AI Agents for Scientific Discovery

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26 papers in the last four weeks, up 44% on the four weeks before. 0.3% of all new papers.

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Latest papers 175

Sep 13, 2026cs.AI

El Agente Potente: High-Throughput Agentic Atomistic Simulations

Foundational machine-learning interatomic potentials (MLIPs) are transforming atomistic simulations by achieving near-ab initio accuracy across large chemical spaces at a fraction of the computational cost. A central challenge in using these tools for high-throughput property calculations is translating high-level scientific intent into adaptive simulation campaigns without compromising workflow rigour. We introduce El Agente Potente, an agentic system that combines typed execution graphs with a complementary coding mode for MLIPs-driven atomistic simulations. Typed execution graphs provide structured and provenance-aware execution for standardized workflows, with large language models (LLMs) restricted to planning and routing while deterministic Python components perform scientific computation and validation. Complementing this structured execution, a coding agent constructs customized workflows for tasks requiring greater procedural flexibility while invoking existing Potente functions for supported calculations. We demonstrate El Agente Potente across computational materials discovery, molecular energy-landscape exploration, adsorption, and catalytic reaction workflows, together with systematic benchmarks of reproducibility and LLM token cost. These results establish typed execution graphs and code-based workflow construction as complementary mechanisms for agentic scientific computing, combining controlled, auditable execution with the flexibility required for customized atomistic simulations

Tsz Wai Ko, Jiaru Bai, Thomas Swanick +6

Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada · 2Vector Institute for Artificial Intelligence, W1140-108 College St., Schwartz Reisman Innovation Campus, Toronto, ON M5G 0C6, Canada · Department of Computer Science, University of Toronto, 40 St George St., Toronto, ON M5S 2E4, Canada +7

AI Agents for Scientific Discovery Scientific Workflow Automation Computational Materials Science

Sep 8, 2026cs.LG

MLIP Detective: Active Failure Mode Discovery Beyond Benchmark Scores for Machine-Learning Interatomic Potentials

Universal machine-learning interatomic potentials (u-MLIPs) aim to generalize across diverse configurations. Benchmarks enable reproducible evaluation but may not expose failures outside their predefined scope. Here, we show that physics-informed search can complement benchmark-based evaluation by uncovering hidden failure modes. We introduce MLIP Detective, an agentic framework for active failure mode discovery. Starting from benchmark evidence, MLIP Detective generates falsifiable, physics-informed failure hypotheses, screens them with inexpensive simulations, and escalates only the most suspicious cases to human experts together with proposed verification protocols. Without issue-specific prompting, MLIP Detective identified and characterized a systematic anomaly in MACE-MPA-0: the model predicted some relaxed adsorbate-surface systems involving O- or F-containing adsorbates to be higher in energy than their corresponding separated fragments. Using cross-model comparisons, MLIP Detective further inferred a likely training-data origin for the anomaly, consistent with recent reports.

Ryuhei Okuno, Nontawat Charoenphakdee, Kaoru Hisama +1

Preferred Networks

AI Agents for Scientific Discovery Machine Learning Interatomic Potentials

Sep 7, 2026cs.LG

Online Surrogate Repair: Decoupling High-Fidelity Feedback from Search Length in Closed-Loop Discovery

Closed-loop AI scientists can generate candidate designs at low marginal computational cost, whereas reliable feedback may require wet-lab synthesis, characterization, or high-fidelity computation. Addressing this imbalance through custom laboratory automation remains infrastructure-intensive and costly, while replacing new experiments with a fixed surrogate leaves persistent model errors that can be amplified by optimization. We propose \emph{online surrogate repair} (OSR), a closed-loop algorithm that uses sparse high-fidelity evaluations to update the surrogate throughout a longer agent search conducted primarily with inexpensive surrogate feedback. An acquisition rule selects which designs from the agent's accumulated proposals receive high-fidelity evaluation, and the resulting labels update the surrogate used in subsequent episodes. Across controlled synthetic environments, we demonstrate that improving global surrogate fit does not necessarily reduce maximum regret, whereas Q90-UCB and expected improvement (EI) substantially reduce regret by directing evaluations toward regions that determine the optimizer's decisions. On MADE, controls receiving high-fidelity feedback after every episode require

6.36

--

7.23\times

more oracle queries to match Online EI under two LLM orchestrators and

10.27\times

more under the non-LLM Chemeleon+MLIP workflow. Online surrogate repair introduces a novel third feedback regime between fixed-surrogate operation and high-fidelity feedback after every episode, separating the frequency of high-fidelity evaluation from the duration of the agent's search.

Xiaotang Feng, Philip Torr, Bruno Andreis

Department of Engineering Science, University of Oxford · Department of Physics, University of Oxford · Slater Labs

AI Agents for Scientific Discovery Surrogate-Assisted Optimization Adaptive Sampling

Sep 7, 2026cs.MA

Scores Alone Do Not Prove Discovery: The Discovery Certification Protocol for Auditing AI Research Agents

AI research agents combine public information and experimental feedback to produce measurable results. The Discovery Certification Protocol (DCP) turns an outcome claim into an executable audit under a registered model, information boundary, and budget. Gate 1 validates useful improvement. Gate 2 tests recovery by matched agents given the starting information and observed Web content, with run history and new measurements withheld. Core requires adequate registered controls, zero recoveries, and a finite-sample recovery bound. Optional Gate 3 compares truthful and neutral feedback from a shared checkpoint; Evidence adds a supported effect and a null-policy equivalence check. Controlled SQLite and virtual catalyst audits pass both decision kernels. On real-data response surfaces, Yacht and Ionosphere pass the Core kernel after zero recoveries in 96 attempts, with an upper bound of 0.0468. Each target combines ten observed utilities and six predictions into a 16-entry data product. Yacht scores 0.7677 on reconstruction of all 32 switch effects, with utility-prediction MAE 0.0315 on its six unmeasured configurations. Fresh truthful continuations recover the target level in 9/30 and 16/30 trials, respectively, separating achieved utility from process repeatability. A deterministic verifier reproduces these local decisions from frozen records.

