Daily Papers

Mechanistic interpretability is often motivated for alignment auditing, where a model's verbal explanations can be absent, incomplete, or misleading. Yet many evaluations do not control whether black-box prompting alone can recover the target behavior, so apparent gains from white-box tools may reflect elicitation rather than internal signal; we call this the elicitation confounder. We introduce Pando, a model-organism benchmark that breaks this confound via an explanation axis: models are trained to produce either faithful explanations of the true rule, no explanation, or confident but unfaithful explanations of a disjoint distractor rule. Across 720 finetuned models implementing hidden decision-tree rules, agents predict held-out model decisions from 10 labeled query-response pairs, optionally augmented with one interpretability tool output. When explanations are faithful, black-box elicitation matches or exceeds all white-box methods; when explanations are absent or misleading, gradient-based attribution improves accuracy by 3-5 percentage points, and relevance patching, RelP, gives the largest gains, while logit lens, sparse autoencoders, and circuit tracing provide no reliable benefit. Variance decomposition suggests gradients track decision computation, which fields causally drive the output, whereas other readouts are dominated by task representation, biases toward field identity and value. We release all models, code, and evaluation infrastructure.

Many methods have been proposed for removing batch effects and aligning single-cell RNA (scRNA) datasets. However, performance is typically evaluated based on multiple parameters and few datasets, creating challenges in assessing which method is best for aligning data at scale. Here, we introduce the K-Neighbors Intersection (KNI) score, a single score that both penalizes batch effects and measures accuracy at cross-dataset cell-type label prediction alongside carefully curated small (scMARK) and large (scREF) benchmarks comprising 11 and 46 human scRNA studies respectively, where we have standardized author labels. Using the KNI score, we evaluate and optimize approaches for cross-dataset single-cell RNA integration. We introduce Batch Adversarial single-cell Variational Inference (BA-scVI), as a new variant of scVI that uses adversarial training to penalize batch-effects in the encoder and decoder, and show this approach outperforms other methods. In the resulting aligned space, we find that the granularity of cell-type groupings is conserved, supporting the notion that whole-organism cell-type maps can be created by a single model without loss of information.

The application of deep learning methods, particularly foundation models, in biological research has surged in recent years. These models can be text-based or trained on underlying biological data, especially omics data of various types. However, comparing the performance of these models consistently has proven to be a challenge due to differences in training data and downstream tasks. To tackle this problem, we developed an architecture-agnostic benchmarking approach that, instead of evaluating the models directly, leverages entity representation vectors from each model and trains simple predictive models for each benchmarking task. This ensures that all types of models are evaluated using the same input and output types. Here we focus on gene properties collected from professionally curated bioinformatics databases. These gene properties are categorized into five major groups: genomic properties, regulatory functions, localization, biological processes, and protein properties. Overall, we define hundreds of tasks based on these databases, which include binary, multi-label, and multi-class classification tasks. We apply these benchmark tasks to evaluate expression-based models, large language models, protein language models, DNA-based models, and traditional baselines. Our findings suggest that text-based models and protein language models generally outperform expression-based models in genomic properties and regulatory functions tasks, whereas expression-based models demonstrate superior performance in localization tasks. These results should aid in the development of more informed artificial intelligence strategies for biological understanding and therapeutic discovery. To ensure the reproducibility and transparency of our findings, we have made the source code and benchmark data publicly accessible for further investigation and expansion at github.com/BiomedSciAI/gene-benchmark.

The rapid evolution of large language models (LLMs) has expanded their capabilities from basic dialogue to advanced scientific reasoning. However, existing benchmarks in biology often fail to assess a critical skill required of researchers: the ability to integrate experimental results with contextual knowledge to derive meaningful conclusions. To address this gap, we introduce BABE(Biology Arena BEnchmark), a comprehensive benchmark designed to evaluate the experimental reasoning capabilities of biological AI systems. BABE is uniquely constructed from peer-reviewed research papers and real-world biological studies, ensuring that tasks reflect the complexity and interdisciplinary nature of actual scientific inquiry. BABE challenges models to perform causal reasoning and cross-scale inference. Our benchmark provides a robust framework for assessing how well AI systems can reason like practicing scientists, offering a more authentic measure of their potential to contribute to biological research.

Benchmarks shape scientific conclusions about model capabilities and steer model development. This creates a feedback loop: stronger benchmarks drive better models, and better models demand more discriminative benchmarks. Ensuring benchmark reliability is therefore essential for trustworthy evaluation and meaningful progress. In this work, we study benchmark reliability from a distributional perspective and introduce benchmark harmony, which measures how uniformly a model's performance is distributed across the subdomains of a benchmark. We posit that high harmony is a desirable benchmark property, indicating that the aggregate metric reflects uniform competence across subdomains. Across 19 multiple-choice benchmarks and five model families, we map each benchmark onto a mean-variance plane of harmony computed across models, where high mean and low variance signal more reliable evaluation. Our analysis shows that less harmonious benchmarks can give misleading results, since overall accuracy may be disproportionately influenced by specific subdomains. For instance, ARC-Easy is overwhelmed by questions on Biological Concepts, overshadowing other critical subdomains such as Geography, Physics, Chemistry, and Environmental Science. By recommending that harmony should be reported alongside accuracy, we reframe evaluation from simple performance averages to a more robust, distributionally reliable measurement of performance.

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

This paper introduces BioAgent Bench, a benchmark dataset and an evaluation suite designed for measuring the performance and robustness of AI agents in common bioinformatics tasks. The benchmark contains curated end-to-end tasks (e.g., RNA-seq, variant calling, metagenomics) with prompts that specify concrete output artifacts to support automated assessment, including stress testing under controlled perturbations. We evaluate frontier closed-source and open-weight models across multiple agent harnesses, and use an LLM-based grader to score pipeline progress and outcome validity. We find that frontier agents can complete multi-step bioinformatics pipelines without elaborate custom scaffolding, often producing the requested final artifacts reliably. However, robustness tests reveal failure modes under controlled perturbations (corrupted inputs, decoy files, and prompt bloat), indicating that correct high-level pipeline construction does not guarantee reliable step-level reasoning. Finally, because bioinformatics workflows may involve sensitive patient data, proprietary references, or unpublished IP, closed-source models can be unsuitable under strict privacy constraints; in such settings, open-weight models may be preferable despite lower completion rates. We release the dataset and evaluation suite publicly.

Large Language Models (LLMs) and LLM-based agents show great promise in accelerating scientific research. Existing benchmarks for measuring this potential and guiding future development continue to evolve from pure recall and rote knowledge tasks, towards more practical work such as literature review and experimental planning. Bioinformatics is a domain where fully autonomous AI-driven discovery may be near, but no extensive benchmarks for measuring progress have been introduced to date. We therefore present the Bioinformatics Benchmark (BixBench), a dataset comprising over 50 real-world scenarios of practical biological data analysis with nearly 300 associated open-answer questions designed to measure the ability of LLM-based agents to explore biological datasets, perform long, multi-step analytical trajectories, and interpret the nuanced results of those analyses. We evaluate the performance of two frontier LLMs (GPT-4o and Claude 3.5 Sonnet) using a custom agent framework we open source. We find that even the latest frontier models only achieve 17% accuracy in the open-answer regime, and no better than random in a multiple-choice setting. By exposing the current limitations of frontier models, we hope BixBench can spur the development of agents capable of conducting rigorous bioinformatic analysis and accelerate scientific discovery.

Biological protocols are fundamental to reproducible and safe life science research. While LLMs excel on general tasks, their systematic evaluation on these highly specialized, accuracy-critical, and inherently procedural texts remains limited. In this work, we present BioProBench, the first large-scale, integrated multi-task benchmark for biological protocol understanding and reasoning. While limited benchmarks have touched upon specific aspects like protocol QA, BioProBench provides a comprehensive suite of five core tasks: Protocol Question Answering, Step Ordering, Error Correction, Protocol Generation, and Protocol Reasoning, enabling a holistic evaluation of LLMs on procedural biological texts. Built upon 27K original protocols, it yields nearly 556K high-quality structured instances. We evaluate 12 mainstream open/closed-source LLMs on BioProBench. Experimental results reveal that while top models preform well on surface understanding tasks, struggle significantly with deep reasoning and structured generation tasks like ordering and generation. Furthermore, model comparisons reveal diverse performance: certain open-source models approach closed-source levels on some tasks, yet bio-specific small models lag behind general LLMs, indicating limitations on complex procedural content. Overall, our findings underscore that procedural reasoning within biological protocols represents a significant challenge for current LLMs. BioProBench serves as a standardized framework to diagnose these specific limitations and guide the development of AI systems better equipped for safely automating complex scientific procedures. The code and data are available at: https://github.com/YuyangSunshine/bioprotocolbench and https://huggingface.co/datasets/GreatCaptainNemo/BioProBench.

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench

ImageNet-1K linear-probe transfer accuracy remains the default proxy for visual representation quality, yet it no longer predicts performance on scientific imagery. Across 46 modern vision model checkpoints, ImageNet top-1 accuracy explains only 34% of variance on ecology tasks and mis-ranks 30% of models above 75% accuracy. We present BioBench, an open ecology vision benchmark that captures what ImageNet misses. BioBench unifies 9 publicly released, application-driven tasks, 4 taxonomic kingdoms, and 6 acquisition modalities (drone RGB, web video, micrographs, in-situ and specimen photos, camera-trap frames), totaling 3.1M images. A single Python API downloads data, fits lightweight classifiers to frozen backbones, and reports class-balanced macro-F1 (plus domain metrics for FishNet and FungiCLEF); ViT-L models evaluate in 6 hours on an A6000 GPU. BioBench provides new signal for computer vision in ecology and a template recipe for building reliable AI-for-science benchmarks in any domain. Code and predictions are available at https://github.com/samuelstevens/biobench and results at https://samuelstevens.me/biobench.

While the field of Quality-Diversity (QD) has grown into a distinct branch of stochastic optimization, a few problems, in particular locomotion and navigation tasks, have become de facto standards. Are such benchmarks sufficient? Are they representative of the key challenges faced by QD algorithms? Do they provide the ability to focus on one particular challenge by properly disentangling it from others? Do they have much predictive power in terms of scalability and generalization? Existing benchmarks are not standardized, and there is currently no MNIST equivalent for QD. Inspired by recent works on Reinforcement Learning benchmarks, we argue that the identification of challenges faced by QD methods and the development of targeted, challenging, scalable but affordable benchmarks is an important step. As an initial effort, we identify three problems that are challenging in sparse reward settings, and propose associated benchmarks: (1) Behavior metric bias, which can result from the use of metrics that do not match the structure of the behavior space. (2) Behavioral Plateaus, with varying characteristics, such that escaping them would require adaptive QD algorithms and (3) Evolvability Traps, where small variations in genotype result in large behavioral changes. The environments that we propose satisfy the properties listed above.

As single-cell RNA sequencing datasets grow in adoption, scale, and complexity, data analysis remains a bottleneck for many research groups. Although frontier AI agents have improved dramatically at software engineering and general data analysis, it remains unclear whether they can extract biological insight from messy, real-world single-cell datasets. We introduce scBench, a benchmark of 394 verifiable problems derived from practical scRNA-seq workflows spanning six sequencing platforms and seven task categories. Each problem provides a snapshot of experimental data immediately prior to an analysis step and a deterministic grader that evaluates recovery of a key biological result. Benchmark data on eight frontier models shows that accuracy ranges from 29-53%, with strong model-task and model-platform interactions. Platform choice affects accuracy as much as model choice, with 40+ percentage point drops on less-documented technologies. scBench complements SpatialBench to cover the two dominant single-cell modalities, serving both as a measurement tool and a diagnostic lens for developing agents that can analyze real scRNA-seq datasets faithfully and reproducibly.

In recent years, with the rapid development of the depth and breadth of large language models' capabilities, various corresponding evaluation benchmarks have been emerging in increasing numbers. As a quantitative assessment tool for model performance, benchmarks are not only a core means to measure model capabilities but also a key element in guiding the direction of model development and promoting technological innovation. We systematically review the current status and development of large language model benchmarks for the first time, categorizing 283 representative benchmarks into three categories: general capabilities, domain-specific, and target-specific. General capability benchmarks cover aspects such as core linguistics, knowledge, and reasoning; domain-specific benchmarks focus on fields like natural sciences, humanities and social sciences, and engineering technology; target-specific benchmarks pay attention to risks, reliability, agents, etc. We point out that current benchmarks have problems such as inflated scores caused by data contamination, unfair evaluation due to cultural and linguistic biases, and lack of evaluation on process credibility and dynamic environments, and provide a referable design paradigm for future benchmark innovation.

Benchmarking multi-object tracking and object detection model performance is an essential step in machine learning model development, as it allows researchers to evaluate model detection and tracker performance on human-generated 'test' data, facilitating consistent comparisons between models and trackers and aiding performance optimization. In this study, a novel benchmark video dataset was developed and used to assess the performance of several Monterey Bay Aquarium Research Institute object detection models and a FathomNet single-class object detection model together with several trackers. The dataset consists of four video sequences representing midwater and benthic deep-sea habitats. Performance was evaluated using Higher Order Tracking Accuracy, a metric that balances detection, localization, and association accuracy. To the best of our knowledge, this is the first publicly available benchmark for multi-object tracking in deep-sea video footage. We provide the benchmark data, a clearly documented workflow for generating additional benchmark videos, as well as example Python notebooks for computing metrics.

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.

