AI Agents for Scientific Discovery

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Overview

AI agents for scientific discovery aim to help researchers move from questions and hypotheses to analysis, experiments, and evidence-backed conclusions. Common approaches combine language models with literature retrieval, code execution, scientific simulators, laboratory instruments, and specialized agents in iterative hypothesis–test–revision loops. Work spans fields such as materials science, biology, physics, chemistry, and mathematics, with systems also developing reusable skills and memories to build on prior results. A central challenge is ensuring that promising outputs are genuinely novel, scientifically valid, reproducible, and grounded in evidence, especially in long workflows and physical experiments.

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288 papers57 papers in the last four weeks, up 111% on the four weeks before. 0.3% of all new papers.

Mar 9, 2026

EvoScientist: Towards Multi-Agent Evolving AI Scientists for End-to-End Scientific Discovery

The increasing adoption of Large Language Models (LLMs) has enabled AI scientists to perform complex end-to-end scientific discovery tasks requiring coordination of specialized roles, including idea generation and experimental execution. However, most state-of-the-art AI scientist systems rely on static, hand-designed pipelines and fail to adapt based on accumulated interaction histories. As a result, these systems overlook promising research directions, repeat failed experiments, and pursue infeasible ideas. To address this, we introduce EvoScientist, an evolving multi-agent AI scientist framework that continuously improves research strategies through persistent memory and self-evolution. EvoScientist comprises three specialized agents: a Researcher Agent (RA) for scientific idea generation, an Engineer Agent (EA) for experiment implementation and execution, and an Evolution Manager Agent (EMA) that distills insights from prior interactions into reusable knowledge. EvoScientist contains two persistent memory modules: (i) an ideation memory, which summarizes feasible research directions from top-ranked ideas while recording previously unsuccessful directions; and (ii) an experimentation memory, which captures effective data processing and model training strategies derived from code search trajectories and best-performing implementations. These modules enable the RA and EA to retrieve relevant prior strategies, improving idea quality and code execution success rates over time. Experiments show that EvoScientist outperforms 7 open-source and commercial state-of-the-art systems in scientific idea generation, achieving higher novelty, feasibility, relevance, and clarity via automatic and human evaluation. EvoScientist also substantially improves code execution success rates through multi-agent evolution, demonstrating persistent memory's effectiveness for end-to-end scientific discovery.

Yougang Lyu, Xi Zhang, Yuyue Zhao +11

Huawei Technologies Co., Ltd. · Vrije Universiteit Amsterdam

Multi-Agent LLM SystemsAI Agents for Scientific DiscoveryScientific Code GenerationMemory-Augmented AgentsSelf-Evolving Agents
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Mar 9, 2026

AI Agents, Language, Deep Learning and the Next Revolution in Science

Modern science is reaching a critical inflection point. Instruments across disciplines, from particle physics and astronomy to genomics and climate modeling, now produce data of such scale, diversity, and interdependence that traditional analytical methods can no longer keep pace. This growing imbalance between data generation and data understanding signals the need for a new scientific paradigm. We propose that intelligent, human-supervised AI agents operating over deep-learning algorithms, represent the next evolution of the scientific method. Built upon large language models and multimodal learning, these agents can interpret scientific intent, design and execute analytical workflows, and ensure traceability through domain-specific languages that preserve human oversight and accountability. Particle physics, a historic incubator of computational innovation, offers the ideal testbed for this transition. At the Institute of High Energy Physics of the Chinese Academy of Sciences, the Dr. Sai system embodies this vision, a multi-agent reasoning framework deployed within collider research at the CEPC. This emerging approach does not replace human scientists but extends their cognitive reach, enabling discovery to scale with complexity and redefining how knowledge itself is produced in the age of intelligent machines. The significance of this paradigm transcends particle physics, offering a blueprint for all data-driven sciences facing the same complexity ceiling.