Jingjie Ning, Shanshan Zhong, Xiaochuan Li +1

School of Computer Science, Carnegie Mellon University

AI Agents for Scientific Discovery Algorithmic Auditing AI Agent Auditing AI Agent Evaluation

Sep 4, 2026cs.AI

TruthInsightBench: An Evidence-Grounded Benchmark for Automated Evaluation of Open-Ended Scientific Discovery Agents

Autonomous coding agents are increasingly proposed as AI-scientist systems that conduct analyses and write research reports, but executing a prescribed analysis is not the same as making a discovery. Existing benchmarks are configured for reproduction: tasks, data, and rubrics are built around a hidden target study, and recovery of its result is rewarded. We present TruthInsightBench, a benchmark configured for discovery. Its 40 blind tasks, drawn from 40 peer-reviewed studies across 10 scientific domains, expose only a neutral scientific objective and frozen data; source conclusions, expected values, and analysis paths are withheld, leaving the agent to determine what claim the data support. A fixed LLM-based judge scores the evidentiary maturity of an agent's own claims along six dimensions, operationalized as 29 artifact-grounded items, with automated, deterministic aggregation and no per-instance human grading, so evaluation can be repeated automatically as agents evolve. On one frozen base model, four coding agents form a narrow plateau (58.4-60.3 of 100) with no statistically reliable pairwise separation: they execute and document analyses competently, with comparatively strong evidence auditability and novelty, but largely lack the discriminating acts that establish a trustworthy claim (controls, robustness, falsifiability, and cross-dataset generalization). The bottleneck is scientific judgment rather than coding, and genuine discovery remains out of reach. TruthInsightBench makes this gap a measurable target; data and scoring code are at https://github.com/TruthInsight-stack/TruthInsightBench.

Zhibo Yang, Chen Zhang, Yuewei Zhang +1

TruthInsight-AI

AI Agents for Scientific Discovery AI Agent Benchmarks Autonomous Scientific Discovery Automated Evaluation

Sep 1, 2026cond-mat.mtrl-sci

Autonomous discovery of new structure-plausibility laws for explainable and rapid crystal diagnosis and screening

Crystal generators and tool-using agents propose structures faster than density functional theory (DFT) energy and phonon calculations or experiments can assess them. Deciding which candidates merit expensive assessment is therefore the bottleneck, yet most screens test little beyond atomic overlap and give no chemical reason for failure. Here, our agents generate, test and actively refute two million candidate laws, leaving eight Plausibility Rules for Inorganic Structures (PRIS). These laws encode five mechanisms: short-range repulsion, ionic contact and packing, electrostatic balance, bond-valence conservation and crystallographic site complexity. Experimental structures satisfy our law sets at 82--99%, but satisfy Pauling's rules 2--5 together at only 6.5%. The strictest set detects 87.9% of damaged crystal structures, whereas distance cutoffs detect only 1.6--3.2%. PRIS plausibility is linearly correlated with synthesizability, so the PRIS-derived synthesis score (PSS) explainably screens 83.7% of hard-to-synthesize structures while retaining 80.7% of experimental structures. In a property-conditioned inverse-design run, PRIS and PSS can reduce the DFT validation queue by up to 67.3% and keep 99.2% of the candidates whose DFT-validated bulk moduli reach the design target. Beyond screening, PRIS explains why GNoME remains enriched in rare low-symmetry structures and reveals how wrong-element assignments in falsified crystal reports hide behind plausible coordinates. PRIS moves screening from a pass-or-fail verdict to a chemical reason for failure, showing that autonomous agents can discover, by active refutation, physicochemical laws that guide calculations and experiments.

Zhilong Song, Lixue Cheng

Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China. · IAS Center for AI for Scientific Discoveries, Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China. · Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Kowloon, Hong Kong 999077, China.

AI Agents for Scientific Discovery Crystal Structure Prediction Virtual Screening Materials Science Computational Materials Science

Aug 31, 2026cs.AI

Dr. Claw: An AI Scientist Workspace for Vibe Research

Command-line coding agents (e.g., Claude Code, Gemini CLI) can already read and write files and sustain long sessions, yet end-to-end research still fragments across chat tools, IDEs, terminals, and writing environments, and the decisions that make it auditable are rarely preserved. We present Dr. Claw, an open-source workspace that wraps existing coding-agent executors in a controllable and auditable human-in-the-loop workflow rather than introducing another autonomous agent. Persistent state objects, a reusable skill library, and multi-executor coordination link human decisions to AI execution, turning planning, execution, and writing into one traceable, recoverable loop. We demonstrate Dr. Claw through an interactive three-view scenario and a failure-recovery walkthrough, and evaluate it against a bare command-line agent sharing the same backend executor, so the comparison contrasts the whole orchestration layer (task graph, state objects, and skill library) with the agent it wraps. Holding the executor fixed, Dr. Claw scores higher on research completeness while persisting an auditable, recoverable process trail. Demo access: repository https://github.com/OpenLAIR/dr-claw, released under AGPL-3.0 with GPL-3.0 upstream components.

Dingjie Song, Hanrong Zhang, Dawei Liu +10

Lehigh University · University of Illinois Chicago · University of Pennsylvania +3

AI Agents for Scientific Discovery Coding Agents LLM Agent Orchestration Human-in-the-Loop AI LLM Agent Harnesses

Aug 31, 2026cs.CL

PaperGym: Rubric-Centered Evolution for Research-Plan Generation

Research planning is the decisive capability of AI scientists. Yet a research plan admits no verifiable answer, so reinforcement learning lacks the environment it requires: tasks paired with a critic. Rubrics extracted from scientific papers can supply the critic. Existing pipelines, however, draw the question and the criteria from the same content, so the reward can be earned by paraphrase. The rubric is further compressed into a single scalar per rollout. We introduce PaperGym, a unified framework that turns each research paper into a complete training environment. PaperGym exploits the structure of a paper: the question is synthesized from the research goal and background, while the criteria are derived from the method and experiments. The criteria span methodological innovation and experimental design, and criterion leakage falls to 3.7%, versus 11.90% to 34.10% in existing datasets. Training uses the rubric twice: first as privileged context for OPSD's self-teacher, then as the reward for GRPO. Across Qwen3-1.7B/4B/8B, this schedule outperforms supervised fine-tuning, either stage alone, and the reverse ordering, improving five-benchmark averages by +5.6, +5.0, and +4.8 points. With the recipe held fixed, models trained on PaperGym-20k win 58.1% of three-way comparisons, against 28.2% for RubricHub Science. The trained Qwen3-8B reaches 73.48 on ResearchQA, above the far larger Kimi K2.6. We release the pipeline, the 20,000-instance corpus PaperGym-20k, and the benchmarks PaperGym-Innov and PaperGym-Design.