Can the rapid advances in code generation, function calling, and data analysis using large language models (LLMs) help automate the search and verification of hypotheses purely from a set of provided datasets? To evaluate this question, we present DiscoveryBench, the first comprehensive benchmark that formalizes the multi-step process of data-driven discovery. The benchmark is designed to systematically assess current model capabilities in discovery tasks and provide a useful resource for improving them. Our benchmark contains 264 tasks collected across 6 diverse domains, such as sociology and engineering, by manually deriving discovery workflows from published papers to approximate the real-world challenges faced by researchers, where each task is defined by a dataset, its metadata, and a discovery goal in natural language. We additionally provide 903 synthetic tasks to conduct controlled evaluations across task complexity. Furthermore, our structured formalism of data-driven discovery enables a facet-based evaluation that provides useful insights into different failure modes. We evaluate several popular LLM-based reasoning frameworks using both open and closed LLMs as baselines on DiscoveryBench and find that even the best system scores only 25%. Our benchmark, thus, illustrates the challenges in autonomous data-driven discovery and serves as a valuable resource for the community to make progress.

AI agents hold the potential to revolutionize scientific productivity by automating literature reviews, replicating experiments, analyzing data, and even proposing new directions of inquiry; indeed, there are now many such agents, ranging from general-purpose "deep research" systems to specialized science-specific agents, such as AI Scientist and AIGS. Rigorous evaluation of these agents is critical for progress. Yet existing benchmarks fall short on several fronts: they (1) fail to provide holistic, product-informed measures of real-world use cases such as science research; (2) lack reproducible agent tools necessary for a controlled comparison of core agentic capabilities; (3) do not account for confounding variables such as model cost and tool access; (4) do not provide standardized interfaces for quick agent prototyping and evaluation; and (5) lack comprehensive baseline agents necessary to identify true advances. In response, we define principles and tooling for more rigorously benchmarking agents. Using these, we present AstaBench, a suite that provides the first holistic measure of agentic ability to perform scientific research, comprising 2400+ problems spanning the entire scientific discovery process and multiple scientific domains, and including many problems inspired by actual user requests to deployed Asta agents. Our suite comes with the first scientific research environment with production-grade search tools that enable controlled, reproducible evaluation, better accounting for confounders. Alongside, we provide a comprehensive suite of nine science-optimized classes of Asta agents and numerous baselines. Our extensive evaluation of 57 agents across 22 agent classes reveals several interesting findings, most importantly that despite meaningful progress on certain individual aspects, AI remains far from solving the challenge of science research assistance.

Recent advances in machine learning and large-scale biological data collections have revived the prospect of building a virtual cell, a computational model of cellular behavior that could accelerate biological discovery. One of the most compelling promises of this vision is the ability to perform in silico phenotypic screens, in which a model predicts the effects of cellular perturbations in unseen biological contexts. This task combines heterogeneous textual inputs with diverse phenotypic outputs, making it particularly well-suited to LLMs and agentic systems. Yet, no standard benchmark currently exists for this task, as existing efforts focus on narrower molecular readouts that are only indirectly aligned with the phenotypic endpoints driving many real-world drug discovery workflows. In this work, we present AssayBench, a benchmark for phenotypic screen prediction, built from 1,920 publicly available CRISPR screens spanning five broad classes of cellular phenotypes. We formulate the screen prediction task as a gene rank prediction for each screen and introduce the adjusted nDCG, a continuous metric for comparing performance across heterogeneous assays. Our extensive evaluation shows that existing methods remain far from empirically estimated performance ceilings and zero-shot generalist LLMs outperform biology-specific LLMs and trainable baselines. Optimization techniques such as fine-tuning, ensembling, and prompt optimization can further improve LLM performance on this task. Overall, AssayBench offers a practical testbed for measuring progress toward in silico phenotypic screening and, more broadly, virtual cell models.

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

Because large language models are expensive to pretrain on different datasets, using smaller-scale experiments to decide on data is crucial for reducing costs. Which benchmarks and methods of making decisions from observed performance at small scale most accurately predict the datasets that yield the best large models? To empower open exploration of this question, we release models, data, and evaluations in DataDecide -- the most extensive open suite of models over differences in data and scale. We conduct controlled pretraining experiments across 25 corpora with differing sources, deduplication, and filtering up to 100B tokens, model sizes up to 1B parameters, and 3 random seeds. We find that the ranking of models at a single, small size (e.g., 150M parameters) is a strong baseline for predicting best models at our larger target scale (1B) (~80% of com parisons correct). No scaling law methods among 8 baselines exceed the compute-decision frontier of single-scale predictions, but DataDecide can measure improvement in future scaling laws. We also identify that using continuous likelihood metrics as proxies in small experiments makes benchmarks including MMLU, ARC, HellaSwag, MBPP, and HumanEval >80% predictable at the target 1B scale with just 0.01% of the compute.

Reward models are critical in techniques like Reinforcement Learning from Human Feedback (RLHF) and Inference Scaling Laws, where they guide language model alignment and select optimal responses. Despite their importance, existing reward model benchmarks often evaluate models by asking them to distinguish between responses generated by models of varying power. However, this approach fails to assess reward models on subtle but critical content changes and variations in style, resulting in a low correlation with policy model performance. To this end, we introduce RM-Bench, a novel benchmark designed to evaluate reward models based on their sensitivity to subtle content differences and resistance to style biases. Extensive experiments demonstrate that RM-Bench strongly correlates with policy model performance, making it a reliable reference for selecting reward models to align language models effectively. We evaluate nearly 40 reward models on RM-Bench. Our results reveal that even state-of-the-art models achieve an average performance of only 46.6%, which falls short of random-level accuracy (50%) when faced with style bias interference. These findings highlight the significant room for improvement in current reward models. Related code and data are available at https://github.com/THU-KEG/RM-Bench.

Language models (LMs) perform well on standardized coding benchmarks but struggle with real-world software engineering tasks such as resolving GitHub issues in SWE-Bench, especially when model parameters are less than 100B. While smaller models are preferable in practice due to their lower computational cost, improving their performance remains challenging. Existing approaches primarily rely on supervised fine-tuning (SFT) with high-quality data, which is expensive to curate at scale. An alternative is test-time scaling: generating multiple outputs, scoring them using a verifier, and selecting the best one. Although effective, this strategy often requires excessive sampling and costly scoring, limiting its practical application. We propose Evolutionary Test-Time Scaling (EvoScale), a sample-efficient method that treats generation as an evolutionary process. By iteratively refining outputs via selection and mutation, EvoScale shifts the output distribution toward higher-scoring regions, reducing the number of samples needed to find correct solutions. To reduce the overhead from repeatedly sampling and selection, we train the model to self-evolve using reinforcement learning (RL). Rather than relying on external verifiers at inference time, the model learns to self-improve the scores of its own generations across iterations. Evaluated on SWE-Bench-Verified, EvoScale enables our 32B model, Satori-SWE-32B, to match or exceed the performance of models with over 100B parameters while using a few samples. Code, data, and models will be fully open-sourced.

We present ORCA (Omni Research on Calculation in AI) Benchmark - a novel benchmark that evaluates large language models (LLMs) on multi-domain, real-life quantitative reasoning using verified outputs from Omni's calculator engine. In 500 natural-language tasks across domains such as finance, physics, health, and statistics, the five state-of-the-art systems (ChatGPT-5, Gemini~2.5~Flash, Claude~Sonnet~4.5, Grok~4, and DeepSeek~V3.2) achieved only 45--63,% accuracy, with errors mainly related to rounding (35,%) and calculation mistakes (33,%). Results in specific domains indicate strengths in mathematics and engineering, but weaknesses in physics and natural sciences. Correlation analysis (r approx 0.40--0.65) shows that the models often fail together but differ in the types of errors they make, highlighting their partial complementarity rather than redundancy. Unlike standard math datasets, ORCA evaluates step-by-step reasoning, numerical precision, and domain generalization across real problems from finance, physics, health, and statistics.

The effective application of foundation models to translational research in immune-mediated diseases requires multimodal patient-level representations that can capture complex phenotypes emerging from multicellular interactions. Yet most current biological foundation models focus only on single-cell resolution and are evaluated on technical metrics often disconnected from actual drug development tasks and challenges. Here, we introduce EVA, the first cross-species, multimodal foundation model of immunology and inflammation, a therapeutic area where shared pathogenic mechanisms create unique opportunities for transfer learning. EVA harmonizes transcriptomics data across species, platforms, and resolutions, and integrates histology data to produce rich, unified patient representations. We establish clear scaling laws, demonstrating that increasing model size and compute translates to improvements in both pretraining and downstream tasks performance. We introduce a comprehensive evaluation suite of 39 tasks spanning the drug development pipeline: zero-shot target efficacy and gene function prediction for discovery, cross-species or cross-diseases molecular perturbations for preclinical development, and patient stratification with treatment response prediction or disease activity prediction for clinical trials applications. We benchmark EVA against several state-of-the-art biological foundation models and baselines on these tasks, and demonstrate state-of-the-art results on each task category. Using mechanistic interpretability, we further identify biological meaningful features, revealing intertwined representations across species and technologies. We release an open version of EVA for transcriptomics to accelerate research on immune-mediated diseases.

The code of nature, embedded in DNA and RNA genomes since the origin of life, holds immense potential to impact both humans and ecosystems through genome modeling. Genomic Foundation Models (GFMs) have emerged as a transformative approach to decoding the genome. As GFMs scale up and reshape the landscape of AI-driven genomics, the field faces an urgent need for rigorous and reproducible evaluation. We present OmniGenBench, a modular benchmarking platform designed to unify the data, model, benchmarking, and interpretability layers across GFMs. OmniGenBench enables standardized, one-command evaluation of any GFM across five benchmark suites, with seamless integration of over 31 open-source models. Through automated pipelines and community-extensible features, the platform addresses critical reproducibility challenges, including data transparency, model interoperability, benchmark fragmentation, and black-box interpretability. OmniGenBench aims to serve as foundational infrastructure for reproducible genomic AI research, accelerating trustworthy discovery and collaborative innovation in the era of genome-scale modeling.

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

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Evaluations are limited by benchmark availability. As models evolve, there is a need to create benchmarks that can measure progress on new generative capabilities. However, creating new benchmarks through human annotations is slow and expensive, restricting comprehensive evaluations for any capability. We introduce BENCHAGENTS, a framework that methodically leverages large language models (LLMs) to automate benchmark creation for complex capabilities while inherently ensuring data and metric quality. BENCHAGENTS decomposes the benchmark creation process into planning, generation, data verification, and evaluation, each of which is executed by an LLM agent. These agents interact with each other and utilize human-in-the-loop feedback from benchmark developers to explicitly improve and flexibly control data diversity and quality. We use BENCHAGENTS to create benchmarks to evaluate capabilities related to planning and constraint satisfaction during text generation. We then use these benchmarks to study seven state-of-the-art models and extract new insights on common failure modes and model differences.

The literature has witnessed an emerging interest in AI agents for automated assessment of scientific papers. Existing benchmarks focus primarily on the computational aspect of this task, testing agents' ability to reproduce or replicate research outcomes when having access to the code and data. This setting, while foundational, (1) fails to capture the inconsistent availability of new data for replication as opposed to reproduction, and (2) lacks ground-truth diversity by focusing only on reproducible papers, thereby failing to evaluate an agent's ability to identify non-replicable research. Furthermore, most benchmarks only evaluate outcomes rather than the replication process. In response, we introduce ReplicatorBench, an end-to-end benchmark, including human-verified replicable and non-replicable research claims in social and behavioral sciences for evaluating AI agents in research replication across three stages: (1) extraction and retrieval of replication data; (2) design and execution of computational experiments; and (3) interpretation of results, allowing a test of AI agents' capability to mimic the activities of human replicators in real world. To set a baseline of AI agents' capability, we develop ReplicatorAgent, an agentic framework equipped with necessary tools, like web search and iterative interaction with sandboxed environments, to accomplish tasks in ReplicatorBench. We evaluate ReplicatorAgent across four underlying large language models (LLMs), as well as different design choices of programming language and levels of code access. Our findings reveal that while current LLM agents are capable of effectively designing and executing computational experiments, they struggle with retrieving resources, such as new data, necessary to replicate a claim. All code and data are publicly available at https://github.com/CenterForOpenScience/llm-benchmarking.

We introduce MABe22, a large-scale, multi-agent video and trajectory benchmark to assess the quality of learned behavior representations. This dataset is collected from a variety of biology experiments, and includes triplets of interacting mice (4.7 million frames video+pose tracking data, 10 million frames pose only), symbiotic beetle-ant interactions (10 million frames video data), and groups of interacting flies (4.4 million frames of pose tracking data). Accompanying these data, we introduce a panel of real-life downstream analysis tasks to assess the quality of learned representations by evaluating how well they preserve information about the experimental conditions (e.g. strain, time of day, optogenetic stimulation) and animal behavior. We test multiple state-of-the-art self-supervised video and trajectory representation learning methods to demonstrate the use of our benchmark, revealing that methods developed using human action datasets do not fully translate to animal datasets. We hope that our benchmark and dataset encourage a broader exploration of behavior representation learning methods across species and settings.

As the demand for comprehensive evaluations of diverse model capabilities steadily increases, benchmark suites have correspondingly grown significantly in scale. Despite notable advances in redundancy reduction and subset-level performance prediction, a systematic framework that effectively integrates these methods to ensure both prediction accuracy and ranking consistency is still largely elusive. In this paper, we first perform a sample-level analysis of benchmark redundancy and identify several highly similar samples that can be eliminated. Besides, we frame benchmark compression as an optimization problem with the aim of score reconstruction. Building on these, we then propose EssenceBench, a coarse-to-fine framework utilizing an iterative Genetic Algorithm (GA), which takes the advantages of fitness-based subset search and attribution-based sample search. Compared to previous methods, our approach yields superior compression results with lower reconstruction error and markedly higher efficiency. In particular, on the HellaSwag benchmark (10K samples), our method preserves the ranking of all models shifting within 5% using 25x fewer samples, and achieves 95% ranking preservation shifting within 5% using only 200x fewer samples.