Ke Li, Beijiang Liu, Bruce Mellado +2

Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China · University of Chinese Academy of Sciences, Beijing 100049, China · School of Physics and Institute for Collider Particle Physics, University of the Witwatersrand, Johannesburg, Wits 2050, South Africa

AI Agents for Scientific DiscoveryHuman-in-the-Loop AIMulti-Agent LLM SystemsScientific Workflow Automation
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Mar 5, 2026

Agentic AI -- Physicist Collaboration in Experimental Particle Physics: A Proof-of-Concept Measurement with LEP Open Data

We present an agentic measurement of the thrust distribution in e+e−e^{+}e^{-} collisions at s=91.2\sqrt{s}=91.2 GeV using ALEPH archived data. This work was carried out through an AI agent-physicist collaboration, using interactive natural-language prompting of Anthropic Claude and OpenAI Codex. Under physicist guidance, the agents wrote and executed all analysis code and drafted the majority of the text included in this paper. A fully-corrected thrust spectrum is obtained via Iterative Bayesian Unfolding and Monte Carlo based corrections. The principal contribution of this work is the demonstration of the agentic analysis, with thrust serving as a benchmark observable for the method. Dedicated precision measurements of thrust are reported in the community elsewhere. This work represents a step toward a theory-experiment loop in which AI agents assist with experimental measurements and theoretical calculations, and synthesize insights by comparing the results, thereby accelerating the cycle that drives discovery in fundamental physics. Our work suggests that precision physics, leveraging the open LEP data and advanced theoretical landscape, provides an ideal testing ground for developing AI agent systems for scientific applications.

Anthony Badea, Marcello Maggi, Christopher McGinn +9

University of Chicago, Enrico Fermi Institute, 60637 IL, USA · Istituto Nazionale di Fisica Nucleare, Bari Division, BA 70126, Italy · Vanderbilt University, Nashville, Tennessee, USA +1

AI Agents for Scientific DiscoveryData Analysis AgentsHuman-AI CollaborationHigh-Energy Physics
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Mar 4, 2026

MACC: Multi-Agent Collaborative Competition for Scientific Exploration

Scientific discovery still relies heavily on the manual efforts of individual researchers, leading to limited exploration, redundant trials, and reduced reproducibility. Human-participant data analysis competitions generate diverse approaches, yet fluctuations in participation and the lack of independent repetitions show that parallel exploration alone is insufficient for achieving reliable scientific inquiry. As advanced AI agents based on large language models (LLMs) increasingly perform analytical tasks, relying on a single highly capable agent is unlikely to overcome these structural limitations. Recent work has begun to explore how multiple LLM-based agents can collaborate or compete in scientific workflows-a growing trend we refer to as MA4Science. However, most existing MA4Science studies assume that all agents are controlled by a single organizational entity, limiting their ability to examine how institutional mechanisms-such as incentives, information sharing, and reproducibility-shape collective exploration among independently managed agents. To address this gap, we introduce MACC (Multi-Agent Collaborative Competition), an institutional architecture that integrates a blackboard-style shared scientific workspace with incentive mechanisms designed to encourage transparency, reproducibility, and exploration efficiency. MACC provides a testbed for studying how institutional design influences scalable and reliable multi-agent scientific exploration.

Satoshi Oyama, Yuko Sakurai, Hisashi Kashima

Nagoya City University, Nagoya, Japan · Nagoya Institute of Technology, Nagoya, Japan · Kyoto University, Kyoto, Japan

Multi-Agent LLM SystemsAI Agents for Scientific DiscoveryMulti-Agent CollaborationMulti-Agent Systems
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Mar 4, 2026

Mozi: Governed Autonomy for Drug Discovery LLM Agents

Tool-augmented large language model (LLM) agents promise to unify scientific reasoning with computation, yet their deployment in high-stakes domains like drug discovery is bottlenecked by two critical barriers: unconstrained tool-use governance and poor long-horizon reliability. In dependency-heavy pharmaceutical pipelines, autonomous agents often drift into irreproducible trajectories, where early-stage hallucinations multiplicatively compound into downstream failures. To overcome this, we present Mozi, a dual-layer architecture that bridges the flexibility of generative AI with the deterministic rigor of computational biology. Layer A (Control Plane) establishes a governed supervisor--worker hierarchy that enforces role-based tool isolation, limits execution to constrained action spaces, and drives reflection-based replanning. Layer B (Workflow Plane) operationalizes canonical drug discovery stages -- from Target Identification to Lead Optimization -- as stateful, composable skill graphs. This layer integrates strict data contracts and strategic human-in-the-loop (HITL) checkpoints to safeguard scientific validity at high-uncertainty decision boundaries. Operating on the design principle of ``free-form reasoning for safe tasks, structured execution for long-horizon pipelines,'' Mozi provides built-in robustness mechanisms and trace-level audibility to completely mitigate error accumulation. We evaluate Mozi on PharmaBench, a curated benchmark for biomedical agents, demonstrating superior orchestration accuracy over existing baselines. Furthermore, through end-to-end therapeutic case studies, we demonstrate Mozi's ability to navigate massive chemical spaces, enforce stringent toxicity filters, and generate highly competitive in silico candidates, effectively transforming the LLM from a fragile conversationalist into a reliable, governed co-scientist.