Yuhan Wang, Zhengxi Lu, Yuchen Yan +6

Zhejiang University · Apple

AI Agents for Scientific Discovery Rubric-Based RL Rubric-Based Evaluation Rubric-Guided Generation

Aug 30, 2026cs.AI

Ideation Arena: Evaluating LLM Generated Research Ideas with Battle-style Human Expert Assessment

Evaluating research ideas generated by LLMs is difficult because their scientific value cannot be fully determined by objective criteria, and no single reference answer specifies what counts as a good idea. To address this challenge, we introduce Ideation Arena, a battle style platform that evaluates research ideas through pairwise human assessment. Ideation Arena evaluates ideas generated by 14 frontier LLMs and 5 research agent architectures built on 2 base models. To ensure a common starting point, Ideation Arena builds shared literature contexts from papers familiar to the participating researchers and provides the same contexts to all LLMs and agents. We collect over 6,000 double blind pairwise comparisons from 105 active computer science researchers and construct an Elo rating leaderboard of proposal-stage expert preferences in computer science under a shared closed-context protocol. We validate the rankings through interrater agreement and robustness analyses, showing that the leaderboard remains stable under changes in annotator composition and domain coverage. Our results show substantial variation in agent effectiveness, with some frameworks improving ideation quality over their backbones and others offering little benefit or even underperforming their base models. We further construct Ideation Arena Eval, a benchmark for assessing whether automated evaluators align with human preferences in research ideation. Experiments with current LLM judges show that they still cannot reliably reproduce expert preferences, with the best judge reaching 72.56% Soft Accuracy on Overall Quality. Our code, data, and leaderboards are available at https://github.com/foss12138/Research-Ideation-Arena.

Zhiyu Chen, Keyu Zhao, Jigao Fu +8

1Fudan University · 3Tsinghua University · 4Zhongguancun Institute of Artificial Intelligence +1

AI Agents for Scientific Discovery LLM-as-a-Judge AI Agent Evaluation Human-in-the-Loop Evaluation AI Agent Benchmarks Research Idea Generation

Aug 28, 2026physics.optics

HALO: A Physics-Aware LLM Agent Framework for Nanophotonic Design

Language models have recently been applied to nanophotonic design, but it remains unclear whether they can reliably translate optical objectives into simulation-ready designs, execute electromagnetic analysis, and revise decisions from numerical feedback. We introduce HALO, a physics-aware framework that couples language-model planners with typed design specifications, electromagnetic simulation, diagnostic evaluation, and optional reuse of prior failure trajectories in an iterative design loop. We further introduce HALO-Bench, a 52-task benchmark spanning lab-derived, paper-derived, and open-ended nanophotonic design tasks under a shared evaluation protocol. We compare three planner configurations: a Fixed Structured Workflow, an Autonomous Structured Agent using the same simulation interface, and an Autonomous Coding Agent that directly writes and executes simulation code. The Fixed Structured Workflow is the most token-efficient and exhibits no observed code- or path-level failures, while autonomous coding can achieve higher task success with stronger models at the cost of additional operational failures. We also study reuse of prior failed trajectories. On targeted multi-round tasks, retrieved failure feedback reduces both iterations to first success and total token use. These results clarify the tradeoffs between explicit interfaces, autonomous execution, and reusable design experience in scientific agents.

Yubo Zhang, Jinlin Xiang, Zijun Zhao +3

Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, USA

AI Agents for Scientific Discovery LLM Agent Planning Memory-Augmented Language Model Agents

Aug 27, 2026q-bio.MN

Orchestra: Corroboration-Based Regulatory Candidate Discovery via Composed Bioinformatics MCP Agents

Orchestra composes two independently built bioinformatics MCP servers -- RegNetAgents, which infers gene regulatory network topology from ARACNe networks, and CASCADE, which supplies four independent evidence sources (LINCS knockdown, DepMap essentiality, super-enhancer status, DoRothEA transcription-factor confidence) -- into one multi-agent workflow exposed via the Model Context Protocol. Its central architectural claim is that requiring RegNetAgents' topology evidence and CASCADE's experimental evidence to agree on a candidate regulator yields a more trustworthy candidate than either alone -- not previously tested directly, since RegNetAgents' own validation asked only whether its candidate lists beat chance. We test this on the TCGA tumor-acquired regulator tier (regulators in a gene's tumor ARACNe network but absent from the GREmLN population-averaged baseline), selecting candidates by ARACNe mutual-information (MI) edge weight. On RegNetAgents' published BRCA/COAD focal-gene panel plus matched negative controls, agreement among at least 2 of the 4 CASCADE sources predicts OncoKB cancer-gene status among focal genes (odds ratio 2.89, Benjamini-Hochberg-adjusted p=0.0166) but not among negative controls (p=0.0721); a single source is not diagnostic for either group. The pattern replicates and strengthens in a third cancer type, STAD, on a separately constructed panel (odds ratio 5.82), and against an independently curated ground truth (the Sanger COSMIC Cancer Gene Census). MI edge weight is the strongest single predictor overall (p=0.0003); a logistic-regression likelihood-ratio test confirms corroboration adds value beyond it in both panels (p=0.0234; p=0.0001). Every experiment invokes Orchestra's real agentic entry point.