As foundation models grow rapidly in capability and deployment, evaluating their scientific understanding becomes increasingly critical. Existing science benchmarks have made progress towards broad **Range**, wide **Reach**, and high **Rigor**, yet they often face two major challenges: **data leakage risks** that compromise benchmarking validity, and **evaluation inefficiency** due to large-scale testing. To address these issues, we introduce the **Ever-Evolving Science Exam (EESE)**, a dynamic benchmark designed to reliably assess scientific capabilities in foundation models. Our approach consists of two components: 1) a non-public **EESE-Pool** with over 100K expertly constructed science instances (question-answer pairs) across 5 disciplines and 500+ subfields, built through a multi-stage pipeline ensuring **Range**, **Reach**, and **Rigor**, 2) a periodically updated 500-instance subset **EESE**, sampled and validated to enable leakage-resilient, low-overhead evaluations. Experiments on 32 open- and closed-source models demonstrate that EESE effectively differentiates the strengths and weaknesses of models in scientific fields and cognitive dimensions. Overall, EESE provides a robust, scalable, and forward-compatible solution for science benchmark design, offering a realistic measure of how well foundation models handle science questions. The project page is at: https://github.com/aiben-ch/EESE.

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

Existing benchmarks have proven effective for assessing the performance of fully trained large language models. However, we find striking differences in the early training stages of small models, where benchmarks often fail to provide meaningful or discriminative signals. To explore how these differences arise, this competition tackles the challenge of designing scientific knowledge evaluation tasks specifically tailored for measuring early training progress of language models. Participants are invited to develop novel evaluation methodologies or adapt existing benchmarks to better capture performance differences among language models. To support this effort, we provide three pre-trained small models (0.5B, 1B, and 3B parameters), along with intermediate checkpoints sampled during training up to 200B tokens. All experiments and development work can be run on widely available free cloud-based GPU platforms, making participation accessible to researchers with limited computational resources. Submissions will be evaluated based on three criteria: the quality of the performance signal they produce, the consistency of model rankings at 1 trillion tokens of training, and their relevance to the scientific knowledge domain. By promoting the design of tailored evaluation strategies for early training, this competition aims to attract a broad range of participants from various disciplines, including those who may not be machine learning experts or have access to dedicated GPU resources. Ultimately, this initiative seeks to make foundational LLM research more systematic and benchmark-informed from the earliest phases of model development.

Recently, there has been great interest in learning how to best represent proteins, specifically with fixed-length embeddings. Deep learning has become a popular tool for protein representation learning as a model's hidden layers produce potentially useful vector embeddings. TAPE introduced a number of benchmark tasks and showed that semi-supervised learning, via pretraining language models on a large protein corpus, improved performance on downstream tasks. Two of the tasks (fluorescence prediction and stability prediction) involve learning fitness landscapes. In this paper, we show that CNN models trained solely using supervised learning both compete with and sometimes outperform the best models from TAPE that leverage expensive pretraining on large protein datasets. These CNN models are sufficiently simple and small that they can be trained using a Google Colab notebook. We also find for the fluorescence task that linear regression outperforms our models and the TAPE models. The benchmarking tasks proposed by TAPE are excellent measures of a model's ability to predict protein function and should be used going forward. However, we believe it is important to add baselines from simple models to put the performance of the semi-supervised models that have been reported so far into perspective.

Evaluation is critical for assessing capabilities, tracking scientific progress, and informing model selection. In this paper, we present three desiderata for a good benchmark for language models: (i) salience (e.g., knowledge about World War II is more salient than a random day in history), (ii) novelty (i.e., the benchmark reveals new trends in model rankings not shown by previous benchmarks), and (iii) difficulty (i.e., the benchmark should be difficult for existing models, leaving headroom for future improvement). We operationalize these three desiderata and cast benchmark creation as a search problem, that of finding benchmarks that that satisfy all three desiderata. To tackle this search problem, we present AutoBencher, which uses a language model to automatically search for datasets that meet the three desiderata. AutoBencher uses privileged information (e.g. relevant documents) to construct reliable datasets, and adaptivity with reranking to optimize for the search objective. We use AutoBencher to create datasets for math, multilingual, and knowledge-intensive question answering. The scalability of AutoBencher allows it to test fine-grained categories and tail knowledge, creating datasets that are on average 27% more novel and 22% more difficult than existing benchmarks. A closer investigation of our constructed datasets shows that we can identify specific gaps in LM knowledge in language models that are not captured by existing benchmarks, such as Gemini Pro performing much worse on question answering about the Permian Extinction and Fordism, while OpenAGI-7B performing surprisingly well on QA about COVID-19.

Language models demonstrate both quantitative improvement and new qualitative capabilities with increasing scale. Despite their potentially transformative impact, these new capabilities are as yet poorly characterized. In order to inform future research, prepare for disruptive new model capabilities, and ameliorate socially harmful effects, it is vital that we understand the present and near-future capabilities and limitations of language models. To address this challenge, we introduce the Beyond the Imitation Game benchmark (BIG-bench). BIG-bench currently consists of 204 tasks, contributed by 442 authors across 132 institutions. Task topics are diverse, drawing problems from linguistics, childhood development, math, common-sense reasoning, biology, physics, social bias, software development, and beyond. BIG-bench focuses on tasks that are believed to be beyond the capabilities of current language models. We evaluate the behavior of OpenAI's GPT models, Google-internal dense transformer architectures, and Switch-style sparse transformers on BIG-bench, across model sizes spanning millions to hundreds of billions of parameters. In addition, a team of human expert raters performed all tasks in order to provide a strong baseline. Findings include: model performance and calibration both improve with scale, but are poor in absolute terms (and when compared with rater performance); performance is remarkably similar across model classes, though with benefits from sparsity; tasks that improve gradually and predictably commonly involve a large knowledge or memorization component, whereas tasks that exhibit "breakthrough" behavior at a critical scale often involve multiple steps or components, or brittle metrics; social bias typically increases with scale in settings with ambiguous context, but this can be improved with prompting.

The rapid progress and widespread deployment of LLMs and LLM-powered agents has outpaced our ability to evaluate them. Hand-crafted, static benchmarks are the primary tool for assessing model capabilities, but these quickly become saturated. In contrast, dynamic benchmarks evolve alongside the models they evaluate, but are expensive to create and continuously update. To address these challenges, we develop BeTaL (Benchmark Tuning with an LLM-in-the-loop), a framework that leverages environment design principles to automate the process of dynamic benchmark design. BeTaL works by parameterizing key design choices in base benchmark templates and uses LLMs to reason through the resulting parameter space to obtain target properties (such as difficulty and realism) in a cost-efficient manner. We validate this approach on its ability to create benchmarks with desired difficulty levels. Using BeTaL, we create two new benchmarks and extend a popular agentic benchmark tau-bench. Extensive evaluation on these three tasks and multiple target difficulty levels shows that BeTaL produces benchmarks much closer to the desired difficulty, with average deviations ranging from 5.3% to 13.2% -- a 2-4x improvement over the baselines.

The large-scale training of multi-modal models on data scraped from the web has shown outstanding utility in infusing these models with the required world knowledge to perform effectively on multiple downstream tasks. However, one downside of scraping data from the web can be the potential sacrifice of the benchmarks on which the abilities of these models are often evaluated. To safeguard against test data contamination and to truly test the abilities of these foundation models we propose LiveXiv: A scalable evolving live benchmark based on scientific ArXiv papers. LiveXiv accesses domain-specific manuscripts at any given timestamp and proposes to automatically generate visual question-answer pairs (VQA). This is done without any human-in-the-loop, using the multi-modal content in the manuscripts, like graphs, charts, and tables. Moreover, we introduce an efficient evaluation approach that estimates the performance of all models on the evolving benchmark using evaluations of only a subset of models. This significantly reduces the overall evaluation cost. We benchmark multiple open and proprietary Large Multi-modal Models (LMMs) on the first version of our benchmark, showing its challenging nature and exposing the models true abilities, avoiding contamination. Lastly, in our commitment to high quality, we have collected and evaluated a manually verified subset. By comparing its overall results to our automatic annotations, we have found that the performance variance is indeed minimal (<2.5%). Our dataset is available online on HuggingFace, and our code will be available here.

Reward models are used throughout the post-training of language models to capture nuanced signals from preference data and provide a training target for optimization across instruction following, reasoning, safety, and more domains. The community has begun establishing best practices for evaluating reward models, from the development of benchmarks that test capabilities in specific skill areas to others that test agreement with human preferences. At the same time, progress in evaluation has not been mirrored by the effectiveness of reward models in downstream tasks -- simpler direct alignment algorithms are reported to work better in many cases. This paper introduces RewardBench 2, a new multi-skill reward modeling benchmark designed to bring new, challenging data for accuracy-based reward model evaluation -- models score about 20 points on average lower on RewardBench 2 compared to the first RewardBench -- while being highly correlated with downstream performance. Compared to most other benchmarks, RewardBench 2 sources new human prompts instead of existing prompts from downstream evaluations, facilitating more rigorous evaluation practices. In this paper, we describe our benchmark construction process and report how existing models perform on it, while quantifying how performance on the benchmark correlates with downstream use of the models in both inference-time scaling algorithms, like best-of-N sampling, and RLHF training algorithms like proximal policy optimization.

Data science agents promise to accelerate discovery and insight-generation by turning data into executable analyses and findings. Yet existing data science benchmarks fall short due to fragmented evaluation interfaces that make cross-benchmark comparison difficult, narrow task coverage and a lack of rigorous data grounding. In particular, we show that a substantial portion of tasks in current benchmarks can be solved without using the actual data. To address these limitations, we introduce DSGym, a standardized framework for evaluating and training data science agents in self-contained execution environments. Unlike static benchmarks, DSGym provides a modular architecture that makes it easy to add tasks, agent scaffolds, and tools, positioning it as a live, extensible testbed. We curate DSGym-Tasks, a holistic task suite that standardizes and refines existing benchmarks via quality and shortcut solvability filtering. We further expand coverage with (1) DSBio: expert-derived bioinformatics tasks grounded in literature and (2) DSPredict: challenging prediction tasks spanning domains such as computer vision, molecular prediction, and single-cell perturbation. Beyond evaluation, DSGym enables agent training via execution-verified data synthesis pipeline. As a case study, we build a 2,000-example training set and trained a 4B model in DSGym that outperforms GPT-4o on standardized analysis benchmarks. Overall, DSGym enables rigorous end-to-end measurement of whether agents can plan, implement, and validate data analyses in realistic scientific context.

We introduce MIRAGE, a new benchmark for multimodal expert-level reasoning and decision-making in consultative interaction settings. Designed for the agriculture domain, MIRAGE captures the full complexity of expert consultations by combining natural user queries, expert-authored responses, and image-based context, offering a high-fidelity benchmark for evaluating models on grounded reasoning, clarification strategies, and long-form generation in a real-world, knowledge-intensive domain. Grounded in over 35,000 real user-expert interactions and curated through a carefully designed multi-step pipeline, MIRAGE spans diverse crop health, pest diagnosis, and crop management scenarios. The benchmark includes more than 7,000 unique biological entities, covering plant species, pests, and diseases, making it one of the most taxonomically diverse benchmarks available for vision-language models, grounded in the real world. Unlike existing benchmarks that rely on well-specified user inputs and closed-set taxonomies, MIRAGE features underspecified, context-rich scenarios with open-world settings, requiring models to infer latent knowledge gaps, handle rare entities, and either proactively guide the interaction or respond. Project Page: https://mirage-benchmark.github.io

Large language models (LLMs) trained on internet-scale corpora can exhibit systematic biases that increase the probability of unwanted behavior. In this study, we examined potential biases towards synthetic vs. biological technological solutions across four domains (materials, energy, manufacturing, and algorithms). A sample of 5 frontier and 5 open-weight models were measured using 50 curated Bioalignment prompts with a Kelly criterion-inspired evaluation framework. According to this metric, most models were not bioaligned in that they exhibit biases in favor of synthetic (non-biological) solutions. We next examined if fine-tuning could increase the preferences of two open-weight models, Llama 3.2-3B-Instruct and Qwen2.5-3B-Instruct, for biological-based approaches. A curated corpus of ~22M tokens from 6,636 PMC articles emphasizing biological problem-solving was used first to fine-tune Llama 3B with a mixed corpus of continued training and instruction-formatted. This was then extended to Qwen 3B using instruction-formatted only. We found that QLoRA fine-tuning significantly increased the scoring of biological solutions for both models without degrading general capabilities (Holm-Bonferroni-corrected p < 0.001 and p < 0.01, respectively). This suggests that even a small amount of fine-tuning can change how models weigh the relative value of biological and bioinspired vs. synthetic approaches. Although this work focused on small open-weight LLMs, it may be extensible to much larger models and could be used to develop models that favor bio-based approaches. We release the benchmark, corpus, code, and adapter weights.

The rapid proliferation of benchmarks for evaluating large language models (LLMs) has created an urgent need for systematic methods to assess benchmark quality itself. We propose Benchmark^2, a comprehensive framework comprising three complementary metrics: (1) Cross-Benchmark Ranking Consistency, measuring whether a benchmark produces model rankings aligned with peer benchmarks; (2) Discriminability Score, quantifying a benchmark's ability to differentiate between models; and (3) Capability Alignment Deviation, identifying problematic instances where stronger models fail but weaker models succeed within the same model family. We conduct extensive experiments across 15 benchmarks spanning mathematics, reasoning, and knowledge domains, evaluating 11 LLMs across four model families. Our analysis reveals significant quality variations among existing benchmarks and demonstrates that selective benchmark construction based on our metrics can achieve comparable evaluation performance with substantially reduced test sets.

Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical scientific use-cases more fragmented and less clear in pathways to impact. This paper introduces an ontology for scientific benchmarking developed through a unified, community-driven effort that extends the MLCommons ecosystem to cover physics, chemistry, materials science, biology, climate science, and more. Building on prior initiatives such as XAI-BENCH, FastML Science Benchmarks, PDEBench, and the SciMLBench framework, our effort consolidates a large set of disparate benchmarks and frameworks into a single taxonomy of scientific, application, and system-level benchmarks. New benchmarks can be added through an open submission workflow coordinated by the MLCommons Science Working Group and evaluated against a six-category rating rubric that promotes and identifies high-quality benchmarks, enabling stakeholders to select benchmarks that meet their specific needs. The architecture is extensible, supporting future scientific and AI/ML motifs, and we discuss methods for identifying emerging computing patterns for unique scientific workloads. The MLCommons Science Benchmarks Ontology provides a standardized, scalable foundation for reproducible, cross-domain benchmarking in scientific machine learning. A companion webpage for this work has also been developed as the effort evolves: https://mlcommons-science.github.io/benchmark/

Data scaling and standardized evaluation benchmarks have driven significant advances in natural language processing and computer vision. However, robotics faces unique challenges in scaling data and establishing evaluation protocols. Collecting real-world data is resource-intensive and inefficient, while benchmarking in real-world scenarios remains highly complex. Synthetic data and simulation offer promising alternatives, yet existing efforts often fall short in data quality, diversity, and benchmark standardization. To address these challenges, we introduce RoboVerse, a comprehensive framework comprising a simulation platform, a synthetic dataset, and unified benchmarks. Our simulation platform supports multiple simulators and robotic embodiments, enabling seamless transitions between different environments. The synthetic dataset, featuring high-fidelity physics and photorealistic rendering, is constructed through multiple approaches. Additionally, we propose unified benchmarks for imitation learning and reinforcement learning, enabling evaluation across different levels of generalization. At the core of the simulation platform is MetaSim, an infrastructure that abstracts diverse simulation environments into a universal interface. It restructures existing simulation environments into a simulator-agnostic configuration system, as well as an API aligning different simulator functionalities, such as launching simulation environments, loading assets with initial states, stepping the physics engine, etc. This abstraction ensures interoperability and extensibility. Comprehensive experiments demonstrate that RoboVerse enhances the performance of imitation learning, reinforcement learning, world model learning, and sim-to-real transfer. These results validate the reliability of our dataset and benchmarks, establishing RoboVerse as a robust solution for advancing robot learning.

Benchmark quality is critical for meaningful evaluation and sustained progress in time series forecasting, particularly given the recent rise of pretrained models. Existing benchmarks often have narrow domain coverage or overlook important real-world settings, such as tasks with covariates. Additionally, their aggregation procedures often lack statistical rigor, making it unclear whether observed performance differences reflect true improvements or random variation. Many benchmarks also fail to provide infrastructure for consistent evaluation or are too rigid to integrate into existing pipelines. To address these gaps, we propose fev-bench, a benchmark comprising 100 forecasting tasks across seven domains, including 46 tasks with covariates. Supporting the benchmark, we introduce fev, a lightweight Python library for benchmarking forecasting models that emphasizes reproducibility and seamless integration with existing workflows. Usingfev, fev-bench employs principled aggregation methods with bootstrapped confidence intervals to report model performance along two complementary dimensions: win rates and skill scores. We report results on fev-bench for various pretrained, statistical and baseline models, and identify promising directions for future research.

As language models improve and become capable of performing more complex tasks across modalities, evaluating them automatically becomes increasingly challenging. Developing strong and robust task-specific automatic metrics gets harder, and human-annotated test sets -- which are expensive to create -- saturate more quickly. A compelling alternative is to design reliable strategies to automate the creation of test data and evaluation, but previous attempts either rely on pre-existing data, or focus solely on individual tasks. We present Zero-shot Benchmarking (ZSB), a framework for creating high-quality benchmarks for any task by leveraging language models for both synthetic test data creation and evaluation. ZSB is simple and flexible: it requires only the creation of a prompt for data generation and one for evaluation; it is scalable to tasks and languages where collecting real-world data is costly or impractical; it is model-agnostic, allowing the creation of increasingly challenging benchmarks as models improve. To assess the effectiveness of our framework, we create benchmarks for five text-only tasks and a multi-modal one: general capabilities in four languages (English, Chinese, French, and Korean), translation, and general vision-language capabilities in English. We then rank a broad range of open and closed systems on our benchmarks. ZSB rankings consistently correlate strongly with human rankings, outperforming widely-adopted standard benchmarks. Through ablations, we find that strong benchmarks can be created with open models, and that judge model size and dataset variety are crucial drivers of performance. We release all our benchmarks, and code to reproduce our experiments and to produce new benchmarks.

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.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

Artificial intelligence systems are increasingly deployed in biomedical research. However, current evaluation frameworks may inadequately assess their effectiveness as research collaborators. This rapid review examines benchmarking practices for AI systems in preclinical biomedical research. Three major databases and two preprint servers were searched from January 1, 2018 to October 31, 2025, identifying 14 benchmarks that assess AI capabilities in literature understanding, experimental design, and hypothesis generation. The results revealed that all current benchmarks assess isolated component capabilities, including data analysis quality, hypothesis validity, and experimental protocol design. However, authentic research collaboration requires integrated workflows spanning multiple sessions, with contextual memory, adaptive dialogue, and constraint propagation. This gap implies that systems excelling on component benchmarks may fail as practical research co-pilots. A process-oriented evaluation framework is proposed that addresses four critical dimensions absent from current benchmarks: dialogue quality, workflow orchestration, session continuity, and researcher experience. These dimensions are essential for evaluating AI systems as research co-pilots rather than as isolated task executors.

In Machine Learning, a benchmark refers to an ensemble of datasets associated with one or multiple metrics together with a way to aggregate different systems performances. They are instrumental in (i) assessing the progress of new methods along different axes and (ii) selecting the best systems for practical use. This is particularly the case for NLP with the development of large pre-trained models (e.g. GPT, BERT) that are expected to generalize well on a variety of tasks. While the community mainly focused on developing new datasets and metrics, there has been little interest in the aggregation procedure, which is often reduced to a simple average over various performance measures. However, this procedure can be problematic when the metrics are on a different scale, which may lead to spurious conclusions. This paper proposes a new procedure to rank systems based on their performance across different tasks. Motivated by the social choice theory, the final system ordering is obtained through aggregating the rankings induced by each task and is theoretically grounded. We conduct extensive numerical experiments (on over 270k scores) to assess the soundness of our approach both on synthetic and real scores (e.g. GLUE, EXTREM, SEVAL, TAC, FLICKR). In particular, we show that our method yields different conclusions on state-of-the-art systems than the mean-aggregation procedure while being both more reliable and robust.

Automating AI research holds immense potential for accelerating scientific progress, yet current AI agents struggle with the complexities of rigorous, end-to-end experimentation. We introduce EXP-Bench, a novel benchmark designed to systematically evaluate AI agents on complete research experiments sourced from influential AI publications. Given a research question and incomplete starter code, EXP-Bench challenges AI agents to formulate hypotheses, design and implement experimental procedures, execute them, and analyze results. To enable the creation of such intricate and authentic tasks with high-fidelity, we design a semi-autonomous pipeline to extract and structure crucial experimental details from these research papers and their associated open-source code. With the pipeline, EXP-Bench curated 461 AI research tasks from 51 top-tier AI research papers. Evaluations of leading LLM-based agents, such as OpenHands and IterativeAgent on EXP-Bench demonstrate partial capabilities: while scores on individual experimental aspects such as design or implementation correctness occasionally reach 20-35%, the success rate for complete, executable experiments was a mere 0.5%. By identifying these bottlenecks and providing realistic step-by-step experiment procedures, EXP-Bench serves as a vital tool for future AI agents to improve their ability to conduct AI research experiments. EXP-Bench is open-sourced at https://github.com/Just-Curieous/Curie/tree/main/benchmark/exp_bench.

We introduce a benchmark to evaluate the capability of AI to solve problems in theoretical physics, focusing on high-energy theory and cosmology. The first iteration of our benchmark consists of 57 problems of varying difficulty, from undergraduate to research level. These problems are novel in the sense that they do not come from public problem collections. We evaluate our data set on various open and closed language models, including o3-mini, o1, DeepSeek-R1, GPT-4o and versions of Llama and Qwen. While we find impressive progress in model performance with the most recent models, our research-level difficulty problems are mostly unsolved. We address challenges of auto-verifiability and grading, and discuss common failure modes. While currently state-of-the art models are still of limited use for researchers, our results show that AI assisted theoretical physics research may become possible in the near future. We discuss the main obstacles towards this goal and possible strategies to overcome them. The public problems and solutions, results for various models, and updates to the data set and score distribution, are available on the website of the dataset tpbench.org.

Time series forecasting is critical across finance, healthcare, and cloud computing, yet progress is constrained by a fundamental bottleneck: the scarcity of large-scale, high-quality benchmarks. To address this gap, we introduce QuitoBench, a regime-balanced benchmark for time series forecasting with coverage across eight trendtimesseasonalitytimesforecastability (TSF) regimes, designed to capture forecasting-relevant properties rather than application-defined domain labels. The benchmark is built upon Quito, a billion-scale time series corpus of application traffic from Alipay spanning nine business domains. Benchmarking 10 models from deep learning, foundation models, and statistical baselines across 232,200 evaluation instances, we report four key findings: (i) a context-length crossover where deep learning models lead at short context (L=96) but foundation models dominate at long context (L ge 576); (ii) forecastability is the dominant difficulty driver, producing a 3.64 times MAE gap across regimes; (iii) deep learning models match or surpass foundation models at 59 times fewer parameters; and (iv) scaling the amount of training data provides substantially greater benefit than scaling model size for both model families. These findings are validated by strong cross-benchmark and cross-metric consistency. Our open-source release enables reproducible, regime-aware evaluation for time series forecasting research.

Accelerating scientific discovery requires the identification of which experiments would yield the best outcomes before committing resources to costly physical validation. While existing benchmarks evaluate LLMs on scientific knowledge and reasoning, their ability to predict experimental outcomes - a task where AI could significantly exceed human capabilities - remains largely underexplored. We introduce SciPredict, a benchmark comprising 405 tasks derived from recent empirical studies in 33 specialized sub-fields of physics, biology, and chemistry. SciPredict addresses two critical questions: (a) can LLMs predict the outcome of scientific experiments with sufficient accuracy? and (b) can such predictions be reliably used in the scientific research process? Evaluations reveal fundamental limitations on both fronts. Model accuracies are 14-26% and human expert performance is approx20%. Although some frontier models exceed human performance model accuracy is still far below what would enable reliable experimental guidance. Even within the limited performance, models fail to distinguish reliable predictions from unreliable ones, achieving only approx20% accuracy regardless of their confidence or whether they judge outcomes as predictable without physical experimentation. Human experts, in contrast, demonstrate strong calibration: their accuracy increases from approx5% to approx80% as they deem outcomes more predictable without conducting the experiment. SciPredict establishes a rigorous framework demonstrating that superhuman performance in experimental science requires not just better predictions, but better awareness of prediction reliability. For reproducibility all our data and code are provided at https://github.com/scaleapi/scipredict

The pursuit of general-purpose robotics has yielded impressive foundation models, yet simulation-based benchmarking remains a bottleneck due to rapid performance saturation and a lack of true generalization testing. Existing benchmarks often exhibit significant domain overlap between training and evaluation, trivializing success rates and obscuring insights into robustness. We introduce RoboLab, a simulation benchmarking framework designed to address these challenges. Concretely, our framework is designed to answer two questions: (1) to what extent can we understand the performance of a real-world policy by analyzing its behavior in simulation, and (2) which external factors most strongly affect that behavior under controlled perturbations. First, RoboLab enables human-authored and LLM-enabled generation of scenes and tasks in a robot- and policy-agnostic manner within a physically realistic and photorealistic simulation. With this, we propose the RoboLab-120 benchmark, consisting of 120 tasks categorized into three competency axes: visual, procedural, relational competency, across three difficulty levels. Second, we introduce a systematic analysis of real-world policies that quantify both their performance and the sensitivity of their behavior to controlled perturbations, indicating that high-fidelity simulation can serve as a proxy for analyzing performance and its dependence on external factors. Evaluation with RoboLab exposes significant performance gap in current state-of-the-art models. By providing granular metrics and a scalable toolset, RoboLab offers a scalable framework for evaluating the true generalization capabilities of task-generalist robotic policies.

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.

Evaluating the real-world applicability of large language models (LLMs) provides valuable insights for their development and use in software development tasks. Existing benchmarks often focus on standalone coding problems or specific libraries, overlooking multi-file, project-based scenarios and lacking a rigorous evaluation of consistency. The HackerRank-ASTRA Benchmark introduces project-based coding problems that mirror real-world scenarios. It evaluates model consistency through 32 runs (k = 32) and median standard deviation while incorporating taxonomy-level analysis to assess sub-skill capabilities. Initial evaluations on 65 problems show that the top three models -- o1, o1-preview, and Claude-3.5-Sonnet-1022 -- achieved comparable average scores of 75%, with no statistically significant differences in performance. Notably, Claude-3.5-Sonnet-1022 demonstrated the highest consistency across problems, with low variability (SD = 0.0497), which was statistically significant compared to other models, highlighting its reliability for real-world software development tasks.