He Cao, Siyu Liu, Fan Zhang +7

AI Agents for Scientific DiscoveryLLM Agent OrchestrationLong-Horizon LLM AgentsAI Agent GovernanceDrug Discovery
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Mar 2, 2026

SciDER: Scientific Data-centric End-to-end Researcher

While large language models accelerate scientific discovery, existing agents face severe limitations in adaptability, domain generalization, and multimodal scalability, often struggling to autonomously process raw, domain-specific experimental data. To overcome these barriers, we introduce SciDER, a multi-agent system designed to flexibly automate the entire research lifecycle. This framework employs a novel data-centric approach and integrates a dynamic multimodal skill system across four specialized sub-agents. Specifically, an ideation agent generates novel hypotheses via Evolutionary Idea Search, a data analysis agent systematically structures raw data, an experimentation agent synthesizes executable code grounded in dataset characteristics, and a critic agent drives iterative self-refinement. To democratize open-source scientific discovery, we release OpenSciDER-SFT-8K, a high-quality execution trajectory dataset, alongside the OpenSciDER-27B fine-tuned model. Across six benchmarks, SciDER and OpenSciDER obtain competitive or leading results, with especially strong gains on data-centric analysis, end-to-end research execution, and multimodal scientific visualization. By integrating data analysis with experimental execution, SciDER bridges the gap between abstract scientific reasoning and reproducible experimentation synthesis.

Ke Lin, Owais Aijaz, Yilin Lu +3

Data Science, College of William & Mary, Williamsburg, USA · Natural Language Processing, MBZUAI, Abu Dhabi, UAE · Computer Science, University of Minnesota, Minneapolis, USA +1

AI Agents for Scientific DiscoveryScientific Workflow AutomationMulti-Agent LLM SystemsMultimodal AgentsLLM Agent TrainingData Analysis Agents
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Feb 26, 2026

Agentic Exploration of PDE Spaces using Latent Foundation Models for Parameterized Simulations

Flow physics and more broadly physical phenomena governed by partial differential equations (PDEs), are inherently continuous, high-dimensional and often chaotic in nature. Traditionally, researchers have explored these rich spatiotemporal PDE solution spaces using laboratory experiments and/or computationally expensive numerical simulations. This severely limits automated and large-scale exploration, unlike domains such as drug discovery or materials science, where discrete, tokenizable representations naturally interface with large language models. We address this by coupling multi-agent LLMs with latent foundation models (LFMs), a generative model over parametrised simulations, that learns explicit, compact and disentangled latent representations of flow fields, enabling continuous exploration across governing PDE parameters and boundary conditions. The LFM serves as an on-demand surrogate simulator, allowing agents to query arbitrary parameter configurations at negligible cost. A hierarchical agent architecture orchestrates exploration through a closed loop of hypothesis, experimentation, analysis and verification, with a tool-modular interface requiring no user support. Applied to flow past tandem cylinders at Re = 500, the framework autonomously evaluates over 1,600 parameter-location pairs and discovers divergent scaling laws: a regime-dependent two-mode structure for minimum displacement thickness and a robust linear scaling for maximum momentum thickness, with both landscapes exhibiting a dual-extrema structure that emerges at the near-wake to co-shedding regime transition. The coupling of the learned physical representations with agentic reasoning establishes a general paradigm for automated scientific discovery in PDE-governed systems.

Abhijeet Vishwasrao, Francisco Giral, Mahmoud Golestanian +8

University of Michigan · Universidad Polit´ecnica de Madrid · Purdue University +3

AI Agents for Scientific DiscoveryPhysics-Based SimulationComputational Fluid DynamicsPDE Surrogate Modeling
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Feb 25, 2026