Jose A. Bird

Independent Researcher, Bird AI Solutions

Cancer Genomics Multi-Agent Orchestration AI Agents for Scientific Discovery Evidence-Grounded Reasoning Gene Regulatory Network Inference Oncology+1

Aug 21, 2026cs.LG

Designing a Robust LLM-Based Evaluation System for Agentic AI in Drug Discovery Through Human Alignment

Agentic large language model (LLM) systems are reshaping scientific workflows in chemistry and drug discovery, but evaluating their open-ended, tool-augmented outputs remains a fundamental bottleneck. The LLM-as-a-Judge paradigm has emerged as a scalable alternative, but existing drug discovery benchmarks deploy LLM judges without validating their alignment with human experts. In this work, we present an LLM-as-a-Judge evaluation framework for ChatInvent, an agentic drug discovery assistant deployed at AstraZeneca, with five contributions. First, we define four output-quality evaluation dimensions---Completeness, Relevancy, Structural Clarity, and Scope Adherence---alongside deterministic Tool Call Correctness checks. Second, we validate the judge through a human alignment study with five expert annotators, comparing Gemini 3.1 Pro, Claude Opus 4.7, GPT-5, and Llama 3.1 70B as candidate judges. Third, we optimize the best-performing judge using few-shot demonstrations of human-annotated examples, improving alignment with the human majority vote from 0.80 to 0.86. Fourth, applying the optimized judge to 70 held-out questions, we surface concrete limitations and find no strong evidence that informal phrasing degrades output quality; it may, however, still be helpful to have the LLM rewrite the original question before querying the agent. Finally, we extend the framework to 38 adversarial questions that are ambiguous, invalid, out-of-scope or ethically sensitive, and show that the agent's refusal behavior is guided by the stated intent of a request. Our framework provides a reusable template for human-aligned evaluation of agentic systems in scientific domains.

Emma Granqvist, Rocío Mercado, Samuel Genheden

Molecular AI, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden · Department of Computer Science and Engineering, Section for Data Science and AI, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden · Science for Life Laboratory (SciLifeLab), Gothenburg, Sweden

AI Agents for Scientific Discovery LLM-as-a-Judge LLM Agent Evaluation Human-in-the-Loop Evaluation Drug Discovery

Aug 19, 2026physics.chem-ph

Science Done on a Machine by a Machine: AI Agents in Computational Chemistry

We are witnessing an explosion of agentic systems for computational chemistry: from four in 2024 to seventeen in 2025 and over sixty now, surveyed here. What is delegated to these systems is shifting from single calculations to whole in silico experiments and even manuscript writing. The ultimate destination is a fully autonomous AI scientist, where the entirety of computational chemistry is performed on a machine by a machine, without human supervision. Our survey shows that these systems are turning into vetted chemistry skills on general-purpose coding agents, and that they must be evaluated not only on their final answers but also on whether their calculations actually support these answers. The role of the human computational chemist is shifting from performing calculations to directing and supervising them, and the field should invest in the judgement that makes the supervision reliable: we propose a reporting standard, an evaluation reproducing published studies, a controlled comparison with general-purpose coding agents, and how to teach.

Pavlo O. Dral, Hassan Nawaz, Arif Ullah

State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen, Fujian 361005, China · Institute of Physics, Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University in Toruń, ul. Grudziadzka 5, 87-100 Toruń, Poland · Institute of Advanced Studies, Nicolaus Copernicus University in Toruń, ul. Wileńska 4, 87-100 Toruń, Poland +2

AI Agents for Scientific Discovery AI Agent Evaluation Scientific Reproducibility Autonomous Research Agents

Aug 13, 2026cs.AI

OmniScientist: An Omni-Modal Omni-Discipline AI Scientist

Recent advances in foundation models have enabled AI scientists to automate increasingly complete research workflows, from hypothesis generation and code execution to manuscript preparation. Yet workflow coverage alone does not provide access to the full evidence on which scientific discovery depends. Existing systems typically reason over text, code, labels, or precomputed summaries, leaving scientifically decisive spatial, temporal, cross-channel, and procedural relations unavailable to the agent. We introduce OmniScientist, an end-to-end, omni-modal AI scientist that conducts multidisciplinary research directly from heterogeneous raw evidence. A perception layer and 3 autonomous agents for ideation, experiment, and writeup operate within a deterministic pipeline, allowing observations to shape research questions, experimental decisions, and final claims throughout the research lifecycle. By running idea, rigour, and claim checks in code, the system enforces novelty screening, statistical validity, execution provenance, and numerical traceability. We evaluate OmniScientist on 36 real-data cases spanning 5 discipline families, 4 families of scientific evidence, and modalities including images, signals, audio, video, 3-D structures, trajectories, tables, formulae, and graphs. The system completes the full path from raw data to a compiled manuscript in all 36 cases and achieves a mean overall paper score of 6.3 with the reference reasoning backbone. In paired comparisons against a blind variant that receives only precomputed scalar features, direct perception improves all 7 evaluation dimensions and wins 85% of head-to-head judgments. These results show that lifecycle-wide perception is essential for evidence-grounded scientific discovery and provides a practical path toward broadly capable AI scientists.

Bobo Li, Hao Fei, Tianjie Ju +2

1National University of Singapore · University of Oxford

AI Agents for Scientific Discovery Scientific Discovery Autonomous Scientific Discovery Evidence-Grounded Generation Scientific Workflow Automation

Aug 13, 2026cs.LG

Intern-S2-Preview: Scientific Agentic Foundation Model

Scientific discovery increasingly requires AI systems that can reason over scientific evidence of heterogeneous modalities, interact with scientific tools and environments, and sustain progress across long task horizons. We present Intern-S2-Preview, a series of scientific agentic foundation models designed to support multimodal scientific understanding, reasoning, generation, and long-horizon tasks. The training pipeline begins with scientific multimodal pre-training over rendered scientific documents, interleaved image-text data, and diverse scientific corpora. Starting from the pretrained checkpoint, we apply a unified post-training pipeline consisting of supervised fine-tuning, scalable multi-task reinforcement learning (RL), black- and white-box agentic RL, and on-policy distillation. This pipeline is supported by practical techniques that improve rollout and training stability and efficiency, including partial rollout with off-policy correction, adaptive length regularization, online speculative decoding, robust multi-task optimization, and trace-aware experience assembly for agentic tasks. At the architecture level, Intern-S2-Preview-397B extends time series modelling from efficient long-sequence understanding to numerical forecasting, while Memory Decoder is studied as a separate memory-augmented path for rapid scientific specialization without modifying the frozen 397B backbone. Evaluations across scientific, multimodal, agentic, and general-purpose benchmarks show that Intern-S2-Preview-397B achieves competitive or leading results in multiple settings. The time series modules improve scientific signal understanding and forecasting on SciTS, while the separate Intern-MemDec-4B extension improves the Biology-Instructions average score from 56.92 to 60.32 without modifying the frozen 397B backbone.