Protein design aims to compose amino-acid sequences that fold into stable three-dimensional structures while satisfying targeted functional properties. The field is increasingly shifting toward vibe protein design, where a single model is expected to generate novel sequences, engineer existing proteins, and reason about protein characteristics through flexible natural-language constraints. Large language models (LLMs) have emerged as a leading paradigm in this space. However, existing evaluation benchmarks often limit their scope to a partial aspect of protein design, while others restrict design objectives to structured input schemas, lacking an integrated framework that evaluates the broad spectrum of protein design competence under open-ended intents. To this end, we present Vibe Protein design Benchmark (VibeProteinBench), a language-interfaced benchmark that probes generalist capabilities through three complementary stages mirroring a computational protein design workflow: recognition, engineering, and generation. Each stage is grounded in expert-curated mechanistic rationales and multi-faceted in silico validation, to computationally verify whether model outputs are biologically plausible. Evaluations across diverse general-purpose and domain-specialized LLMs reveal that no model achieves strong performance across all three stages, suggesting that generalist protein design remains a substantial open challenge for current LLMs.

Existing benchmarks for frontier models often test specialized, ``PhD-level'' knowledge that is difficult for non-experts to grasp. In contrast, we present a benchmark based on the NPR Sunday Puzzle Challenge that requires only general knowledge. Our benchmark is challenging for both humans and models, however correct solutions are easy to verify, and models' mistakes are easy to spot. Our work reveals capability gaps that are not evident in existing benchmarks: OpenAI o1 significantly outperforms other reasoning models that are on par on benchmarks that test specialized knowledge. Furthermore, our analysis of reasoning outputs uncovers new kinds of failures. DeepSeek R1, for instance, often concedes with ``I give up'' before providing an answer that it knows is wrong. R1 can also be remarkably ``uncertain'' in its output and in rare cases, it does not ``finish thinking,'' which suggests the need for an inference-time technique to ``wrap up'' before the context window limit is reached. We also quantify the effectiveness of reasoning longer with R1 and Gemini Thinking to identify the point beyond which more reasoning is unlikely to improve accuracy on our benchmark.

Benchmarks are essential for quantitatively tracking progress in AI. As AI agents become increasingly capable, researchers and practitioners have introduced agentic benchmarks to evaluate agents on complex, real-world tasks. These benchmarks typically measure agent capabilities by evaluating task outcomes via specific reward designs. However, we show that many agentic benchmarks have issues task setup or reward design. For example, SWE-bench Verified uses insufficient test cases, while TAU-bench counts empty responses as successful. Such issues can lead to under- or overestimation agents' performance by up to 100% in relative terms. To make agentic evaluation rigorous, we introduce the Agentic Benchmark Checklist (ABC), a set of guidelines that we synthesized from our benchmark-building experience, a survey of best practices, and previously reported issues. When applied to CVE-Bench, a benchmark with a particularly complex evaluation design, ABC reduces the performance overestimation by 33%.

Manual labeling of animal images remains a significant bottleneck in ecological research, limiting the scale and efficiency of biodiversity monitoring efforts. This study investigates whether state-of-the-art Vision Transformer (ViT) foundation models can reduce thousands of unlabeled animal images directly to species-level clusters. We present a comprehensive benchmarking framework evaluating five ViT models combined with five dimensionality reduction techniques and four clustering algorithms, two supervised and two unsupervised, across 60 species (30 mammals and 30 birds), with each test using a random subset of 200 validated images per species. We investigate when clustering succeeds at species-level, where it fails, and whether clustering within the species-level reveals ecologically meaningful patterns such as sex, age, or phenotypic variation. Our results demonstrate near-perfect species-level clustering (V-measure: 0.958) using DINOv3 embeddings with t-SNE and supervised hierarchical clustering methods. Unsupervised approaches achieve competitive performance (0.943) while requiring no prior species knowledge, rejecting only 1.14% of images as outliers requiring expert review. We further demonstrate robustness to realistic long-tailed distributions of species and show that intentional over-clustering can reliably extract intra-specific variation including age classes, sexual dimorphism, and pelage differences. We introduce an open-source benchmarking toolkit and provide recommendations for ecologists to select appropriate methods for sorting their specific taxonomic groups and data.

We introduce TimeSeriesGym, a scalable benchmarking framework for evaluating Artificial Intelligence (AI) agents on time series machine learning engineering challenges. Existing benchmarks lack scalability, focus narrowly on model building in well-defined settings, and evaluate only a limited set of research artifacts (e.g., CSV submission files). To make AI agent benchmarking more relevant to the practice of machine learning engineering, our framework scales along two critical dimensions. First, recognizing that effective ML engineering requires a range of diverse skills, TimeSeriesGym incorporates challenges from diverse sources spanning multiple domains and tasks. We design challenges to evaluate both isolated capabilities (including data handling, understanding research repositories, and code translation) and their combinations, and rather than addressing each challenge independently, we develop tools that support designing multiple challenges at scale. Second, we implement evaluation mechanisms for multiple research artifacts, including submission files, code, and models, using both precise numeric measures and more flexible LLM-based evaluation approaches. This dual strategy balances objective assessment with contextual judgment. Although our initial focus is on time series applications, our framework can be readily extended to other data modalities, broadly enhancing the comprehensiveness and practical utility of agentic AI evaluation. We open-source our benchmarking framework to facilitate future research on the ML engineering capabilities of AI agents.

Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To address this gap, we introduce SciHorizon-GENE, a large-scale gene-centric benchmark constructed from authoritative biological databases. The benchmark integrates curated knowledge for over 190K human genes and comprises more than 540K questions covering diverse gene-to-function reasoning scenarios relevant to cell type annotation, functional interpretation, and mechanism-oriented analysis. Motivated by behavioral patterns observed in preliminary examinations, SciHorizon-GENE evaluates LLMs along four biologically critical perspectives: research attention sensitivity, hallucination tendency, answer completeness, and literature influence, explicitly targeting failure modes that limit the safe adoption of LLMs in biological interpretation pipelines. We systematically evaluate a wide range of state-of-the-art general-purpose and biomedical LLMs, revealing substantial heterogeneity in gene-level reasoning capabilities and persistent challenges in generating faithful, complete, and literature-grounded functional interpretations. Our benchmark establishes a systematic foundation for analyzing LLM behavior at the gene scale and offers insights for model selection and development, with direct relevance to knowledge-enhanced biological interpretation.

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.

Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development. These methods are evaluated on different SAbDab snapshots, non-overlapping test sets, and incompatible metrics, and the literature fragments the design problem into numerous sub-tasks with no common definition. We introduce Chimera-Bench (CDR Modeling with Epitope-guided Redesign), a unified benchmark built around a single canonical task: epitope-conditioned CDR sequence-structure co-design. Chimera-Bench provides (1) a curated, deduplicated dataset of 2,922 antibody-antigen complexes with epitope and paratope annotations; (2) three biologically motivated splits testing generalization to unseen epitopes, unseen antigen folds, and prospective temporal targets; and (3) a comprehensive evaluation protocol with five metric groups including novel epitope-specificity measures. We benchmark representative methods spanning different generative paradigms and report results across all splits. Chimera-Bench is the largest dataset of its kind for the antibody design problem, allowing the community to develop and test novel methods and evaluate their generalizability. The source code and data are available at: https://github.com/mansoor181/chimera-bench.git

We introduce MLE-bench, a benchmark for measuring how well AI agents perform at machine learning engineering. To this end, we curate 75 ML engineering-related competitions from Kaggle, creating a diverse set of challenging tasks that test real-world ML engineering skills such as training models, preparing datasets, and running experiments. We establish human baselines for each competition using Kaggle's publicly available leaderboards. We use open-source agent scaffolds to evaluate several frontier language models on our benchmark, finding that the best-performing setup--OpenAI's o1-preview with AIDE scaffolding--achieves at least the level of a Kaggle bronze medal in 16.9% of competitions. In addition to our main results, we investigate various forms of resource scaling for AI agents and the impact of contamination from pre-training. We open-source our benchmark code (github.com/openai/mle-bench/) to facilitate future research in understanding the ML engineering capabilities of AI agents.

We introduce a new, highly challenging benchmark and a dataset -- FungiTastic -- based on data continuously collected over a twenty-year span. The dataset originates in fungal records labeled and curated by experts. It consists of about 350k multi-modal observations that include more than 650k photographs from 5k fine-grained categories and diverse accompanying information, e.g., acquisition metadata, satellite images, and body part segmentation. FungiTastic is the only benchmark that includes a test set with partially DNA-sequenced ground truth of unprecedented label reliability. The benchmark is designed to support (i) standard close-set classification, (ii) open-set classification, (iii) multi-modal classification, (iv) few-shot learning, (v) domain shift, and many more. We provide baseline methods tailored for almost all the use-cases. We provide a multitude of ready-to-use pre-trained models on HuggingFace and a framework for model training. A comprehensive documentation describing the dataset features and the baselines are available at https://bohemianvra.github.io/FungiTastic/ and https://www.kaggle.com/datasets/picekl/fungitastic.

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.

Efficient experiment reproduction is critical to accelerating progress in artificial intelligence. However, the inherent complexity of method design and training procedures presents substantial challenges for automation. Notably, reproducing experiments often requires implicit domain-specific knowledge not explicitly documented in the original papers. To address this, we introduce the paper lineage algorithm, which identifies and extracts implicit knowledge from the relevant references cited by the target paper. Building on this idea, we propose AutoReproduce, a multi-agent framework capable of automatically reproducing experiments described in research papers in an end-to-end manner. AutoReproduce enhances code executability by generating unit tests alongside the reproduction process. To evaluate the reproduction capability, we construct ReproduceBench, a benchmark annotated with verified implementations, and introduce novel evaluation metrics to assess both the reproduction and execution fidelity. Experimental results demonstrate that AutoReproduce outperforms the existing strong agent baselines on all five evaluation metrics by a peak margin of over 70%. In particular, compared to the official implementations, AutoReproduce achieves an average performance gap of 22.1% on 89.74% of the executable experiment runs. The code will be available at https://github.com/AI9Stars/AutoReproduce.

Recent advances in video generation have opened new avenues for macroscopic simulation of complex dynamic systems, but their application to microscopic phenomena remains largely unexplored. Microscale simulation holds great promise for biomedical applications such as drug discovery, organ-on-chip systems, and disease mechanism studies, while also showing potential in education and interactive visualization. In this work, we introduce MicroWorldBench, a multi-level rubric-based benchmark for microscale simulation tasks. MicroWorldBench enables systematic, rubric-based evaluation through 459 unique expert-annotated criteria spanning multiple microscale simulation task (e.g., organ-level processes, cellular dynamics, and subcellular molecular interactions) and evaluation dimensions (e.g., scientific fidelity, visual quality, instruction following). MicroWorldBench reveals that current SOTA video generation models fail in microscale simulation, showing violations of physical laws, temporal inconsistency, and misalignment with expert criteria. To address these limitations, we construct MicroSim-10K, a high-quality, expert-verified simulation dataset. Leveraging this dataset, we train MicroVerse, a video generation model tailored for microscale simulation. MicroVerse can accurately reproduce complex microscale mechanism. Our work first introduce the concept of Micro-World Simulation and present a proof of concept, paving the way for applications in biology, education, and scientific visualization. Our work demonstrates the potential of educational microscale simulations of biological mechanisms. Our data and code are publicly available at https://github.com/FreedomIntelligence/MicroVerse

With the growing popularity of deep learning and foundation models for tabular data, the need for standardized and reliable benchmarks is higher than ever. However, current benchmarks are static. Their design is not updated even if flaws are discovered, model versions are updated, or new models are released. To address this, we introduce TabArena, the first continuously maintained living tabular benchmarking system. To launch TabArena, we manually curate a representative collection of datasets and well-implemented models, conduct a large-scale benchmarking study to initialize a public leaderboard, and assemble a team of experienced maintainers. Our results highlight the influence of validation method and ensembling of hyperparameter configurations to benchmark models at their full potential. While gradient-boosted trees are still strong contenders on practical tabular datasets, we observe that deep learning methods have caught up under larger time budgets with ensembling. At the same time, foundation models excel on smaller datasets. Finally, we show that ensembles across models advance the state-of-the-art in tabular machine learning and investigate the contributions of individual models. We launch TabArena with a public leaderboard, reproducible code, and maintenance protocols to create a living benchmark available at https://tabarena.ai.

Systematic literature reviews are essential for synthesizing scientific evidence but are costly, difficult to scale and time-intensive, creating bottlenecks for evidence-based policy. We study whether large language models can automate the complete systematic review workflow, from article retrieval, article screening, data extraction to report synthesis. Applied to epidemiological reviews of nine WHO-designated priority pathogens and validated against expert-curated ground truth, our open-source agentic pipeline (AgentSLR) achieves performance comparable to human researchers while reducing review time from approximately 7 weeks to 20 hours (a 58x speed-up). Our comparison of five frontier models reveals that performance on SLR is driven less by model size or inference cost than by each model's distinctive capabilities. Through human-in-the-loop validation, we identify key failure modes. Our results demonstrate that agentic AI can substantially accelerate scientific evidence synthesis in specialised domains.

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.

Large language models (LLMs) are increasingly applied to scientific research, yet prevailing science benchmarks probe decontextualized knowledge and overlook the iterative reasoning, hypothesis generation, and observation interpretation that drive scientific discovery. We introduce a scenario-grounded benchmark that evaluates LLMs across biology, chemistry, materials, and physics, where domain experts define research projects of genuine interest and decompose them into modular research scenarios from which vetted questions are sampled. The framework assesses models at two levels: (i) question-level accuracy on scenario-tied items and (ii) project-level performance, where models must propose testable hypotheses, design simulations or experiments, and interpret results. Applying this two-phase scientific discovery evaluation (SDE) framework to state-of-the-art LLMs reveals a consistent performance gap relative to general science benchmarks, diminishing return of scaling up model sizes and reasoning, and systematic weaknesses shared across top-tier models from different providers. Large performance variation in research scenarios leads to changing choices of the best performing model on scientific discovery projects evaluated, suggesting all current LLMs are distant to general scientific "superintelligence". Nevertheless, LLMs already demonstrate promise in a great variety of scientific discovery projects, including cases where constituent scenario scores are low, highlighting the role of guided exploration and serendipity in discovery. This SDE framework offers a reproducible benchmark for discovery-relevant evaluation of LLMs and charts practical paths to advance their development toward scientific discovery.