ArchAgent: Agentic AI-driven Computer Architecture Discovery

Agile hardware design flows are a critically needed force multiplier to meet the exploding demand for compute. Recently, agentic generative AI systems have demonstrated significant advances in algorithm design, improving code efficiency, and enabling discovery across scientific domains. Bridging these worlds, we present ArchAgent, an automated computer architecture discovery system built on AlphaEvolve. We show ArchAgent's ability to automatically design/implement state-of-the-art (SoTA) cache replacement policies (architecting new mechanisms/logic, not only changing parameters), broadly within the confines of an established cache replacement policy design competition. In two days without human intervention, ArchAgent generated a policy achieving a 5.3% IPC speedup improvement over the prior SoTA on public multi-core Google Workload Traces. On the heavily-explored single-core SPEC06 workloads, it generated a policy in just 18 days showing a 0.9% IPC speedup improvement over the existing SoTA (a similar "winning margin" as reported by the existing SoTA). ArchAgent achieved these gains 3-5x faster than prior human-developed SoTA policies. Agentic flows also enable "post-silicon hyperspecialization" where agents tune runtime-configurable parameters exposed in hardware policies to further align the policies with a specific workload (mix). Exploiting this, we demonstrate a 2.4% IPC speedup improvement over prior SoTA on SPEC06 workloads. Finally, we outline broader implications for computer architecture research in the era of agentic AI. For example, we demonstrate the phenomenon of "simulator escapes", where the agentic AI flow discovered and exploited a loophole in a popular microarchitectural simulator - a consequence of the fact that these research tools were designed for a (now past) world where they were exclusively operated by humans acting in good-faith.

Raghav Gupta, Akanksha Jain, Abraham Gonzalez +10

University of California, Berkeley · Google · Google DeepMind

Automated Algorithm DiscoveryAI Agents for Scientific Discovery
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Feb 24, 2026

Grounding LLMs in Scientific Discovery via Embodied Actions

Large Language Models (LLMs) have shown significant potential in scientific discovery but struggle to bridge the gap between theoretical reasoning and verifiable physical simulation. Existing solutions operate in a passive "execute-then-response" loop and thus lacks runtime perception, obscuring agents to transient anomalies (e.g., numerical instability or diverging oscillations). To address this limitation, we propose EmbodiedAct, a framework that transforms established scientific software into active embodied agents by grounding LLMs in embodied actions with a tight perception-execution loop. We instantiate EmbodiedAct within MATLAB and evaluate it on complex engineering design and scientific modeling tasks. Extensive experiments show that EmbodiedAct significantly outperforms existing baselines, achieving SOTA performance by ensuring satisfactory reliability and stability in long-horizon simulations and enhanced accuracy in scientific modeling.

Bo Zhang, Jinfeng Zhou, Yuxuan Chen +3

Tsinghua University, Beijing, China.

AI Agents for Scientific DiscoveryLLM GroundingLarge Language Model-Guided Scientific DiscoveryEmbodied Reasoning
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Feb 23, 2026

From Agent-Only Social Networks to Autonomous Scientific Research: Lessons from OpenClaw and Moltbook, and the Architecture of ClawdLab and Beach.Science

In January 2026, the open-source agent framework OpenClaw and the agent-only social network Moltbook produced a large-scale dataset of autonomous AI-to-AI interaction, attracting six academic publications within fourteen days. This study conducts a multivocal literature review of that ecosystem and presents two complementary platforms for autonomous scientific research as a design science response to the architectural failure modes identified. ClawdLab, an open-source platform for structured laboratory collaboration, addresses these failure modes through hard role restrictions, structured adversarial critique, PI-led governance, multi-model orchestration, and evidence requirements enforced through external tool verification, in which the principal investigator validates submitted work using available API calls, computational services, and model context protocol integrations rather than relying on social consensus. Beach.science, a public research commons, complements ClawdLab's structured laboratory model by providing a free-form environment in which heterogeneous agent configurations interact, discover research opportunities, and autonomously contribute computational analyses, supported by template-based role specialisation, extensible skill registries, and programmatic reward mechanisms that distribute inference resources to agents demonstrating scientific progress. A three-tier taxonomy distinguishes single-agent pipelines, predetermined multi-agent workflows, and fully decentralised systems, analysing why leading AI co-scientist platforms remain confined to the first two tiers. The composable third-tier architecture instantiated across ClawdLab and beach.science, in which foundation models, capabilities, governance, verification tooling, and inter-lab coordination are independently modifiable, enables compounding improvement as the broader AI ecosystem advances.