Lei Bai, Jiaqi Cao, Chiyu Chen +122

AI Agents for Scientific Discovery Time Series Forecasting Multimodal Reasoning Memory-Augmented Language Model Agents

Aug 13, 2026cs.LG

Training AI Scientists to Replicate Research

The replicability of papers is a cornerstone of scientific knowledge, ensuring the reliability of existing results and providing a base for further experiments. The act of replication typically illuminates details that were previously underspecified, and thus requires similar hypothesis-driven exploration to open-ended research. In this work, we develop Replica, a scalable task space for paper replication. To provide reward signal, we introduce an auto-generated rubric-based judge that has low noise and agrees with human assessment of replication quality. We post-train Faraday, a 27B-parameter "AI Scientist" agent that leverages coding agents as tools, surpassing the performance of Claude Opus 4.8 and GPT-5.5 on held-out replication tasks. Qualitative analysis of individual rollouts reveals that Faraday adopts a more scientifically-principled approach. We believe that our results provide a stepping stone towards AI agents capable of long-horizon scientific innovation without requiring complex harnesses.

Damon Falck, Samer Sabri, Anja Surina +8

1Inherent

AI Agents for Scientific Discovery AI Agent Benchmarks LLM Agent Training Scientific Reproducibility

Aug 12, 2026cs.AI

Mechanist: AI as a Scientific Instrument for Discovering the Mechanisms of Intelligence

AI models have achieved remarkable success across diverse domains, yet the mechanisms underlying their capabilities and the risks they may pose remain poorly understood. As AI development becomes faster and increasingly automated, mechanistic exploration remains largely manual, widening the gap between what models can do and our ability to understand and control them. To bridge this gap, we introduce Mechanist, an agentic system that uses AI as a scientific instrument for the autonomous discovery of mechanisms underlying AI intelligence. To support autonomous mechanistic discovery, we construct an interpretability-focused knowledge graph of approximately 13,000 papers and integrate it with a multidisciplinary database of 43 million papers spanning 26 fields. We further curate a library of 32 foundational methods for mechanism analysis, causal intervention, and validation. Compared with Claude Code and existing AI-scientist systems, Mechanist generates more valuable mechanism hypotheses and executes experiments more reliably. Mechanist also demonstrates a progression from discovering model behaviors to explaining and controlling AI models. Specifically, Mechanist first uncovers a counterintuitive safety risk in scientific laboratories, showing that unsafe traits can transfer across modalities through apparently safe training data. Mechanist then develops a mechanism theory of belief, revealing how models represent world knowledge, form beliefs, infer the beliefs of others, and how these mechanisms emerge during pretraining. Finally, Mechanist translates these mechanistic insights into practical interventions that improve model performance across diverse scenarios and steer scientific foundation models toward generating DNA sequences with specified properties.

Mengru Wang, Junfeng Fang, Shuofei Qiao +16

Zhejiang University · National University of Singapore · Heriot-Watt University +3

AI Agents for Scientific Discovery Mechanistic Interpretability Large Language Model-Guided Scientific Discovery Autonomous Research Agents

Aug 11, 2026cs.AI

ChemWorld: Programmable Chemical Worlds for Controlled and Replayable Agent Experimentation

Autonomous chemistry increasingly depends on environments in which agents can repeatedly act, observe, and adapt.Physical laboratories provide essential real-material evidence but are costly to repeat and difficult to use for tightly matched interventions, whereas most digital environments keep the underlying experimental world largely fixed. We introduce ChemWorld, a programmable chemical environment in which reusable process and observation components are compiled into executable worlds. ChemWorld separates the public experimental contract available to an agent from evaluator-owned chemical and material laws. Researchers can therefore vary world composition and operating conditions, or change a single hidden law while holding the public task and interaction conditions fixed. Transactional execution records operations, failures, resource changes, and state transitions, allowing complete environment-action trajectories to be replayed exactly and audited. Full-census qualification covered the reference registry, 52 generated compositions, and module, interface, compilation, and invalid-action tests. Eight deterministic experimental cases demonstrated shared lifecycle semantics, failure recovery, and exact replay, while six parent-child world-fork pairs isolated the effects of single private-law interventions under matched public conditions. An independent agent also completed a full lifecycle in a non-reference world through the same public interface. Within the declared component and model domain, ChemWorld provides a controlled and replayable substrate for studying experimentation across systematically varied chemical worlds, complementary to physical-laboratory evidence and calibration.

Jiangjie Qiu, Yijun Li, Xiaonan Wang

Beijing Key Laboratory of Artificial Intelligence for Advanced Chemical Engineering Materials, State Key Laboratory of Chemical Engineering and Low-Carbon Technology, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China

AI Agents for Scientific Discovery Scientific Reproducibility Autonomous Experimentation

Aug 11, 2026cs.AI

Tree-of-Ideas: Automated Research Ideation via Cross-Trajectory Reasoning over Scholarly Evolution

Effective research ideation requires moving beyond a static understanding of prior work to trace how research problems and solutions evolve across the literature. Existing methods either treat papers as unstructured context or model scholarly evolution as isolated citation chains, overlooking interactions among research trajectories. We propose Tree-of-Ideas (ToI), a two-stage framework. EvoTrace reconstructs branching scholarly trajectories from citations, tracking evolving methods, resolved problems, and gaps. EvoAgent then reasons across trajectories to identify convergent problems and complementary solutions, generating grounded research ideas. Across six AI research topics, ToI achieves the highest score among automatic methods (6.27 vs. 5.36 for the strongest baseline on a 10-point scale), with strong Novelty (6.36) and Groundedness (7.00). Also, its score approaches that of human-paper references (6.29), demonstrating the value of cross-path evolutionary reasoning.