The rapid advancement of Large Language Models (LLMs) necessitates robust evaluation methodologies. Current benchmarking approaches often rely on comparing model outputs against predefined prompts and reference outputs. Relying on predefined reference outputs hinders flexible adaptation of benchmarks to the rapidly evolving capabilities of LLMs. This limitation necessitates periodic efforts to prepare new benchmarks. To keep pace with rapidly evolving LLM capabilities, we propose a more flexible benchmarking approach. Our method, \textbf{Varco Arena}, provides reference-free benchmarking of LLMs in tournament style. \textbf{Varco Arena} directly compares LLM outputs across a diverse set of prompts, determining model rankings through a single-elimination tournament structure. This direct pairwise comparison offers two key advantages: (1) Direct comparison, unmediated by reference text, more effectively orders competing LLMs, resulting in more reliable rankings, and (2) reference-free approach to benchmarking adds flexibility in updating benchmark prompts by eliminating the need for quality references. Our empirical results, supported by simulation experiments, demonstrate that the \textbf{Varco Arena} tournament approach aligns better with the current Elo model for benchmarking LLMs. The alignment is measured in terms of Spearman correlation, showing improvement over current practice of benchmarking that use reference outputs as comparison anchors.

We introduce CheeseBench, a benchmark that evaluates large language models (LLMs) on nine classical behavioral neuroscience paradigms (Morris water maze, Barnes maze, T-maze, radial arm maze, star maze, operant chamber, shuttle box, conditioned place preference, and delayed non-match to sample), spanning six cognitive dimensions. Each task is grounded in peer-reviewed rodent protocols with approximate animal baselines. The agent receives a unified system prompt with no task-specific instructions and must discover goals purely from ASCII text observations and reward signals, much like a rodent placed into an unfamiliar apparatus. We evaluate six open-weight LLMs (3B to 72B parameters) on text-based ASCII renderings and compare against both a random baseline and a graph-based reinforcement learning agent. Our best model (Qwen2.5-VL-7B) reaches 52.6% average success on ASCII input, compared to 32.1% for random agents and 78.9% for approximate rodent baselines. We find that (1) scaling beyond 7B yields diminishing returns, (2) longer context history degrades performance, (3) chain-of-thought prompting hurts rather than helps, and (4) a vision-language architecture provides an advantage at 7B but hurts at 32B. Because the same model's performance ranges from 20% to 57% depending on interface parameters alone, these results characterize the agent-plus-interface system, not the model in isolation. Under this unified zero-shot ASCII protocol, current open-weight LLM agents remain well below approximate rodent reference values, particularly on tasks requiring spatial navigation and within-trial state tracking.

Model-learning agents should gather information to learn world models that support many downstream tasks and inferences, such as predicting unobserved states, estimating near- and far-term consequences of actions, planning action sequences, and detecting changes in dynamics. Current methods for learning and evaluating world models diverge from this goal: training and evaluation are anchored to next-frame prediction, and success is scored by reward maximization in the same environment. We propose WorldTest, a protocol to evaluate model-learning agents that separates reward-free interaction from a scored test phase in a different but related environment. WorldTest is open-endedx2014models should support many different tasks unknown ahead of timex2014and agnostic to model representation, allowing comparison across approaches. We instantiated WorldTest with AutumnBench, a suite of 43 interactive grid-world environments and 129 tasks across three families: masked-frame prediction, planning, and predicting changes to the causal dynamics. We compared 517 human participants and three frontier models on AutumnBench. We found that humans outperform the models, and scaling compute improves performance only in some environments but not others. WorldTest provides a novel templatex2014reward-free exploration, derived tests, and behavior-based scoringx2014to evaluate what agents learn about environment dynamics, and AutumnBench exposes significant headroom in world-model learning.

Due to the high computational demands executing a rigorous comparison between hyperparameter optimization (HPO) methods is often cumbersome. The goal of this paper is to facilitate a better empirical evaluation of HPO methods by providing benchmarks that are cheap to evaluate, but still represent realistic use cases. We believe these benchmarks provide an easy and efficient way to conduct reproducible experiments for neural hyperparameter search. Our benchmarks consist of a large grid of configurations of a feed forward neural network on four different regression datasets including architectural hyperparameters and hyperparameters concerning the training pipeline. Based on this data, we performed an in-depth analysis to gain a better understanding of the properties of the optimization problem, as well as of the importance of different types of hyperparameters. Second, we exhaustively compared various different state-of-the-art methods from the hyperparameter optimization literature on these benchmarks in terms of performance and robustness.

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

Composer 2 is a specialized model designed for agentic software engineering. The model demonstrates strong long-term planning and coding intelligence while maintaining the ability to efficiently solve problems for interactive use. The model is trained in two phases: first, continued pretraining to improve the model's knowledge and latent coding ability, followed by large-scale reinforcement learning to improve end-to-end coding performance through stronger reasoning, accurate multi-step execution, and coherence on long-horizon realistic coding problems. We develop infrastructure to support training in the same Cursor harness that is used by the deployed model, with equivalent tools and structure, and use environments that match real problems closely. To measure the ability of the model on increasingly difficult tasks, we introduce a benchmark derived from real software engineering problems in large codebases including our own. Composer 2 is a frontier-level coding model and demonstrates a process for training strong domain-specialized models. On our CursorBench evaluations the model achieves a major improvement in accuracy compared to previous Composer models (61.3). On public benchmarks the model scores 61.7 on Terminal-Bench and 73.7 on SWE-bench Multilingual in our harness, comparable to state-of-the-art systems.

Large Language Models (LLMs) based autonomous agents demonstrate multifaceted capabilities to contribute substantially to economic production. However, existing benchmarks remain focused on single agentic capability, failing to capture long-horizon real-world scenarios. Moreover, the reliance on human-in-the-loop feedback for realistic tasks creates a scalability bottleneck, hindering automated rollout collection and evaluation. To bridge this gap, we introduce AgencyBench, a comprehensive benchmark derived from daily AI usage, evaluating 6 core agentic capabilities across 32 real-world scenarios, comprising 138 tasks with specific queries, deliverables, and rubrics. These scenarios require an average of 90 tool calls, 1 million tokens, and hours of execution time to resolve. To enable automated evaluation, we employ a user simulation agent to provide iterative feedback, and a Docker sandbox to conduct visual and functional rubric-based assessment. Experiments reveal that closed-source models significantly outperform open-source models (48.4% vs 32.1%). Further analysis reveals significant disparities across models in resource efficiency, feedback-driven self-correction, and specific tool-use preferences. Finally, we investigate the impact of agentic scaffolds, observing that proprietary models demonstrate superior performance within their native ecosystems (e.g., Claude-4.5-Opus via Claude-Agent-SDK), while open-source models exhibit distinct performance peaks, suggesting potential optimization for specific execution frameworks. AgencyBench serves as a critical testbed for next-generation agents, highlighting the necessity of co-optimizing model architecture with agentic frameworks. We believe this work sheds light on the future direction of autonomous agents, and we release the full benchmark and evaluation toolkit at https://github.com/GAIR-NLP/AgencyBench.

The BrowserGym ecosystem addresses the growing need for efficient evaluation and benchmarking of web agents, particularly those leveraging automation and Large Language Models (LLMs) for web interaction tasks. Many existing benchmarks suffer from fragmentation and inconsistent evaluation methodologies, making it challenging to achieve reliable comparisons and reproducible results. BrowserGym aims to solve this by providing a unified, gym-like environment with well-defined observation and action spaces, facilitating standardized evaluation across diverse benchmarks. Combined with AgentLab, a complementary framework that aids in agent creation, testing, and analysis, BrowserGym offers flexibility for integrating new benchmarks while ensuring consistent evaluation and comprehensive experiment management. This standardized approach seeks to reduce the time and complexity of developing web agents, supporting more reliable comparisons and facilitating in-depth analysis of agent behaviors, and could result in more adaptable, capable agents, ultimately accelerating innovation in LLM-driven automation. As a supporting evidence, we conduct the first large-scale, multi-benchmark web agent experiment and compare the performance of 6 state-of-the-art LLMs across all benchmarks currently available in BrowserGym. Among other findings, our results highlight a large discrepancy between OpenAI and Anthropic's latests models, with Claude-3.5-Sonnet leading the way on almost all benchmarks, except on vision-related tasks where GPT-4o is superior. Despite these advancements, our results emphasize that building robust and efficient web agents remains a significant challenge, due to the inherent complexity of real-world web environments and the limitations of current models.

We present HealthBench, an open-source benchmark measuring the performance and safety of large language models in healthcare. HealthBench consists of 5,000 multi-turn conversations between a model and an individual user or healthcare professional. Responses are evaluated using conversation-specific rubrics created by 262 physicians. Unlike previous multiple-choice or short-answer benchmarks, HealthBench enables realistic, open-ended evaluation through 48,562 unique rubric criteria spanning several health contexts (e.g., emergencies, transforming clinical data, global health) and behavioral dimensions (e.g., accuracy, instruction following, communication). HealthBench performance over the last two years reflects steady initial progress (compare GPT-3.5 Turbo's 16% to GPT-4o's 32%) and more rapid recent improvements (o3 scores 60%). Smaller models have especially improved: GPT-4.1 nano outperforms GPT-4o and is 25 times cheaper. We additionally release two HealthBench variations: HealthBench Consensus, which includes 34 particularly important dimensions of model behavior validated via physician consensus, and HealthBench Hard, where the current top score is 32%. We hope that HealthBench grounds progress towards model development and applications that benefit human health.

Artificial intelligence systems for scientific discovery have demonstrated remarkable potential, yet existing approaches remain largely proprietary and operate in batch-processing modes requiring hours per research cycle, precluding real-time researcher guidance. This paper introduces Deep Research, a multi-agent system enabling interactive scientific investigation with turnaround times measured in minutes. The architecture comprises specialized agents for planning, data analysis, literature search, and novelty detection, unified through a persistent world state that maintains context across iterative research cycles. Two operational modes support different workflows: semi-autonomous mode with selective human checkpoints, and fully autonomous mode for extended investigations. Evaluation on the BixBench computational biology benchmark demonstrated state-of-the-art performance, achieving 48.8% accuracy on open response and 64.4% on multiple-choice evaluation, exceeding existing baselines by 14 to 26 percentage points. Analysis of architectural constraints, including open access literature limitations and challenges inherent to automated novelty assessment, informs practical deployment considerations for AI-assisted scientific workflows.

Large language models are emerging as scientific assistants, but evaluating their ability to reason from empirical data remains challenging. Benchmarks derived from published studies and human annotations inherit publication bias, known-knowledge bias, label noise, and substantial storage requirements. We present InfiniteScienceGym, a procedurally generated benchmark of scientific repositories paired with a verifiable question-answering task. From a seed, the simulator deterministically generates a self-contained repository with realistic directory structure, files, and tabular data, and a privileged QA generator produces both answerable and unanswerable questions with exact ground truth. This makes it possible to evaluate evidence-grounded reasoning, abstention, and tool-mediated analysis in a controlled setting without distributing a large static corpus. InfiniteScienceGym complements real scientific benchmarks by targeting blind spots and failure modes that are hard to evaluate using published datasets alone. Evaluating both proprietary and open-weight models, we find that none achieve more than 45% accuracy overall, that recognizing unanswerable questions remains a major weakness, and that stronger models tend to use tools more effectively rather than simply consuming more tokens.

Rigorous and reproducible evaluation is critical for assessing the state of the art and for guiding scientific advances in Artificial Intelligence. Evaluation is challenging in practice due to several reasons, including benchmark saturation, lack of transparency in methods used for measurement, development challenges in extracting measurements for generative tasks, and, more generally, the extensive number of capabilities required for a well-rounded comparison across models. We make three contributions to alleviate the above challenges. First, we present Eureka, an open-source framework for standardizing evaluations of large foundation models beyond single-score reporting and rankings. Second, we introduce Eureka-Bench as an extensible collection of benchmarks testing capabilities that (i) are still challenging for state-of-the-art models and (ii) represent fundamental but overlooked language and multimodal capabilities. The inherent space for improvement in non-saturated benchmarks enables us to discover meaningful differences between models at a capability level. Third, using Eureka, we conduct an analysis of 12 state-of-the-art models, providing in-depth insights into failure understanding and model comparison, which can be leveraged to plan targeted improvements. In contrast to recent trends in reports and leaderboards showing absolute rankings and claims for one model or another to be the best, our analysis shows that there is no such best model. Different models have different strengths, but there are models that appear more often than others as best performers for some capabilities. Despite the recent improvements, current models still struggle with several fundamental capabilities including detailed image understanding, benefiting from multimodal input when available rather than fully relying on language, factuality and grounding for information retrieval, and over refusals.