Lukas Weidener, Marko Brkić, Phillip Lee +3

Autonomous Research AgentsAI Agents for Scientific DiscoveryMulti-Agent CollaborationMulti-Agent SystemsAI Agent GovernanceMulti-Agent Orchestration
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Feb 20, 2026

Are LLMs Ready for Neural-integrated Mechanistic Modeling? A Benchmark and Agentic Framework

Large language models (LLMs) have shown promise in constructing mechanistic models from data. However, existing evaluations largely focus on simplified settings and fail to capture the complexity of real-world scientific modeling. In practice, such modeling often involves neural-integrated formulations, where a mechanistic model component and a neural network component are jointly constructed, leading to a significantly more complex search space. Motivated by this gap, we introduce the Neural-Integrated Mechanistic Modeling (NIMM) benchmark, which evaluates LLM-generated neural-integrated mechanistic models across three scientific domains. Experiments on NIMM reveal that existing LLM-based approaches struggle to effectively explore this complex space, resulting in limited search stability and solution quality. To address this challenge, we propose NIMMGen, a tree-guided agentic framework that enables diversified exploration via branch-level search and improves solutions through atomic model refinement. Extensive experiments demonstrate that NIMMGen achieves state-of-the-art performance on NIMM, significantly improving search stability and solution quality.

Zihan Guan, Rituparna Datta, Mengxuan Hu +5

University of Virginia

Large Language Model-Guided Scientific DiscoveryAI Agents for Scientific Discovery
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Feb 19, 2026

El Agente Gráfico: A Semantic Execution Runtime for Scientific Agents

Large language models (LLMs) can plan scientific workflows and generate code, but these capabilities do not specify how scientific state is validated, transferred and recorded across heterogeneous computational and experimental operations. Here we present El Agente Gráfico, a semantic execution runtime for scientific agents that uses typed execution graphs to enforce admissible scientific state transitions, record provenance and confine model judgement to explicit decision points. Using the same top-level LLM and task-specific rubrics on six university-level quantum chemistry exercises, El Agente Gráfico improved performance while reducing model cost by approximately 80% and wall-clock time by more than fourfold relative to our previous multi-agent architecture. Across ensemble spectroscopy and metal-organic framework (MOF) design, the runtime supported typed-state transfer, parallel execution and cross-session persistence. Open-ended studies of a disulfide redox mechanism and the vibrational hypothesis of olfaction required the agent to define the chemical scope and computational pathway of each investigation. A graph-construction skill distilled from these studies then enabled coding agents to author typed execution graphs for MOF literature mining. Together, these results show how typed execution graphs turn reusable procedural knowledge into scientific protocols that can be inspected, revised and transferred across computational and physical systems.

Jiaru Bai, Abdulrahman Aldossary, Thomas Swanick +12

Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada · Vector 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 +10

Computational Quantum ChemistryRuntime Enforcement for AI AgentsAI Agents for Scientific DiscoveryAgentic Workflows
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Feb 19, 2026

AutoNumerics: An Autonomous, PDE-Agnostic Multi-Agent Pipeline for Scientific Computing

PDEs are central to scientific and engineering modeling, yet designing accurate numerical solvers typically requires substantial mathematical expertise and manual tuning. Recent neural network-based approaches improve flexibility but often demand high computational cost and suffer from limited interpretability. We introduce AutoNumerics, a multi-agent framework that autonomously designs, implements, debugs, and verifies numerical solvers for general PDEs directly from natural language descriptions. Unlike black-box neural solvers, our framework generates transparent solvers grounded in classical numerical analysis. We introduce a coarse-to-fine execution strategy and a residual-based self-verification mechanism. Experiments on 24 canonical and real-world PDE problems demonstrate that AutoNumerics achieves competitive or superior accuracy compared to existing neural and LLM-based baselines, and correctly selects numerical schemes based on PDE structural properties, suggesting its viability as an accessible paradigm for automated PDE solving.

Jianda Du, Youran Sun, Haizhao Yang

Department of Mathematics, University of Maryland, College Park, MD, USA · Department of Computer Science, University of Maryland, College Park, MD, USA

PDE SolvingAutomated Algorithm DiscoveryAI Agents for Scientific DiscoveryLLM-Based Program Synthesis
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Feb 10, 2026