Xun Li, Yiying Yang, Pengtao Li +8

Guangdong Laboratory of Artificial Intelligence and Digital Economy (SZ) · University of Melbourne · University of Sydney +4

AI Agents for Scientific Discovery Research Idea Generation Large Language Model-Guided Scientific Discovery

Aug 10, 2026cs.AI

Agentic Auto-Research is Fuzz Testing

Autonomous research agents can generate experiments faster than researchers can validate them. Researchers have responded by scaling the proposer and ranking more samples with a learned judge or human reviewers. We argue that this generate-and-rank paradigm misses the problem of sparse feedback. Within a declared research problem, an agent follows the control loop of a greybox fuzzer: it proposes a candidate, executes it, observes feedback, and chooses what to try next. A fuzzer rarely finds a bug, but coverage makes partial progress observable on every execution. Fuzzers then use that signal to mutate inputs and allocate effort, rather than only to rank completed runs. Auto-research needs the same two capabilities. First, each experiment should expose a cheap, dense signal of epistemic progress before final scientific validation is available. Second, that signal should determine the next intervention so that the agent searches rather than repeatedly samples. Because the optimized progress signal is guidance rather than a verdict, final validation must still decide what counts as a discovery using evidence protected from adaptive reuse. We propose controlled tests of whether candidate signals predict validated progress, whether feedback-directed search yields more validated discoveries per unit cost than repeated sampling, and whether protected validation reduces false discoveries. Feedback architecture, not only generation, is a central bottleneck in auto-research.

Yifeng He, Jicheng Wang, Yinzhe Zhao +2

University of California, Davis · ARA Lab · Zhejiang University +2

AI Agents for Scientific Discovery Autonomous Experimentation Autonomous Research Agents

Aug 10, 2026cs.AI

Model Discovery Agent: LLM-assisted Bayesian experiment design for data-efficient discovery of mechanistic world models

A primary goal of science is to learn mechanistic world models from limited experimental data, both to explain observations and to predict novel interventions. We introduce the Model Discovery Agent (MDA), which combines LLM proposals for

\mathcal M

-open model discovery, experiment design based on Value of Information, and approximate Bayesian inference over model structures, parameters, and stochastic latent trajectories. We apply MDA to learn symbolic reaction rate laws for ChemBench \citep{kabra2026autoscilab}, partially observed ODE models for GlucoseBench \citep{xie2018simglucose,kovatchev2009insilico}, and partially observed SDE models for a new stochastic single-neuron simulator we create. In the appendix, we also show results on various other domains from BoxingGym \citep{gandhi2025boxinggym}. We show that MDA has improved sample efficiency compared to various baseline methods, and the learned models are good predictors but also provide interpretable abstractions of each domain.

Kevin Murphy

Dept. Computer Science Univ. British Columbia, Canada.

Dynamical Systems AI Agents for Scientific Discovery Bayesian Experimental Design Large Language Model-Guided Scientific Discovery

Aug 10, 2026quant-ph

Multi-agent discovery of practical quantum LDPC codes

Quantum low-density parity-check (qLDPC) codes can encode multiple logical qubits using sparse parity checks, yet searching for useful finite-length instances remains a challenging design problem because code performance must be optimized while satisfying practical constraints. Motivated by recent advances in artificial-intelligence agents for scientific discovery, we develop a multi-agent framework for discovering practical qLDPC codes. The framework combines specialist proposal and review, persistent scientific memory, long-horizon evolution of executable programs, and deterministic construction and evaluation within a closed-loop search. These programs instantiate coset-orbit balanced-product codes, providing a search space that includes bicycle and lifted-product constructions as well as non-normal subgroup actions. To incorporate practical constraints, we restrict the search to binary CSS codes with block length

n\leq400

and overall weight

w\leq10

. Within this regime, the framework discovers codes with leading or competitive rate--distance performance in every weight class considered, with representative instances including

[[288,16,18]]

at

w=7

,

[[288,18,18]]

at

w=9

, and

[[234,28,18]]

at

w=10

. The search also uncovers structurally distinct, high-performing constructions, including a

[[336,12,\leq24]]

candidate and a

[[368,18,16]]

code, both of which are genuine balanced-product constructions with non-normal subgroup actions. When evaluated under code-capacity depolarizing noise using a common BP-OSD decoding protocol, the discovered codes also exhibit low logical failure rates. Together, these results provide hardware-relevant finite-length candidates for further experimental evaluation and show how structured agentic search can contribute to scientific discovery.

Dongheng Qian, Tianyi Li

State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai 200433, China · Shanghai Research Center for Quantum Sciences, Shanghai 201315, China · University of Wisconsin–Madison, Madison, Wisconsin 53706, USA

AI Agents for Scientific Discovery Automated Algorithm Discovery Quantum Error Correction

Aug 7, 2026cs.AI

CAi Copilot: Reducing Operational Workload in Molecular Design through Intent-Driven Agentic Workflows

Early-stage molecular design is an iterative process, not just a task of generating molecules. Researchers turn broad goals into design strategies, refine candidates, assess many properties, and gather evidence before synthesis and tests. AI methods can generate molecules, optimize several goals, predict properties, dock compounds, and account for synthesis. Yet these functions are spread across specialized tools. Experts must still coordinate each step, judge interim results, and integrate evidence. The central challenge is thus to turn research intent into adaptive, traceable runs grounded in scientific tools. We cast this challenge as intent-to-evidence molecular design workflow execution and present CAi Copilot, an expert-oriented agent with three linked layers. The Research Interface Layer turns intent into an executable plan. The Agent Reasoning Layer uses interim results to guide each run. The Execution Substrate supplies molecular tools, metrics, reusable utilities, and backend services. Across 45 tasks, CAi achieves the strongest overall performance, with an outcome score of 84.59, exceeding the next-best result by 18.07 points. Additional benchmarks test how CAi coordinates generation, screening, and multi-criteria evaluation, while exposing limits in long-horizon execution. These results show that CAi turns broad molecular-design intent into transparent, traceable workflows that connect interim decisions to candidate-level evidence.

