awesome-ai-scientists

# Awesome AI Scientists [](https://awesome.re) [](https://github.com/natnew/awesome-ai-scientists/actions/workflows/ci.yml) [](LICENSE) [](https://github.com/natnew/awesome-ai-scientists/stargazers) [](https://github.com/natnew/awesome-ai-scientists/network/members) [](https://github.com/natnew/awesome-ai-scientists/graphs/contributors) [](https://github.com/natnew/awesome-ai-scientists/commits/main) [](https://github.com/natnew/awesome-ai-scientists/issues) [](https://github.com/natnew/awesome-ai-scientists) [](https://github.com/natnew/awesome-ai-scientists/blob/main/CONTRIBUTING.md) A curated collection of resources for building "AI Scientist" systems: AI that assists scientific discovery through literature intelligence, hypothesis generation, experiment planning, tool use, evaluation, and scientific communication.

     

Contents

• Foundational Papers & Systems
• Surveys & Overviews
• Literature Intelligence & Knowledge Extraction
• Hypothesis Generation & Ideation
• Experiment Planning & Design
• Tool-Use & Lab Automation
• Multi-Agent Architectures for Science
• Benchmarks & Evaluation
• Datasets for Scientific AI
• Scientific Communication & Reporting
• Ethics, Safety & Responsible AI for Science
• Domain: Drug Discovery & Chemistry
• Domain: Materials Science
• Domain: Genomics & Biology
• Domain: Climate & Earth Sciences
• Domain: Physics & Mathematics
• Hugging Face Models & Resources
• Agent Frameworks (General-Purpose)
• Meta-Resources & Awesome Lists

Foundational Papers & Systems

Landmark systems that define the AI Scientist paradigm.

• The AI Scientist v1 - Sakana AI, 2024. First end-to-end system for fully automated scientific discovery. Generates ideas, writes code, runs experiments, and produces LaTeX papers with automated peer review at roughly $15 per paper.
• The AI Scientist v2 - Sakana AI, 2025. Adds agentic tree search, removes human-authored templates, and produced the first fully AI-generated paper accepted at an ICLR 2025 workshop.
• Coscientist - Boiko et al., Nature 2023. GPT-4 autonomously designs, plans, and performs chemistry experiments via web search, code execution, and robotic lab control.
• ChemCrow - Bran et al., Nature Machine Intelligence 2024. An LLM augmented with 18 chemistry tools including RDKit, PubChem, retrosynthesis engines, and robotic synthesis tools.
• Google DeepMind AI Co-Scientist - Gottweis et al., 2025. A multi-agent Gemini 2.0 system using generate-debate-evolve with tournament-based Elo ranking.
• Robin - FutureHouse, 2025. An end-to-end drug discovery system that orchestrates specialized agents from literature review through experiment design.
• FunSearch - DeepMind, Nature 2024. Pairs an LLM with a systematic evaluator to search in function space and discover new mathematical constructions.
• Agent Laboratory - Schmidgall et al., 2025. A PhD, postdoc, and reviewer agent pipeline with large cost reductions versus earlier autonomous methods.
• AI-Researcher - NeurIPS 2025. A full pipeline from literature review to publication.
• Kosmos - Supports 200 parallel agent rollouts and large code-generation runs.
• Stanford Ideation Study - Si, Yang, and Hashimoto, 2024. LLM-generated research ideas were judged more novel than expert human ideas in blind evaluation.

Surveys & Overviews

• What’s Missing in Autonomous Research? - Ren et al., 2026. A systematization of 56 autonomous-research systems that separates what a system can produce from what it can defend, and formalizes missing release-gate architecture.
• Scientific Discovery in the Age of AI - Nature, 2023. A broad review of AI breakthroughs across the research lifecycle.
• Agentic AI for Scientific Discovery - 2025. Categorizes existing systems across chemistry, biology, and materials science.
• Towards Scientific Intelligence: LLM-based Scientific Agents - 2025. A taxonomy of LLM-based scientific agent architectures and evaluation benchmarks.

Literature Intelligence & Knowledge Extraction

Tools for searching, retrieving, synthesizing, and extracting knowledge from scientific literature.

RAG & QA Systems

• PaperQA2 - FutureHouse. An agentic RAG system for scientific literature search, summarization, and contradiction detection.
• OpenScholar - Allen AI and UW, Nature 2025. An open retrieval-augmented LM that searches 45M open-access papers.
• Elicit - An AI research assistant for structured literature extraction and screening.
• BGPT - REST, Python, and MCP API for scientific paper search, returning structured study evidence such as methods, sample sizes, limitations, quality scores, conflicts of interest, and data availability.