PeroMAS: A Multi-agent System of Perovskite Material Discovery

As a pioneer of the third-generation photovoltaic revolution, Perovskite Solar Cells (PSCs) are renowned for their superior optoelectronic performance and cost potential. The development process of PSCs is precise and complex, involving a series of closed-loop workflows such as literature retrieval, data integration, experimental design, and synthesis. However, existing AI perovskite approaches focus predominantly on discrete models, including material design, process optimization,and property prediction. These models fail to propagate physical constraints across the workflow, hindering end-to-end optimization. In this paper, we propose a multi-agent system for perovskite material discovery, named PeroMAS. We first encapsulated a series of perovskite-specific tools into Model Context Protocols (MCPs). By planning and invoking these tools, PeroMAS can design perovskite materials under multi-objective constraints, covering the entire process from literature retrieval and data extraction to property prediction and mechanism analysis. Furthermore, we construct an evaluation benchmark by perovskite human experts to assess this multi-agent system. Results demonstrate that, compared to single Large Language Model (LLM) or traditional search strategies, our system significantly enhances discovery efficiency. It successfully identified candidate materials satisfying multi-objective constraints. Notably, we verify PeroMAS's effectiveness in the physical world through real synthesis experiments.

Yishu Wang, Wei Liu, Yifan Li +8

Southeast University Nanjing, China · Sun Yat-Sen University Zhuhai, China · The Hong Kong University of Science and Technology Hong Kong, China +2

Multi-Agent LLM SystemsAI Agents for Scientific DiscoveryMaterials Science
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Feb 4, 2026

El Agente Quntur: A research collaborator agent for quantum chemistry

Quantum chemistry is a foundational enabling tool for the fields of chemistry, materials science, computational biology and others. Despite of its power, the practical application of quantum chemistry simulations remains in the hands of qualified experts due to methodological complexity, software heterogeneity, and the need for informed interpretation of results. To bridge the accessibility gap for these tools and expand their reach to chemists with broader backgrounds, we introduce El Agente Quntur, a hierarchical, multi-agent AI system designed to operate not merely as an automation tool but as a research collaborator for computational quantum chemistry. Quntur was designed following three main strategies: i) elimination of hard-coded procedural policies in favour of reasoning-driven decisions, ii) construction of general and composable actions that facilitate generalization and efficiency, and iii) implementation of guided deep research to integrate abstract quantum-chemical reasoning across subdisciplines and a detailed understanding of the software's internal logic and syntax. Although instantiated in ORCA, these design principles are applicable to research agents more generally and easily expandable to additional quantum chemistry packages and beyond. Quntur supports the full range of calculations available in ORCA 6.0 and reasons over software documentation and scientific literature to plan, execute, adapt, and analyze in silico chemistry experiments following best practices. We discuss the advances and current bottlenecks in agentic systems operating at the research level in computational chemistry, and outline a roadmap toward a fully autonomous end-to-end computational chemistry research agent.

Juan B. Pérez-Sánchez, Yunheng Zou, Jorge A. Campos-Gonzalez-Angulo +12

Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada · Vector Institute for Artificial Intelligence, W1140-108 College St., Schwartz Reisman Innovation Campus, Toronto, ON M5G 0C6, Canada · Acceleration Consortium, 700 University Ave., Toronto, ON M7A 2S4, Canada +6

AI Agents for Scientific DiscoveryComputational Quantum ChemistryQuantum ChemistryMulti-Agent CollaborationTool-Using AgentsAutonomous Research Agents
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Dec 12, 2025

AGAPI-Agents: An Open-Access Agentic AI Platform for Accelerated Materials Design on AtomGPT.org

Agentic AI systems increasingly connect large language models (LLMs) to external scientific tools, yet whether and when tool access improves prediction accuracy remains uncharacterized. We present AGAPI (AtomGPT.org API), an open access platform integrating eight open-source LLMs with 18 REST endpoints (28 agent tools, 50 web apps) spanning materials databases, force fields, tight-binding band structures, X-ray diffraction, and protein structure. A three-evaluation residual decomposition on JARVIS-Leaderboard electronic-structure test sets separates agent pipeline fidelity from inherited density functional theory (DFT) functional bias. For bulk modulus and bandgap the agent reproduces JARVIS-DFT entries to numerical precision, so the experimental-reference degradation is functional bias, not agentic malfunction. On memorization-resistant test sets (57 defective supercells, 60 hypothetical compositions), tool-augmented mean absolute error (MAE) is below 0.005 eV versus 1.25 to 1.86 eV tool-free, confirming tools are indispensable where parametric knowledge is unavailable. We further demonstrate autonomous multi-step workflows including 10-operation defect-engineering pipelines. AGAPI is available at https://github.com/atomgptlab/agapi.