Recent studies operationalize self-improvement through coding agents that edit their own codebases. They grow a tree of self-modifications through expansion strategies that favor higher software engineering benchmark performance, assuming that this implies more promising subsequent self-modifications. However, we identify a mismatch between the agent's self-improvement potential (metaproductivity) and its coding benchmark performance, namely the Metaproductivity-Performance Mismatch. Inspired by Huxley's concept of clade, we propose a metric (CMP) that aggregates the benchmark performances of the descendants of an agent as an indicator of its potential for self-improvement. We show that, in our self-improving coding agent development setting, access to the true CMP is sufficient to simulate how the G\"odel Machine would behave under certain assumptions. We introduce the Huxley-G\"odel Machine (HGM), which, by estimating CMP and using it as guidance, searches the tree of self-modifications. On SWE-bench Verified and Polyglot, HGM outperforms prior self-improving coding agent development methods while using less wall-clock time. Last but not least, HGM demonstrates strong transfer to other coding datasets and large language models. The agent optimized by HGM on SWE-bench Verified with GPT-5-mini and evaluated on SWE-bench Lite with GPT-5 achieves human-level performance, matching the best officially checked results of human-engineered coding agents. Our code is available at https://github.com/metauto-ai/HGM.

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse DNA elements, potentially enabling various genomic prediction, interpretation and design tasks. Despite their potential, existing benchmarks do not adequately assess the capabilities of DNALMs on key downstream applications involving an important class of non-coding DNA elements critical for regulating gene activity. In this study, we introduce DART-Eval, a suite of representative benchmarks specifically focused on regulatory DNA to evaluate model performance across zero-shot, probed, and fine-tuned scenarios against contemporary ab initio models as baselines. Our benchmarks target biologically meaningful downstream tasks such as functional sequence feature discovery, predicting cell-type specific regulatory activity, and counterfactual prediction of the impacts of genetic variants. We find that current DNALMs exhibit inconsistent performance and do not offer compelling gains over alternative baseline models for most tasks, while requiring significantly more computational resources. We discuss potentially promising modeling, data curation, and evaluation strategies for the next generation of DNALMs. Our code is available at https://github.com/kundajelab/DART-Eval.

Large language models are increasingly being used to assess and forecast research ideas, yet we lack scalable ways to evaluate the quality of models' judgments about these scientific ideas. Towards this goal, we introduce PoT, a semi-verifiable benchmarking framework that links scientific idea judgments to downstream signals that become observable later (e.g., citations and shifts in researchers' agendas). PoT freezes a pre-cutoff snapshot of evidence in an offline sandbox and asks models to forecast post-cutoff outcomes, enabling verifiable evaluation when ground truth arrives, scalable benchmarking without exhaustive expert annotation, and analysis of human-model misalignment against signals such as peer-review awards. In addition, PoT provides a controlled testbed for agent-based research judgments that evaluate scientific ideas, comparing tool-using agents to non-agent baselines under prompt ablations and budget scaling. Across 30,000+ instances spanning four benchmark domains, we find that, compared with non-agent baselines, higher interaction budgets generally improve agent performance, while the benefit of tool use is strongly task-dependent. By combining time-partitioned, future-verifiable targets with an offline sandbox for tool use, PoT supports scalable evaluation of agents on future-facing scientific idea judgment tasks.

Automatic evaluation benchmarks such as MT-Bench, Arena-Hard, and Auto-Arena are seeing growing adoption for the evaluation of Large Language Models (LLMs). Existing research has primarily focused on approximating human-based model rankings using limited data and LLM-as-a-Judge. However, the fundamental premise of these studies, which attempts to replicate human rankings, is flawed. Specifically, these benchmarks typically offer only overall scores, limiting their utility to leaderboard rankings, rather than providing feedback that can guide model optimization and support model profiling. Therefore, we advocate for an evaluation paradigm shift from approximating human-based model rankings to providing feedback with analytical value. To this end, we introduce Feedbacker, an evaluation framework that provides comprehensive and fine-grained results, thereby enabling thorough identification of a model's specific strengths and weaknesses. Such feedback not only supports the targeted optimization of the model but also enhances the understanding of its behavior. Feedbacker comprises three key components: an extensible tree-based query taxonomy builder, an automated query synthesis scheme, and a suite of visualization and analysis tools. Furthermore, we propose a novel LLM-as-a-Judge method: PC2 (Pre-Comparison-derived Criteria) pointwise evaluation. This method derives evaluation criteria by pre-comparing the differences between several auxiliary responses, achieving the accuracy of pairwise evaluation while maintaining the time complexity of pointwise evaluation. Finally, leveraging the evaluation results of 17 mainstream LLMs, we demonstrate the usage of Feedbacker and highlight its effectiveness and potential. Our homepage project is available at https://liudan193.github.io/Feedbacker.

Generative world models are increasingly used for video generation, where learned simulators are expected to capture the physical rules that govern real-world dynamics. However, evaluating whether generated videos actually follow these rules remains challenging. Existing physics-focused video benchmarks have made important progress, but they still face three key challenges, including the coarse evaluation frameworks that hide law-specific failures, response biases and fatigue that undermine the validity of annotation judgments, and automated evaluators that are insufficiently physics-aware or difficult to audit. To address those challenges, we introduce PhyGround, a criteria-grounded benchmark for evaluating physical reasoning in video generation. The benchmark contains 250 curated prompts, each augmented with an expected physical outcome, and a taxonomy of 13 physical laws across solid-body mechanics, fluid dynamics, and optics. Each law is operationalized through observable sub-questions to enable per-law diagnostics. We evaluate eight modern video generation models through a large-scale, quality-controlled human study, grounded on social science lab experiment design. A total of 459 annotators provided 5,796 complete annotations and over 37.4K fine-grained labels; after quality control, the retained annotations exhibited high split-half model-ranking correlations (Spearman's rho > 0.90). To support reproducible automated evaluation, we release PhyJudge-9B, an open physics-specialized VLM judge. PhyJudge-9B achieves substantially lower aggregate relative bias than Gemini-3.1-Pro (3.3% vs. 16.6%). We release prompts, human annotations, model checkpoints, and evaluation code on the project page https://phyground.github.io/.

High-quality benchmarks are the foundation for embodied AI research, enabling significant advancements in long-horizon navigation, manipulation and rearrangement tasks. However, as frontier tasks in robotics get more advanced, they require faster simulation speed, more intricate test environments, and larger demonstration datasets. To this end, we present MS-HAB, a holistic benchmark for low-level manipulation and in-home object rearrangement. First, we provide a GPU-accelerated implementation of the Home Assistant Benchmark (HAB). We support realistic low-level control and achieve over 3x the speed of previous magical grasp implementations at similar GPU memory usage. Second, we train extensive reinforcement learning (RL) and imitation learning (IL) baselines for future work to compare against. Finally, we develop a rule-based trajectory filtering system to sample specific demonstrations from our RL policies which match predefined criteria for robot behavior and safety. Combining demonstration filtering with our fast environments enables efficient, controlled data generation at scale.

LLM agents hold significant promise for advancing scientific research. To accelerate this progress, we introduce AIRS-Bench (the AI Research Science Benchmark), a suite of 20 tasks sourced from state-of-the-art machine learning papers. These tasks span diverse domains, including language modeling, mathematics, bioinformatics, and time series forecasting. AIRS-Bench tasks assess agentic capabilities over the full research lifecycle -- including idea generation, experiment analysis and iterative refinement -- without providing baseline code. The AIRS-Bench task format is versatile, enabling easy integration of new tasks and rigorous comparison across different agentic frameworks. We establish baselines using frontier models paired with both sequential and parallel scaffolds. Our results show that agents exceed human SOTA in four tasks but fail to match it in sixteen others. Even when agents surpass human benchmarks, they do not reach the theoretical performance ceiling for the underlying tasks. These findings indicate that AIRS-Bench is far from saturated and offers substantial room for improvement. We open-source the AIRS-Bench task definitions and evaluation code to catalyze further development in autonomous scientific research.

With the advent of highly capable instruction-tuned neural language models, benchmarking in natural language processing (NLP) is increasingly shifting towards pairwise comparison leaderboards, such as LMSYS Arena, from traditional global pointwise scores (e.g., GLUE, BIG-bench, SWE-bench). This paper empirically investigates the strengths and weaknesses of both global scores and pairwise comparisons to aid decision-making in selecting appropriate model evaluation strategies. Through computational experiments on synthetic and real-world datasets using standard global metrics and the popular Bradley-Terry model for pairwise comparisons, we found that while global scores provide more reliable overall rankings, they can underestimate strong models with rare, significant errors or low confidence. Conversely, pairwise comparisons are particularly effective for identifying strong contenders among models with lower global scores, especially where quality metrics are hard to define (e.g., text generation), though they require more comparisons to converge if ties are frequent. Our code and data are available at https://github.com/HSPyroblast/srw-ranking under a permissive license.

Large language models (LLMs) have recently achieved remarkable results in complex multi-step tasks, such as mathematical reasoning and agentic software engineering. However, they often struggle to maintain consistent performance across multiple solution attempts. One effective approach to narrow the gap between average-case and best-case performance is guided test-time search, which explores multiple solution paths to identify the most promising one. Unfortunately, effective search techniques (e.g. MCTS) are often unsuitable for non-serializable RL environments, such as Docker containers, where intermediate environment states cannot be easily saved and restored. We investigate two complementary search strategies applicable to such environments: 1-step lookahead and trajectory selection, both guided by a learned action-value function estimator. On the SWE-bench Verified benchmark, a key testbed for agentic software engineering, we find these methods to double the average success rate of a fine-tuned Qwen-72B model, achieving 40.8%, the new state-of-the-art for open-weights models. Additionally, we show that these techniques are transferable to more advanced closed models, yielding similar improvements with GPT-4o.

Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

The rapid advancement of large language models (LLMs) and multimodal foundation models has sparked growing interest in their potential for scientific research. However, scientific intelligence encompasses a broad spectrum of abilities ranging from understanding fundamental knowledge to conducting creative discovery, and existing benchmarks remain fragmented. Most focus on narrow tasks and fail to reflect the hierarchical and multi-disciplinary nature of real scientific inquiry. We introduce HiSciBench, a hierarchical benchmark designed to evaluate foundation models across five levels that mirror the complete scientific workflow: Scientific Literacy (L1), Literature Parsing (L2), Literature-based Question Answering (L3), Literature Review Generation (L4), and Scientific Discovery (L5). HiSciBench contains 8,735 carefully curated instances spanning six major scientific disciplines, including mathematics, physics, chemistry, biology, geography, and astronomy, and supports multimodal inputs including text, equations, figures, and tables, as well as cross-lingual evaluation. Unlike prior benchmarks that assess isolated abilities, HiSciBench provides an integrated, dependency-aware framework that enables detailed diagnosis of model capabilities across different stages of scientific reasoning. Comprehensive evaluations of leading models, including GPT-5, DeepSeek-R1, and several multimodal systems, reveal substantial performance gaps: while models achieve up to 69\% accuracy on basic literacy tasks, performance declines sharply to 25\% on discovery-level challenges. HiSciBench establishes a new standard for evaluating scientific Intelligence and offers actionable insights for developing models that are not only more capable but also more reliable. The benchmark will be publicly released to facilitate future research.

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.

In this report, we present ML-Dev-Bench, a benchmark aimed at testing agentic capabilities on applied Machine Learning development tasks. While existing benchmarks focus on isolated coding tasks or Kaggle-style competitions, ML-Dev-Bench tests agents' ability to handle the full complexity of ML development workflows. The benchmark assesses performance across critical aspects including dataset handling, model training, improving existing models, debugging, and API integration with popular ML tools. We evaluate three agents - ReAct, Openhands, and AIDE - on a diverse set of 30 tasks, providing insights into their strengths and limitations in handling practical ML development challenges. We open source the benchmark for the benefit of the community at https://github.com/ml-dev-bench/ml-dev-bench{https://github.com/ml-dev-bench/ml-dev-bench}.

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.

We present a new reproducible benchmark for evaluating robot manipulation in the real world, specifically focusing on pick-and-place. Our benchmark uses the YCB objects, a commonly used dataset in the robotics community, to ensure that our results are comparable to other studies. Additionally, the benchmark is designed to be easily reproducible in the real world, making it accessible to researchers and practitioners. We also provide our experimental results and analyzes for model-based and model-free 6D robotic grasping on the benchmark, where representative algorithms are evaluated for object perception, grasping planning, and motion planning. We believe that our benchmark will be a valuable tool for advancing the field of robot manipulation. By providing a standardized evaluation framework, researchers can more easily compare different techniques and algorithms, leading to faster progress in developing robot manipulation methods.

We introduce the first version of KWBench (Knowledge Work Bench), a benchmark for unprompted problem recognition in large language models: can an LLM identify a professional scenario before attempting to solve it. Existing frontier benchmarks have saturated, and most knowledge-work evaluations to date reduce to extraction or task completion against a specification. KWBench targets the step before that: recognizing the governing structure of the situation from raw inputs alone. The benchmark contains 223 tasks sourced from practitioners across acquisitions, contract negotiations, clinical pharmacy, organizational politics, fraud analysis, and incentive design. Each task encodes a formal game-theoretic pattern (principal-agent conflict, signaling, mechanism design failure, strategic omission, coalitional dynamics, strategic interdependence) and carries structured ground truth recording the expert reading of the situation and the anticipated failure modes. Models receive raw data and a task prompt with no indication of problem type. Scoring is a three-tier rubric gated by a mandatory conjunctive check. Mandatory criteria encode the predicted wrong paths. We evaluate 16 models. The best model passes on 27.9% of tasks. The top two models agree on only 31.7% of their passes. Among the top 8, 44 tasks are solved by exactly one model; routing across the top 8 covers 50.7% of the benchmark, nearly double the best single model. Conditional on passing, quality scores converge (approx 83% across models); unconditional scores do not. Same models articulate the relevant game-theoretic concept correctly when asked, then fail to apply it unprompted. We release KWBench to shift how frontier models are evaluated on knowledge work, scoring them on whether they recognize the right problem from the situation alone, not only on how well they execute once the problem has been framed for them.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

AI agents powered by large language models exhibit strong reasoning and problem-solving capabilities, enabling them to assist scientific research tasks such as formula derivation and code generation. However, whether these agents can reliably perform end-to-end reproduction from real scientific papers remains an open question. We introduce PRBench, a benchmark of 30 expert-curated tasks spanning 11 subfields of physics. Each task requires an agent to comprehend the methodology of a published paper, implement the corresponding algorithms from scratch, and produce quantitative results matching the original publication. Agents are provided only with the task instruction and paper content, and operate in a sandboxed execution environment. All tasks are contributed by domain experts from over 20 research groups at the School of Physics, Peking University, each grounded in a real published paper and validated through end-to-end reproduction with verified ground-truth results and detailed scoring rubrics. Using an agentified assessment pipeline, we evaluate a set of coding agents on PRBench and analyze their capabilities across key dimensions of scientific reasoning and execution. The best-performing agent, OpenAI Codex powered by GPT-5.3-Codex, achieves a mean overall score of 34%. All agents exhibit a zero end-to-end callback success rate, with particularly poor performance in data accuracy and code correctness. We further identify systematic failure modes, including errors in formula implementation, inability to debug numerical simulations, and fabrication of output data. Overall, PRBench provides a rigorous benchmark for evaluating progress toward autonomous scientific research.