• Nujan - Split-view scientific paper reader with dual-pane PDF and AI assistance, mathematical derivation breakdowns, methodological critique, and multi-paper synthesis.

• Lune Research - MCP server for full-text search over peer-reviewed computer-science papers, citation traversal, evidence extraction, and claim verification against verbatim source passages; requires a Lune account.
• Nujan - Split-view scientific paper reader with dual-pane PDF and AI assistance, mathematical derivation breakdowns, methodological critique, and multi-paper synthesis.

Knowledge Graphs & Metadata APIs

• OpenAlex - A fully open knowledge graph with hundreds of millions of works, authors, and institutions.
• Semantic Scholar API - Allen AI. A free API with 200M+ papers, citation graphs, recommendations, and AI-generated TL;DRs.
• S2ORC - Allen AI. A large open corpus of machine-readable full-text academic papers.
• ORKG - A machine-actionable platform for comparing research contributions.
• scite.ai - Smart citation analysis that classifies citations as supporting, contrasting, or mentioning.
• Connected Papers - A visual graph tool for exploring citation neighborhoods.
• CORE - An open-access full-text aggregator with hundreds of millions of metadata records.

Scientific Language Models

• Galactica - Meta AI. A 120B-parameter scientific language model trained on papers, textbooks, and knowledge bases.
• SciBERT - Allen AI. BERT trained on 1.14M scientific papers with a scientific vocabulary.
• BioGPT - Microsoft. A biomedical language model with strong QA and relation-extraction performance.
• BioMedLM - Stanford CRFM. A 2.7B-parameter biomedical language model.

Hypothesis Generation & Ideation

Systems for AI-driven hypothesis generation, novelty detection, and research ideation.

• SciMON - Wang et al., ACL 2024. Retrieves inspirations from prior work and iteratively optimizes ideas for novelty.
• ResearchAgent - Microsoft and KAIST, 2024. Defines problems, proposes methods, and designs experiments with reviewing agents.
• IDEAgent - A multi-agent research ideation system that applies quality-diversity search to evolve populations of candidate ideas, retaining diverse, high-quality directions for hypothesis generation.
• Scideator - UW and Allen AI. Decomposes papers into facets and recombines them for structured ideation.
• KG-CoI - Xiong et al., 2024. A knowledge-graph-grounded hypothesis generation system with hallucination detection.
• SpecEvo - Ha et al., NUS, 2026. An evolutionary search framework in which cheap LLMs do most of the exploring and a frontier model steps in at a few checkpoints, matching frontier-only baselines at up to 80% lower API cost. Code.

Experiment Planning & Design

Bayesian optimization, adaptive design, and intelligent experiment selection.

• BoTorch - Meta. A modular Bayesian optimization library on PyTorch.
• Ax Platform - Meta. A production-grade experiment management platform built on BoTorch.
• BayBE - Merck KGaA. Bayesian optimization for chemistry with built-in chemical encodings and transfer learning.
• Dragonfly - Scalable Bayesian optimization for high-dimensional and multi-fidelity problems.
• Summit - Chemical reaction optimization benchmarks and strategies.
• Olympus - Algorithm benchmarking with experimentally derived datasets.
• Phoenics - Bayesian optimization for categorical search spaces.
• GRYFFIN - Descriptor-aware optimization for categorical chemical spaces.

Tool-Use & Lab Automation

Frameworks connecting AI reasoning to scientific databases, code execution, and physical instruments.

Robotic & Cloud Lab Platforms

• Opentrons - Open-source lab robotics with a Python API.
• ChemOS 2.0 - An open-source self-driving lab orchestration platform using SiLA2.
• Emerald Cloud Lab - Remote access to hundreds of instruments with built-in lab information systems.
• Benchling - Biotech data infrastructure with ELN, LIMS, and molecular biology tooling.

Scientific Database APIs

• PubChem - A massive chemistry database with programmatic access via PUG-REST.
• UniProt - Comprehensive protein sequence and functional data.
• ChEMBL - A large database of bioactive compounds with REST access.
• Materials Project - Computed materials data with API access via mp-api.
• PDB (Protein Data Bank) - Experimentally determined macromolecular structures with REST and GraphQL interfaces.

Multi-Agent Architectures for Science

Systems where multiple specialized agents collaborate, debate, and refine scientific work.