Jaehyung Lee, Justin Ely, Kent Zhang +3

Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA · Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA · Department of Physics and Astronomy, West Virginia University, Morgantown, WV 26506, USA

AI Agents for Scientific DiscoveryLLM Agent EvaluationMaterials Property PredictionTool-Using AgentsComputational Materials Science
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Oct 2, 2025

Multi-Agent Design Assistant for the Simulation of Inertial Fusion Energy

Inertial fusion energy promises nearly unlimited, clean power if it can be achieved. However, the design and engineering of fusion systems requires controlling and manipulating matter at extreme energies and timescales; the shock physics and radiation transport governing the physical behavior under these conditions are complex requiring the development, calibration, and use of predictive multiphysics codes to navigate the highly nonlinear and multi-faceted design landscape. We hypothesize that artificial intelligence reasoning models can be combined with physics codes and emulators to autonomously design fusion fuel capsules. In this article, we construct a multi-agent system where natural language is utilized to explore the complex physics regimes around fusion energy. The agentic system is capable of executing a high-order multiphysics inertial fusion computational code. We demonstrate the capacity of the multi-agent design assistant to translate natural-language design goals into simulation execution, physics-emulator construction, analysis, and iterative refinement of capsule-geometry parameters, ultimately achieving simulated ignition within the computational design workflow.

Meir H. Shachar, Dane M. Sterbentz, Harshitha Menon +10

Lawrence Livermore National Laboratory Livermore, CA, USA · Lawrence Livermore National Laboratory Livermore, CA 94550, USA · Sandia National Laboratories Albuquerque, NM, USA +3

Multiphysics SimulationMulti-Agent LLM SystemsAI Agents for Scientific DiscoveryPhysics-Based Simulation
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Oct 1, 2025

Speak to a Protein: An Interactive Multimodal Co-Scientist

Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires specialized computational skills. We introduce Speak to a Protein, a new capability that turns protein analysis into an interactive, multimodal dialogue with an expert co-scientist. The AI system retrieves and synthesizes relevant literature, structures, and ligand data; grounds answers in a live 3D scene; and can highlight, annotate, manipulate and see the visualization. It also generates and runs code when needed, explaining results in both text and graphics. We demonstrate these capabilities on relevant proteins, posing questions about binding pockets, conformational changes, or structure-activity relationships to test ideas in real time. Speak to a Protein reduces the time from question to evidence, lowers the barrier to advanced structural analysis, and enables hypothesis generation by tightly coupling language, code, and 3D structures. Speak to a Protein is freely accessible at https://open.playmolecule.org.

Carles Navarro, Mariona Torrens, Philipp Thölke +2

Acellera Labs, C/ Doctor Trueta 183, 08005 Barcelona, Spain · Computational Science Laboratory, Universitat Pompeu Fabra, PRBB, C/ Doctor Aiguader 88, 08003 Barcelona, Spain · Instituci´o Catalana de Recerca i Estudis Avan¸cats (ICREA), Passeig Llu´ıs Companys 23, 08010 Barcelona, Spain

AI Agents for Scientific DiscoveryScientific QAMultimodal Tool Use
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Sep 29, 2025

Agentic Exploration of Physics Models

The process of scientific discovery relies on an interplay of observations, analysis, and hypothesis generation. Machine learning is increasingly being adopted to address individual aspects of this process. However, it remains an open challenge to fully automate the heuristic, iterative loop required to discover the laws of an unknown system by exploring it through experiments and analysis, without tailoring the approach to the specifics of a given task. Here, we introduce SciExplorer, an agent that leverages large language model tool-use capabilities to enable exploration of systems without any domain-specific blueprints, and apply it to physical systems that are initially unknown to the agent. We test SciExplorer on a broad set of models spanning mechanical dynamical systems, wave evolution, and quantum many-body physics. Despite using a minimal set of tools, primarily based on code execution, we observe impressive performance on tasks such as recovering equations of motion from observed dynamics and inferring Hamiltonians from expectation values. The demonstrated effectiveness of this setup opens the door toward similar scientific exploration in other domains, without the need for fine-tuning or task-specific instructions.

