation and excited-state behavior. Existing molecular datasets typically provide only basic physicochemical descriptors and therefore cannot support data-driven screening or AI-assisted design of photoinitiators. To address this gap, we introduce QuantumChem-200K, a large-scale dataset of over 200,000 organic molecules annotated with eleven quantum-chemical properties, including two-photon absorption (TPA) cross sections, TPA spectral ranges, singlet-triplet intersystem crossing (ISC) energies, toxicity and synthetic accessibility scores, hydrophilicity, solubility, boiling point, molecular weight, and aromaticity. These values are computed using a hybrid workflow that integrates density function theory (DFT), semi-empirical excited-state methods, atomistic quantum solvers, and neural-network predictors. Using QuantumChem-200K, we fine tune the open-source Qwen2.5-32B large language model to create a chemistry AI assistant capable of forward property prediction from SMILES. Benchmarking on 3000 unseen molecules from VQM24 and ZINC20 demonstrates that domain-specific fine-tuning significantly improves accuracy over GPT-4o, Llama-3.1-70B, and the base Qwen2.5-32B model, particularly for TPA and ISC predictions central to photoinitiator design. QuantumChem-200K and the corresponding AI assistant together provide the first scalable platform for high-throughput, LLM-driven photoinitiator screening and accelerated discovery of photosensitive materials.

Recent advancements in artificial intelligence have sparked interest in scientific assistants that could support researchers across the full spectrum of scientific workflows, from literature review to experimental design and data analysis. A key capability for such systems is the ability to process and reason about scientific information in both visual and textual forms - from interpreting spectroscopic data to understanding laboratory setups. Here, we introduce MaCBench, a comprehensive benchmark for evaluating how vision-language models handle real-world chemistry and materials science tasks across three core aspects: data extraction, experimental understanding, and results interpretation. Through a systematic evaluation of leading models, we find that while these systems show promising capabilities in basic perception tasks - achieving near-perfect performance in equipment identification and standardized data extraction - they exhibit fundamental limitations in spatial reasoning, cross-modal information synthesis, and multi-step logical inference. Our insights have important implications beyond chemistry and materials science, suggesting that developing reliable multimodal AI scientific assistants may require advances in curating suitable training data and approaches to training those models.

On-board processing of hyperspectral data with machine learning models would enable unprecedented amount of autonomy for a wide range of tasks, for example methane detection or mineral identification. This can enable early warning system and could allow new capabilities such as automated scheduling across constellations of satellites. Classical methods suffer from high false positive rates and previous deep learning models exhibit prohibitive computational requirements. We propose fast and accurate machine learning architectures which support end-to-end training with data of high spectral dimension without relying on hand-crafted products or spectral band compression preprocessing. We evaluate our models on two tasks related to hyperspectral data processing. With our proposed general architectures, we improve the F1 score of the previous methane detection state-of-the-art models by 27% on a newly created synthetic dataset and by 13% on the previously released large benchmark dataset. We also demonstrate that training models on the synthetic dataset improves performance of models finetuned on the dataset of real events by 6.9% in F1 score in contrast with training from scratch. On a newly created dataset for mineral identification, our models provide 3.5% improvement in the F1 score in contrast to the default versions of the models. With our proposed models we improve the inference speed by 85% in contrast to previous classical and deep learning approaches by removing the dependency on classically computed features. With our architecture, one capture from the EMIT sensor can be processed within 30 seconds on realistic proxy of the ION-SCV 004 satellite.

Training algorithms, broadly construed, are an essential part of every deep learning pipeline. Training algorithm improvements that speed up training across a wide variety of workloads (e.g., better update rules, tuning protocols, learning rate schedules, or data selection schemes) could save time, save computational resources, and lead to better, more accurate, models. Unfortunately, as a community, we are currently unable to reliably identify training algorithm improvements, or even determine the state-of-the-art training algorithm. In this work, using concrete experiments, we argue that real progress in speeding up training requires new benchmarks that resolve three basic challenges faced by empirical comparisons of training algorithms: (1) how to decide when training is complete and precisely measure training time, (2) how to handle the sensitivity of measurements to exact workload details, and (3) how to fairly compare algorithms that require hyperparameter tuning. In order to address these challenges, we introduce a new, competitive, time-to-result benchmark using multiple workloads running on fixed hardware, the AlgoPerf: Training Algorithms benchmark. Our benchmark includes a set of workload variants that make it possible to detect benchmark submissions that are more robust to workload changes than current widely-used methods. Finally, we evaluate baseline submissions constructed using various optimizers that represent current practice, as well as other optimizers that have recently received attention in the literature. These baseline results collectively demonstrate the feasibility of our benchmark, show that non-trivial gaps between methods exist, and set a provisional state-of-the-art for future benchmark submissions to try and surpass.

Building generalist models has recently demonstrated remarkable capabilities in diverse scientific domains. Within the realm of molecular learning, several studies have explored unifying diverse tasks across diverse domains. However, negative conflicts and interference between molecules and knowledge from different domain may have a worse impact in threefold. First, conflicting molecular representations can lead to optimization difficulties for the models. Second, mixing and scaling up training data across diverse tasks is inherently challenging. Third, the computational cost of refined pretraining is prohibitively high. To address these limitations, this paper presents Omni-Mol, a scalable and unified LLM-based framework for direct instruction tuning. Omni-Mol builds on three key components to tackles conflicts: (1) a unified encoding mechanism for any task input; (2) an active-learning-driven data selection strategy that significantly reduces dataset size; (3) a novel design of the adaptive gradient stabilization module and anchor-and-reconcile MoE framework that ensures stable convergence. Experimentally, Omni-Mol achieves state-of-the-art performance across 15 molecular tasks, demonstrates the presence of scaling laws in the molecular domain, and is supported by extensive ablation studies and analyses validating the effectiveness of its design. The code and weights of the powerful AI-driven chemistry generalist are open-sourced at: https://anonymous.4open.science/r/Omni-Mol-8EDB.