Thousands of diverse benchmarks have been developed to measure the quality of large language models (LLMs). Yet prior work has demonstrated that LLM performance is often sufficiently explained by a small set of latent factors, or abilities. This suggests the potential for more efficient and principled benchmarking, but it remains difficult to compare the quality of different methods. Motivated by predictive validity, we argue that the quality of a benchmarking framework should be grounded in how efficiently it enables the prediction of model performance on unseen tasks. To analyze this objective, we collect the "Wide-scale Item Level Dataset" (WILD), a dataset of item-model response pairs, comprising evaluations of 65 models on 109,564 unique items spanning 163 tasks drawn from 27 datasets. This dataset enables the first analysis of how different techniques can predict a model's performance on a large, diverse collection of unseen tasks under different budget constraints. We demonstrate that combining a modified multidimensional item response theory (IRT) model with adaptive item selection driven by optimal experimental design can predict performance on 112 held-out benchmark tasks with a mean absolute error (MAE) of less than 7%, and can do so after observing only 16 items. We further demonstrate that incorporating cost-aware discount factors into our selection criteria can reduce the total tokens needed to reach 7% MAE from 141,000 tokens to only 22,000, an 85% reduction in evaluation cost.

We present DM-Bench, the first benchmark designed to evaluate large language model (LLM) performance across real-world decision-making tasks faced by individuals managing diabetes in their daily lives. Unlike prior health benchmarks that are either generic, clinician-facing or focused on clinical tasks (e.g., diagnosis, triage), DM-Bench introduces a comprehensive evaluation framework tailored to the unique challenges of prototyping patient-facing AI solutions in diabetes, glucose management, metabolic health and related domains. Our benchmark encompasses 7 distinct task categories, reflecting the breadth of real-world questions individuals with diabetes ask, including basic glucose interpretation, educational queries, behavioral associations, advanced decision making and long term planning. Towards this end, we compile a rich dataset comprising one month of time-series data encompassing glucose traces and metrics from continuous glucose monitors (CGMs) and behavioral logs (e.g., eating and activity patterns) from 15,000 individuals across three different diabetes populations (type 1, type 2, pre-diabetes/general health and wellness). Using this data, we generate a total of 360,600 personalized, contextual questions across the 7 tasks. We evaluate model performance on these tasks across 5 metrics: accuracy, groundedness, safety, clarity and actionability. Our analysis of 8 recent LLMs reveals substantial variability across tasks and metrics; no single model consistently outperforms others across all dimensions. By establishing this benchmark, we aim to advance the reliability, safety, effectiveness and practical utility of AI solutions in diabetes care.

Predicting the evolution of complex physical systems remains a central problem in science and engineering. Despite rapid progress in scientific Machine Learning (ML) models, a critical bottleneck is the lack of expensive real-world data, resulting in most current models being trained and validated on simulated data. Beyond limiting the development and evaluation of scientific ML, this gap also hinders research into essential tasks such as sim-to-real transfer. We introduce RealPDEBench, the first benchmark for scientific ML that integrates real-world measurements with paired numerical simulations. RealPDEBench consists of five datasets, three tasks, eight metrics, and ten baselines. We first present five real-world measured datasets with paired simulated datasets across different complex physical systems. We further define three tasks, which allow comparisons between real-world and simulated data, and facilitate the development of methods to bridge the two. Moreover, we design eight evaluation metrics, spanning data-oriented and physics-oriented metrics, and finally benchmark ten representative baselines, including state-of-the-art models, pretrained PDE foundation models, and a traditional method. Experiments reveal significant discrepancies between simulated and real-world data, while showing that pretraining with simulated data consistently improves both accuracy and convergence. In this work, we hope to provide insights from real-world data, advancing scientific ML toward bridging the sim-to-real gap and real-world deployment. Our benchmark, datasets, and instructions are available at https://realpdebench.github.io/.

AI agents may soon become capable of autonomously completing valuable, long-horizon tasks in diverse domains. Current benchmarks either do not measure real-world tasks, or are not sufficiently difficult to meaningfully measure frontier models. To this end, we present Terminal-Bench 2.0: a carefully curated hard benchmark composed of 89 tasks in computer terminal environments inspired by problems from real workflows. Each task features a unique environment, human-written solution, and comprehensive tests for verification. We show that frontier models and agents score less than 65\% on the benchmark and conduct an error analysis to identify areas for model and agent improvement. We publish the dataset and evaluation harness to assist developers and researchers in future work at https://www.tbench.ai/ .

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.

Foundation models (FMs) are transforming computational pathology by offering new ways to analyze histopathology images. However, FMs typically require weeks of training on large databases, making their creation a resource-intensive process. In this paper, we present a training for foundation models from whole slide images using supervised, end-to-end, multitask learning on slide-level labels. Notably, it is the first model to incorporate cancer subtyping, risk estimation, and genetic mutation prediction into one model. The presented model outperforms self-supervised models on seven benchmark tasks while the training only required 5% of the computational resources. The results not only show that supervised training can outperform self-supervision with less data, but also offer a solution to annotation problems, as patient-based labels are widely available through routine clinical processes. Furthermore, an attention module provides a layer of explainability across different tasks and serves as a tumor detector for unseen cancer types. To address the issue of closed-source datasets, the model was fully trained on openly available data. The code and model weights are made available under https://github.com/FraunhoferMEVIS/MedicalMultitaskModeling.

Evaluating the scientific discovery capabilities of large language model based agents, particularly how they cope with varying environmental complexity and utilize prior knowledge, requires specialized benchmarks currently lacking in the landscape. To address this gap, we introduce PhysGym, a novel benchmark suite and simulation platform for rigorously assessing LLM-based scientific reasoning in interactive physics environments. PhysGym's primary contribution lies in its sophisticated control over the level of prior knowledge provided to the agent. This allows researchers to dissect agent performance along axes including the complexity of the problem and the prior knowledge levels. The benchmark comprises a suite of interactive simulations, where agents must actively probe environments, gather data sequentially under constraints and formulate hypotheses about underlying physical laws. PhysGym provides standardized evaluation protocols and metrics for assessing hypothesis accuracy and model fidelity. We demonstrate the benchmark's utility by presenting results from baseline LLMs, showcasing its ability to differentiate capabilities based on varying priors and task complexity.

Existing evaluation of large language model (LLM) agents on scientific discovery lacks objective baselines and metrics to assess the viability of their proposed methods. To address this issue, we introduce MLRC-Bench, a benchmark designed to quantify how effectively language agents can tackle challenging Machine Learning (ML) Research Competitions. Our benchmark highlights open research problems that demand novel methodologies, in contrast to recent benchmarks such as OpenAI's MLE-Bench (Chan et al., 2024) and METR's RE-Bench (Wijk et al., 2024), which focus on well-established research tasks that are largely solvable through sufficient engineering effort. Unlike prior work, e.g., AI Scientist (Lu et al., 2024b), which evaluates the end-to-end agentic pipeline by using LLM-as-a-judge, MLRC-Bench measures the key steps of proposing and implementing novel research methods and evaluates them with newly proposed rigorous protocol and objective metrics. Our curated suite of 7 competition tasks reveals significant challenges for LLM agents. Even the best-performing tested agent (gemini-exp-1206 under MLAB (Huang et al., 2024a)) closes only 9.3% of the gap between baseline and top human participant scores. Furthermore, our analysis reveals a misalignment between the LLM-judged innovation and their actual performance on cutting-edge ML research problems. MLRC-Bench is a dynamic benchmark, which is designed to continually grow with new ML competitions to encourage rigorous and objective evaluations of AI's research capabilities.

An important limitation to the development of Artificial Intelligence (AI)-based solutions for In Vitro Fertilization (IVF) is the absence of a public reference benchmark to train and evaluate deep learning (DL) models. In this work, we describe a fully annotated dataset of 704 videos of developing embryos, for a total of 337k images. We applied ResNet, LSTM, and ResNet-3D architectures to our dataset and demonstrate that they overperform algorithmic approaches to automatically annotate stage development phases. Altogether, we propose the first public benchmark that will allow the community to evaluate morphokinetic models. This is the first step towards deep learning-powered IVF. Of note, we propose highly detailed annotations with 16 different development phases, including early cell division phases, but also late cell divisions, phases after morulation, and very early phases, which have never been used before. We postulate that this original approach will help improve the overall performance of deep learning approaches on time-lapse videos of embryo development, ultimately benefiting infertile patients with improved clinical success rates (Code and data are available at https://gitlab.univ-nantes.fr/E144069X/bench_mk_pred.git).

Many benchmarks for automated causal inference evaluate a system's performance based on a single numerical output, such as an Average Treatment Effect (ATE). This approach conflates two distinct steps in causal analysis: identification-formulating a valid research design under stated assumptions-and estimation-implementing that design numerically on finite data. We introduce CausalReasoningBenchmark, a benchmark of 173 queries across 138 real-world datasets, curated from 85 peer-reviewed research papers and four widely-used causal-inference textbooks. For each query a system must produce (i) a structured identification specification that names the strategy, the treatment, outcome, and control variables, and all design-specific elements, and (ii) a point estimate with a standard error. By scoring these two components separately, our benchmark enables granular diagnosis: it distinguishes failures in causal reasoning from errors in numerical execution. Baseline results with a state-of-the-art LLM show that, while the model correctly identifies the high-level strategy in 84 % of cases, full identification-specification correctness drops to only 30 %, revealing that the bottleneck lies in the nuanced details of research design rather than in computation. CausalReasoningBenchmark is publicly available on Hugging Face and is designed to foster the development of more robust automated causal-inference systems.

We present SciArena, an open and collaborative platform for evaluating foundation models on scientific literature tasks. Unlike traditional benchmarks for scientific literature understanding and synthesis, SciArena engages the research community directly, following the Chatbot Arena evaluation approach of community voting on model comparisons. By leveraging collective intelligence, SciArena offers a community-driven evaluation of model performance on open-ended scientific tasks that demand literature-grounded, long-form responses. The platform currently supports 23 open-source and proprietary foundation models and has collected over 13,000 votes from trusted researchers across diverse scientific domains. We analyze the data collected so far and confirm that the submitted questions are diverse, aligned with real-world literature needs, and that participating researchers demonstrate strong self-consistency and inter-annotator agreement in their evaluations. We discuss the results and insights based on the model ranking leaderboard. To further promote research in building model-based automated evaluation systems for literature tasks, we release SciArena-Eval, a meta-evaluation benchmark based on our collected preference data. The benchmark measures the accuracy of models in judging answer quality by comparing their pairwise assessments with human votes. Our experiments highlight the benchmark's challenges and emphasize the need for more reliable automated evaluation methods.

Perception of toxicity evolves over time and often differs between geographies and cultural backgrounds. Similarly, black-box commercially available APIs for detecting toxicity, such as the Perspective API, are not static, but frequently retrained to address any unattended weaknesses and biases. We evaluate the implications of these changes on the reproducibility of findings that compare the relative merits of models and methods that aim to curb toxicity. Our findings suggest that research that relied on inherited automatic toxicity scores to compare models and techniques may have resulted in inaccurate findings. Rescoring all models from HELM, a widely respected living benchmark, for toxicity with the recent version of the API led to a different ranking of widely used foundation models. We suggest caution in applying apples-to-apples comparisons between studies and lay recommendations for a more structured approach to evaluating toxicity over time. Code and data are available at https://github.com/for-ai/black-box-api-challenges.

Transformers do not scale very well to long sequence lengths largely because of quadratic self-attention complexity. In the recent months, a wide spectrum of efficient, fast Transformers have been proposed to tackle this problem, more often than not claiming superior or comparable model quality to vanilla Transformer models. To this date, there is no well-established consensus on how to evaluate this class of models. Moreover, inconsistent benchmarking on a wide spectrum of tasks and datasets makes it difficult to assess relative model quality amongst many models. This paper proposes a systematic and unified benchmark, LRA, specifically focused on evaluating model quality under long-context scenarios. Our benchmark is a suite of tasks consisting of sequences ranging from 1K to 16K tokens, encompassing a wide range of data types and modalities such as text, natural, synthetic images, and mathematical expressions requiring similarity, structural, and visual-spatial reasoning. We systematically evaluate ten well-established long-range Transformer models (Reformers, Linformers, Linear Transformers, Sinkhorn Transformers, Performers, Synthesizers, Sparse Transformers, and Longformers) on our newly proposed benchmark suite. LRA paves the way towards better understanding this class of efficient Transformer models, facilitates more research in this direction, and presents new challenging tasks to tackle. Our benchmark code will be released at https://github.com/google-research/long-range-arena.