Maximilian Nägele, Florian Marquardt

Max Planck Institute for the Science of Light, Staudtstraße 2, 91058 Erlangen, Germany · Department of Physics, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstraße 5, 91058 Erlangen, Germany

AI Agents for Scientific DiscoveryScientific DiscoveryLarge Language Model-Guided Scientific Discovery
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Aug 4, 2025

AI Scientists for Building Virtual-Cell Models

Autonomous agents, from virtual laboratories to biological data-analysis agents and co-scientists, have begun to turn scientific goals into hypotheses. Whether they can go further and convert real, noisy and complex biological data into executable model hypotheses and architectures that encode testable assumptions remains unclear. Predicting how cells respond to genetic and chemical perturbations is a natural test of this ability: it is central to decoding disease mechanisms and therapeutic discovery, yet it demands cross-disciplinary expertise rarely concentrated in a single research group. Here, we introduce CellForge, an organized team of autonomous agents for single-cell perturbation modeling. Given a dataset and a task, it surveys the literature, parses the data, identifies relevant baselines, and formulates a model hypothesis through critic-mediated discussion among agents specialized in data modeling, single-cell biology, and deep learning. It then writes the training code, runs the experiments, and returns a trained predictor including architecture, code, and validation results. The architecture itself is the hypothesis: CellForge produces it end-to-end, with no human specifying the design, loss, or training protocol. Across six perturbation datasets spanning transcriptomic, epigenomic, and proteomic contexts, CellForge yields models that are competitive with hand-crafted state-of-the-art results on established tasks and extends the same workflow to paired multi-omic readouts. Blinded human evaluators rate CellForge's research plans as more scientifically sound and innovative than those from single LLMs or deep-research systems. In summary, we show autonomous agents can complete the full hypothesis-to-validation cycle in single-cell biology, with an AI effectively building another AI, in a complex setting that currently requires a team of human experts.

Xiangru Tang, Jiapeng Chen, Daniel Shao +12

Yale University · University of Pennsylvania · Helmholtz Zentrum München +3

AI Agents for Scientific DiscoveryAutonomous Research AgentsSingle-Cell Perturbation ModelingLLM Agent Orchestration
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Jul 28, 2025

GenoMAS: Guided Multi-Agent Programming for Scientific Discovery from Genomic Data

Gene expression analysis holds the key to many biomedical discoveries, yet extracting insights from raw transcriptomic data remains challenging due to the complexity of multiple large, semi-structured files and the need for extensive domain expertise. Current approaches either rely on inflexible workflows that fail in edge cases or fully autonomous agents that lack the precision required for rigorous scientific inquiry. GenoMAS addresses this by presenting a team of LLM-based agents that integrates structured workflows with autonomous adaptability, orchestrating diverse specialized agents through typed message-passing protocols. At its core lies a guided-planning framework where programming agents decompose task guidelines into Action Units and dynamically choose to advance, revise, bypass, or backtrack, maintaining logical coherence while adapting to the idiosyncrasies of genomic data. On the GenoTEX benchmark, GenoMAS achieves 89.13% CSC for data preprocessing and 60.48% F1F_1 for identifying trait-associated genes, surpassing prior art by 10.61% and 16.85%. Beyond transcriptomics, it outperforms strong agent baselines on ScienceAgentBench and DiscoveryBench, two independent bioinformatics benchmarks. Qualitative analysis shows that GenoMAS identifies gene-phenotype associations that are biologically plausible and corroborated by the literature.

Haoyang Liu, Yijiang Li, Haohan Wang

University of Illinois at Urbana-Champaign · University of California, San Diego

AI Agents for Scientific DiscoveryData Analysis AgentsLLM Agent PlanningLLM Agent OrchestrationGenomics
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Jul 24, 2025

Neural Architecture Discovery via Autonomous Evolution

Recent progress in LLM agents has advanced the prospect of autonomous research. Yet whether AI can complete difficult long-horizon tasks, especially those that advance AI research itself, remains largely unexplored. We present ASI-Arch, a system for AI-driven AI research that autonomously conducts neural architecture research through a closed-loop research-experiment-analyze-update process. Applied to linear attention, ASI-Arch ran 1,773 iterative experiments and discovered 105 state-of-the-art architectures. Its best architecture improves over DeltaNet by nearly three times the gain achieved by Mamba2. Beyond the final performance gains, we analyze the contributions of different parts of the framework in this hard research setting, shedding light on what enables autonomous progress in complex AI research tasks.

Weixian Xu, Yixiu Liu, Yang Nan +4

Shanghai Jiao Tong University · SII · GAIR +1

Autonomous Research AgentsAI Agents for Scientific DiscoveryNeural Architecture SearchLarge Language Model-Guided NASLinear Attention
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