Zhu Wang, Jiangyu Chen, Yingjun Shang +4

Shanghai Artificial Intelligence Laboratory, Shanghai, China · Nanjing University, Nanjing, China

AI Agents for Scientific Discovery Agentic Workflows Scientific Workflow Automation

Aug 5, 2026cs.DC

Hierarchical Server Architecture for Agentic Science

Agentic science is transforming the landscape of computational work, and is applied to scientific pipelines and workload managers. Scientific workloads require specialized hardware within and between institutions. Automated resource discovery is an essential step for scheduling workloads with specific hardware and environmental requirements. In this paper, we present a hierarchical, dynamic architecture and accompanying software to discover resources across diverse cloud, edge, and HPC systems. The design enables concurrent, asynchronous negotiation, selection, and dispatch of requests for work using secretary agents. The agents probe and discover 51 real and simulated providers across 7 categories. We perform 19,973 negotiation and 6,952 selection simulations to assess reliability of decisions, demonstrating high (87.71%) negotiation accuracy and selection costs comparable to more traditional strategies. Designed for extensibility and currently supporting the US DOE Genesis Mission, this architecture exemplifies the importance of careful coordination between agents, discovery tools, and infrastructure for agentic science.

Vanessa Sochat, Daniel Milroy

Lawrence Livermore National Laboratory Livermore, California, USA

Multi-Agent Coordination AI Agents for Scientific Discovery Online Resource Allocation

Aug 5, 2026cs.AI

Agentic self-driving microscopy benchmarks support qualification but do not necessarily generalize to unseen tasks

Large language model agents are increasingly being developed to control a wide range of scientific characterization tools including microscopes and synchrotron beamlines. Research into agentic control of physical infrastructure is nascent and there are few well-established paradigms for how to engineer an agentic system. There are many choices to make when designing a microscopy agent, including the choice of LLM, the number of agents to use, agent responsibilities and delegation rules, retrieval-augmented generation parameters, and more. When designing and optimizing an agentic microscope controller, researchers not only want to ensure that the agent can correctly perform known tasks but also that the agent can generalize to new tasks that it has not encountered before. In this study, we develop a benchmark and trace-logging framework that reveals a) how different choices of agent architecture impact performance at microscopy tasks and b) the limitations of benchmarks for predicting if a particular agent will perform well on unseen microscopy tasks. The framework was used to evaluate one-, two-, and three-agent graph topologies, five LLMs, RAG and context parameters, and operational constraints across 53 microscopy benchmark tests. In total, 105 agent configurations, 1,949 individual test runs, and 49,109 RAG retrievals were recorded. Direct comparisons showed clear differences in latency, token use, cost, and failure mode between configurations. However, surrogate models trained on agent architecture and test results did not reliably predict an agent's performance on new, unseen tasks. These results show that these benchmarks are useful for qualification, regression testing, diagnosis, and direct comparison, but the current heterogeneous test suite does not support a task-independent global configuration model.

Nathan S Johnson, Ian Abshire

Carl Zeiss Research Microscopy Solutions, 5300 Central Boulevard, Dublin, CA 94568

AI Agents for Scientific Discovery LLM Agent Orchestration LLM Agent Evaluation LLM Agents Agent Benchmarks

Aug 5, 2026cs.AI

Project2Task: Graph-Guided Project-Level Planning for Autonomous Research

Research agents can increasingly search literature, propose hypotheses, generate code, run experiments, and draft manuscripts from a single topic. However, a research project is not merely a larger task: it is a long-horizon agenda that must be advanced through multiple bounded tasks with distinct but related objectives, parallel alternatives, and dependency-aware sequences. Existing single-task systems often treat the project as one oversized task, produce a flat set of vague or overlapping tasks, or leave task boundaries and execution order to manual coordination. We introduce Project2Task, a graph-guided project-level planning layer for autonomous research. Given a project brief, it represents candidate contributions as innovation atoms and organizes them in a directed lineage graph. A lightweight Bernoulli block-model objective selects among horizontal, vertical, and hybrid portfolio decompositions. Project2Task then generates bounded tasks with explicit contribution ownership, repairs overlaps and missing execution fields, and emits dependency-aware task contracts that specify objectives, inputs, expected artifacts, evaluation requirements, boundary constraints, dependencies, and execution order. The contracts are independent of any particular downstream research executor and support integration of task outputs into a coherent project-level result. On a benchmark of ten project briefs yielding roughly 30 tasks, manuscript-based portfolio evaluation gives Project2Task an average quality score of 7.15, compared with 4.58 for the Brief Baseline and 5.31 for the Topic-only Setting. Integrating its contracts with AutoResearchClaw increases average downstream task accuracy from 0.536 to 0.759. These results demonstrate the value of explicit project-to-task planning for producing coherent, non-redundant, and executable research-task portfolios.

Huirui Xu, Runtao Xu, Shuo Ren +1

Institute of Automation, Chinese Academy of Sciences · School of Artificial Intelligence, University of Chinese Academy of Sciences · School of Future Technology, University of Chinese Academy of Sciences +1

AI Agents for Scientific Discovery Graph-Based Planning Task Decomposition Long-Horizon Agent Tasks Autonomous Research Agents

Aug 4, 2026cs.AI

Adversarial Fast-Moving Real-World Domains as Test Beds for Benchmarking AI Scientist Capabilities

Benchmarking the ability of AI scientists to generate novel ideas is notoriously difficult. Existing benchmarks in this field have made progress in evaluating scientific reasoning and research replication, but often rely on synthetic tasks or retrospective targets, which may be confounded by prior exposure. We hypothesize that complex, adversarial, fast-moving real-world domains where expert practitioners independently generate observable outputs can provide a practical solution to fill this gap and evaluate the capabilities needed for AI scientists, including reasoning, novelty, and hypothesis formulation. We instantiate this framework in two structurally different domains, Formula 1 (F1), where models ideate around car design concepts for the 2026 season, and real pre-season innovations provide a ground truth, and Magic: The Gathering (MTG), where models propose decks from a recently updated card pool and are evaluated against 19 Pro Tour (PT) decklists. Across both domains, models produce plausible outputs, but few align with real-world expert solutions. In F1, the best model, GPT-5.2 matched 10 of 40 real innovations with 166 ideas proposed across runs. In MTG, the best deck from Gemini 3 Flash recovered 5 of 7 new-set cards from the third-place PT deck, and across all 108 decks, the cards models selected most often were also the cards most widely adopted by PT decks (Spearman

ρ= 0.74

,

p = 0.0003

). These results suggest that a key capability gap for AI scientists is not idea generation, but filtering, prioritization, and coherent novelty.