• Agon - Sun et al., 2026. An autonomous large-scale omnidisciplinary research system built around Prompt Economy with scientist, coder, and auditor loops coordinated by prompt dispatchers.
• SciAgents - Ghafarollahi and Buehler, MIT 2024. A KG plus multi-agent pipeline for materials discovery built on AutoGen.
• AgenticSciML - 2025. Uses proposers, critics, engineers, retrievers, and evaluators for scientific ML.
• VirSci - Su et al., 2024. Uses agents with different scientific backgrounds to improve research potential.
• AgentRxiv - Schmidgall et al., 2025. A centralized preprint server where autonomous agents publish and build on each other’s work.
• A Society of Researchers - 2026. Proposes institutions and resource-allocation rules that organise large populations of autonomous research agents without a central task manager, with humans limited to governance.
• Multi-Agent Debate - Du et al., ICML 2024. Foundational work showing that debate between LLM instances improves reasoning.
• ChatDev - A multi-agent software development framework adaptable to scientific workflows.
• CAMEL - A role-playing agent communication framework.
• Sage-A1.5 - Intern Science (Shanghai AI Laboratory), 2026. An open-weights 35B mixture-of-experts agentic model that delegates to parallel subagents with separate contexts, checks its own progress and evidence, and leaves inspectable research artefacts. Model.

Benchmarks & Evaluation

Measuring scientific AI capabilities across reasoning, coding, and autonomous research.

• ScienceAgentBench - ICLR 2025. A benchmark with 102 tasks drawn from peer-reviewed scientific workflows.
• GPQA - Rein et al., 2023. Graduate-level Google-proof questions across biology, physics, and chemistry.
• SciCode - NeurIPS 2024. Research coding problems across 16 scientific subdomains.
• MLAgentBench - A benchmark suite for research-agent experimentation ability.
• ST-Bench (multi-agent system generation) - 2026. A benchmark that evaluates how well LLMs generate multi-agent systems for scientific research tasks with spatial and temporal structure.
• SciFact - A benchmark for scientific claim verification.
• SciBench - Open-ended collegiate STEM problem solving.
• BioASQ - Biomedical information retrieval and question answering.
• IdeaBench - A benchmark for evaluating research-idea generation quality.
• IdeaGene-Bench - A benchmark for evaluating scientific lineage reasoning and lineage-grounded idea generation.
• REFUTE - Apache-2.0 benchmark for evaluating scientific critique, falsification, uncertainty calibration, overclaim detection, and evidence-grounded reasoning in LLMs.
• Agent4Sci - Zhong et al., NeurIPS 2026 Datasets & Benchmarks. Twenty long-horizon scientific-ML benchmarks across 11 domains for testing whether frontier agents can beat published best results, with analysis showing most gains came from ML engineering rather than research insight. Code.

Datasets for Scientific AI

Dataset	Domain	Size	Path or link
GPQA	Bio/Physics/Chem	448 questions	idavidrein/gpqa
SciFact	Biomedical claims	1,400 claims	allenai/scifact
SciQ	Science exam QA	13,679 questions	allenai/sciq
PubMedQA	Biomedical research	1K+ labeled	qiaojin/PubMedQA
MMLU-Pro	STEM-heavy QA	12K+ questions	TIGER-Lab/MMLU-Pro
S2ORC	Full-text papers	81.1M papers	Allen AI S2ORC
The Pile	Mixed scientific text	Large	EleutherAI
MoleculeNet	Molecular benchmarks	Multiple datasets	DeepChem docs
MatBench	Materials properties	13 tasks	GitHub
Open Catalyst	Catalysis/DFT	1.3M+ relaxations	OCP project
QM9	Quantum chemistry	134K molecules	Various mirrors

Scientific Communication & Reporting

Automating the last mile from results to manuscripts, figures, and reports.

• AI Scientist Paper Module - Sakana AI. Generates LaTeX manuscripts with figures, citations, and automated review.
• Manubot - Open-source collaborative manuscripts via Markdown and GitHub-based automation.
• SciNote - An open-source ELN with manuscript-writing support.
• SciencePlots - One-line Matplotlib style sheets for publication figures.
• LLM4Papers - An AI editing agent for Overleaf documents.
• Paperpal - Academic language improvement trained on scholarly writing.
• Writefull - An academic English writing assistant with Overleaf integration.
• tikzplotlib - Converts Matplotlib figures to TikZ and PGFPlots for LaTeX.
• ScholarCopilot - TIGER-Lab. LLM trained for academic writing that drafts text with accurate, retrieval-grounded citations.

Ethics, Safety & Responsible AI for Science

Dual-use concerns, hallucination, reproducibility, epistemic integrity, and governance.

Key Papers & Reports

• Dual-use capabilities of concern of biological AI models - Carter, Sandbrink et al., 2025. Proposes evaluation methods with preset risk thresholds and mitigation actions.
• AI Hallucination Taxonomy - Zhou et al., 2024. A classification of distorted information in AI-generated content.
• The ethics of using AI in scientific research - Resnik & Hosseini, 2024. Actionable recommendations for responsible AI use in science.
• AI Scientist Evaluation (ARI) - Beel, Kan & Baumgart, 2025. A critical assessment of AI Scientist v1 limitations, failure modes, and risks.

Policy Frameworks

• EU Living Guidelines on Responsible Use of Generative AI in Research - Guidance on transparency, responsibility, and non-authorship for AI systems.
• UNESCO Recommendation on the Ethics of AI - A global standard with readiness and ethical impact assessment tools.
• OECD AI in Science - Policy proposals on research integrity, open science, and LLM quality standards.

Authorship and Publishing

• Project Rachel: Can an AI Become a Scholarly Author? - Discusses how AI scientists can publish under their own name (arXiv 2511.14819, 2025).

Practical Tools

• SecureDNA - DNA synthesis screening to reduce biosecurity risks.
• Guardrails AI - Validation and control tooling for LLM outputs.
• FactScore - Fine-grained fact verification for model outputs.

Domain: Drug Discovery & Chemistry

Toolkits & Platforms

• RDKit - Industry-standard open-source cheminformatics.
• DeepChem - Deep learning tooling for drug discovery, materials science, and quantum chemistry.
• TorchDrug - A GPU-accelerated graph-based molecular ML platform.
• Open Babel - Chemical file format conversion and molecular toolkit.

Molecular Generation & Docking

• DiffDock - MIT, 2022. Diffusion-based molecular docking.
• REINVENT 4 - AstraZeneca. De novo drug design via reinforcement learning.
• MoleculeSTM - Multi-modal molecular understanding across SMILES, graphs, and text.
• AutoDock Vina - A fast and widely used molecular docking system.
• Uni-Mol - A 3D molecular pretraining framework.

Retrosynthesis & Reactions

• AiZynthFinder - AstraZeneca. Template-based retrosynthetic planning via Monte Carlo tree search.
• RXN for Chemistry - IBM. Transformer-based chemical reaction prediction.
• ASKCOS - MIT’s retrosynthesis and pathway planning platform.

Chemistry Agents

• ChemCrow - An LLM plus chemistry-tools agent system.

Domain: Materials Science

• MACE - Higher-order equivariant message passing for interatomic potentials.
• CHGNet - A universal ML potential trained on Materials Project data.
• M3GNet - A graph neural network potential for the periodic table.
• Matbench Discovery - Benchmarks universal potentials on materials discovery tasks.
• Pymatgen - A comprehensive Python materials analysis library.
• JARVIS - NIST. DFT, ML, and force-field calculations for tens of thousands of materials.
• Materials Project API - Computed materials data with API access.
• CDVAE - Crystal Diffusion VAE for periodic materials generation.
• GNoME - DeepMind, Nature 2023. Predicts millions of stable crystals.

Domain: Genomics & Biology

Protein Structure & Language Models

• AlphaFold - DeepMind’s protein structure prediction system; AlphaFold 2 and 3 weights and code, with AlphaFold 3 extending coverage to DNA, RNA, and ligands.
• OpenFold 3 - Columbia. An open-source AlphaFold 3 reproduction.
• Protenix - ByteDance. Biomolecular structure prediction plus de novo protein-binder design.
• ESM-2 - Meta AI. Protein language modeling up to 15B parameters.
• ESM Cambrian - Next-generation ESM models with major speedups.
• ESMFold - Single-sequence protein folding in Hugging Face Transformers.
• Boltz-1 - Open-source biomolecular structure prediction.
• Chai-1 - Multi-purpose molecular structure prediction.
• RFDiffusion - Baker Lab. Protein design via diffusion models.

Genomic Foundation Models

• Evo 2 - Arc Institute. A 40B-parameter genomic model trained on 9.3T DNA bases.
• Enformer - DeepMind. Predicts gene expression from DNA sequence across long contexts.
• Nucleotide Transformer - InstaDeep and NVIDIA. Foundation models for genomics.
• HyenaDNA - Stanford. Long-range genomic sequence modeling at single-nucleotide resolution.
• DNABERT-2 - A multi-species genome foundation model.