William Bolton, Philip Torr

Department of Engineering Science, University of Oxford, Oxford, United Kingdom.

AI Agents for Scientific Discovery Benchmark Design Scientific Hypothesis Generation AI Agent Benchmarks Research Idea Generation

Aug 3, 2026cs.AI

Long-Horizon Autonomous Architecture Research with a Language-Model Agent: A Behavioural Case Study

We study what happens when a single general-purpose large language model acts as the sole researcher on a long-horizon neural architecture design problem. The agent receives a scientific question, an initial hypothesis and motivation, a compute budget, and research affordances (source and experiment management, experiment tracking, literature access, and persistent memory), then autonomously proposes, implements, evaluates, and records experiments over an extended period. The study comprises three phases, separated by human-declared transitions, that progressively expand the agent's tool surface or problem scale. Across approximately 100 sequential experiments, the agent improves a non-standard Vision Transformer from a weak baseline to a stronger, efficient model on small benchmarks and a usable but sub-SOTA model on ImageNet-1K, while producing a dense behavioural trace. We report four findings.(i)Productivity exhibits a clear phase structure: rapid early gains, a multi-dozen-hypothesis saturation wall, and recovery, with recovery triggered by expanding the action surface rather than changing the underlying model.(ii)A single early hypothesis contributes more to accuracy gain, with later improvements long-tailed.(iii)The preference for greedy, incremental hypotheses is largely workflow-induced: a commit-or-discard evaluation rule is isomorphic to greedy hill-climbing; the remainder reflects risk aversion after bold failures and anchoring on familiar literature. (iv)The agent independently rediscovers established results and, in the unfamiliar regime of pure channel attention, overturns a standard design choice. We conclude that workflow design was at least as influential as agent capability in this study and propose diversified search, budgeted moonshot hypotheses, explicit forks, and regime-aware re-validation as testable directions for future autonomous research.

Aon Safdar, Mohamed Saadeldin

University College Dublin, Ireland

AI Agents for Scientific Discovery Neural Architecture Search Long-Horizon LLM Agents Large Language Model-Guided Scientific Discovery Autonomous Research Agents

Aug 2, 2026cs.AI

Agentic Stage-One Stellarator Optimization: Autonomous Multi-Objective Search for Finite-Beta Equilibria

Stage-one stellarator design searches a high-dimensional family of three-dimensional plasma boundaries and fixed-boundary MHD equilibria for configurations that jointly meet requirements on confinement, field-line topology, force balance, stability proxies, and geometry. These specifications do not provide a general constructive map to a validated finite-beta equilibrium. High-quality targets are commonly developed through iterative numerical optimization whose outcome depends on the initial configuration, active Fourier resolution, objective priorities, and local solver budget. Coordinating this process is computationally costly and expert-intensive, limiting both design throughput and the production of consistently evaluated data. We present a proof of concept for \emph{agentic} stage-one optimization. A bounded language-model agent diagnoses the current equilibrium and selects the next local optimization experiment, while deterministic DESC execution owns prescribed profiles and flux, symmetry, metric evaluation, solver validity, and acceptance. On a common-budget subset from an expanding finite-beta campaign, the number of gate-valid configurations increases from five inputs to nineteen outputs; median Boozer QS RMS decreases from

2.39\times10^{-4}

to

1.07\times10^{-4}

, and median maximum principal curvature decreases from

62.56

to

33.00\,\mathrm{m}^{-1}

. A complementary long route achieves a

9.10\times

QS reduction while repairing magnetic-well and curvature defects. The system also records every attempted local action as transition evidence, yielding 734 structured parent--action--outcome records in the reported experiments. These results show that agentic outer-loop control can sustain finite-beta, multi-objective search and turn repeated optimization into a scalable source of improved equilibria and reusable decision data.

Tingjia Zhang, Zhuoran Meng, Runlai Xu

AI Agents for Scientific Discovery Multi-Objective Optimization Autonomous Experimentation

Aug 1, 2026cs.AI

Tracing the Cascade: A Topology-Aware Evaluation Framework for Scientific Agent Hallucinations

Large language model (LLM) agents are increasingly deployed in scientific research, where reliability is critical and the underlying knowledge is densely interconnected. In such settings, hallucinations are particularly damaging: a single erroneous claim on a foundational concept can propagate through multi-step reasoning and corrupt entire trajectories. Existing hallucination benchmarks largely operate at the surface level, treating facts in isolation and relying on uniform accuracy metrics that ignore this topological structure. We address this gap with SCHEMA, the first evidence-grounded, topology-aware evaluation framework for hallucinations in scientific agents. SCHEMA automatically constructs scientific concept graphs from benchmark seeds and literature evidence, synthesizes graph-grounded tasks spanning claim verification, multi-hop reasoning, open-ended explanation, and experimental code generation, and evaluates agents with two complementary diagnostics. A trajectory hallucination pipeline audits intermediate reasoning at scale via a topology-weighted severity score, while a multi-agent counterfactual attribution module pinpoints the causal mechanism behind selected failures. SCHEMA reveals that hallucinations concentrate at a small set of highly connected knowledge hubs, and that final-answer accuracy decouples from trajectory honesty; models often reach correct conclusions through structurally flawed reasoning. These results indicate that for high-stakes scientific applications, terminal accuracy alone is an insufficient signal of agent reliability, motivating mechanism-level evaluation grounded in knowledge topology. Code is available at https://github.com/circles-post/SCHEMA.

Xinshun Feng, Ziqi Miao, Lijun Li +1

Shanghai Artificial Intelligence Laboratory Shanghai, China

AI Agents for Scientific Discovery Hallucination in Language Models LLM Agent Evaluation LLM Hallucination Detection