Single-Cell & Omics

• scvi-tools - Deep learning tooling for single-cell omics.
• scGPT - A foundation model for single-cell biology.
• Geneformer - Christina Theodoris. A transformer pretrained on 30M single-cell transcriptomes.

Domain: Climate & Earth Sciences

• GraphCast - DeepMind, Science 2023. A fast 10-day weather model at 0.25-degree resolution.
• Aurora - Microsoft, 2025. A 1.3B-parameter atmospheric model spanning weather, chemistry, and air quality.
• Prithvi WxC - IBM and NASA. An open foundation model for weather and climate.
• FourCastNet - NVIDIA. Fourier neural operators for global weather forecasting.
• Pangu-Weather - Huawei, Nature 2023. A 3D neural weather model.
• ClimaX - Microsoft. A foundation model for weather and climate.
• WeatherBench 2 - Google Research and ECMWF. An evaluation framework for data-driven weather models.
• Climate Change AI - A community focused on the intersection of climate change and machine learning.

Domain: Physics & Mathematics

• PySR - Symbolic regression for interpretable scientific equations.
• LaSR - LLM-guided concept evolution for symbolic regression.
• LeanDojo - An end-to-end framework for AI theorem proving in Lean 4.
• AlphaProof - DeepMind’s IMO-level mathematical reasoning system.
• AlphaGeometry 2 - DeepMind’s olympiad geometry theorem prover.
• Learning to Discover Interesting Mathematics - Patel et al., 2026. Trains an LLM conjecturer against a proof-to-statement-length interestingness signal and grows a library of Lean-verified theorems with reduced overlap with Mathlib.
• DeepXDE - Physics-informed neural networks for differential equations.
• torchdiffeq - Neural ordinary differential equations in PyTorch.
• SciML - The Julia ecosystem for scientific ML and differential equation solving.

Hugging Face Models & Resources

Model	HF Path	Domain	Notes
ESM-2 (3B)	facebook/esm2_t36_3B_UR50D	Protein	8M-15B parameter family
ESMFold	facebook/esmfold_v1	Protein structure	Single-sequence folding
ESM Cambrian	EvolutionaryScale/esmc-600m-2024-12	Protein	Up to 6B parameters
BioGPT	microsoft/biogpt	Biomedical NLP	Strong PubMed QA signal
SciBERT	allenai/scibert_scivocab_uncased	Scientific NLP	Scientific vocabulary
BioMedLM	stanford-crfm/BioMedLM	Biomedical	2.7B parameters
Galactica (6.7B)	facebook/galactica-6.7b	General science	Part of a larger family
ChemBERTa	seyonec/ChemBERTa-zinc-base-v1	Molecular	SMILES-trained
Prithvi WxC	ibm-nasa-geospatial/Prithvi-WxC	Weather/Climate	2.3B parameters
Geneformer	ctheodoris/Geneformer	Single-cell	30M transcriptomes

Agent Frameworks (General-Purpose)

Not science-specific, but widely used to build scientific agent systems.

• LangChain - Foundation for many scientific LLM-agent applications.
• LangGraph - Stateful, multi-actor agent orchestration built on LangChain.
• AutoGen / AG2 - Microsoft. A multi-agent conversation framework.
• CrewAI - A role-playing multi-agent framework.
• Semantic Kernel - Microsoft. Enterprise-grade AI orchestration.
• Haystack - An end-to-end NLP and RAG framework from deepset.
• DSPy - Stanford. Programming language-model pipelines instead of hand-tuned prompting.

Meta-Resources & Awesome Lists

• Awesome-LLM-Scientific-Discovery - HKUST. A broad list of LLM resources across the scientific method.
• awesome-ai-for-science - A broad AI-for-science resource list across domains.
• LLMs-in-science - White Lab. A living bibliography of LLM scientific agents.

Contributing

Thrilled to have you here.
Whether it's a quick typo fix, a fresh resource,
a doc polish, or a sweeping overhaul — every contribution helps this list grow.
Jump in and join the community — PRs of every size are welcome. 📝 [Read the contributing guide](/awesome-ai-scientists/CONTRIBUTING.md) · 🐛 [good first issues](https://github.com/natnew/awesome-ai-scientists/issues?q=is%3Aissue+is%3Aopen+label%3A%22good+first+issue%22)

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