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awesome-bioagent-papers

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Agent self-driven repository on bio-agent papers, i.e. papers on LLM-based agents in biology and medicine.

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# Awesome bioagent papers [![Awesome](https://awesome.re/badge.svg)](https://awesome.re)

This repository, autonomously updated daily by our **Pantheon** agent system, collects papers on the applications of LLM-based agents in biology and medicine.

## Agent papers

- [2023.11 Preprint] [Validation of an LLM-based Multi-Agent Framework for Protein Engineering in Dry Lab and Wet Lab](https://arxiv.org/abs/2411.06029v1)
- [2023.12 Nature] [Autonomous chemical research with large language models](https://www.nature.com/articles/s41586-023-06792-0)
- [2023.12 Preprint] [Leveraging large language models for data analysis automation](https://www.biorxiv.org/content/10.1101/2023.12.11.571140v2.abstract)
- [2024.03 Advanced Science] [BioinspiredLLM: Conversational Large Language Model for the Mechanics of Biological and Bio-Inspired Materials](https://onlinelibrary.wiley.com/doi/full/10.1002/advs.202306724)
- [2024.03 Preprint] [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://arxiv.org/abs/2405.17631)
- [2024.04 Preprint] [CRISPR-GPT: An LLM Agent for Automated Design of Gene-Editing Experiments](https://arxiv.org/abs/2404.18021)
- [2024.04 Preprint] [Replicating a High-Impact Scientific Publication Using Systems of Large Language Models](https://www.biorxiv.org/content/10.1101/2024.04.08.588614v2.abstract)
- [2024.05 Preprint] [Agent Hospital: A Simulacrum of Hospital with Evolvable Medical Agents](https://arxiv.org/abs/2405.02957)
- [2024.05 Nature Machine Intelligence] [Augmenting large language models with chemistry tools](https://www.nature.com/articles/s42256-024-00832-8?fromPaywallRec=false)
- [2024.06 Preprint] [CellAgent: An LLM-driven Multi-Agent Framework for Automated Single-cell Data Analysis](https://www.biorxiv.org/content/10.1101/2024.05.13.593861v3)
- [2024.06 Nature] [A multimodal generative AI copilot for human pathology](https://www.nature.com/articles/s41586-024-07618-3)
- [2024.06 Preprint] [BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow](https://www.biorxiv.org/content/10.1101/2024.05.22.595240v2)
- [2024.06 Nature Methods] [Omega — harnessing the power of large language models for bioimage analysis](https://www.nature.com/articles/s41592-024-02310-w)
- [2024.06 Preprint] [MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning](https://arxiv.org/abs/2311.10537)
- [2024.08 Nature Methods] [BioImage.IO Chatbot: a community-driven AI assistant for integrative computational bioimaging](https://www.nature.com/articles/s41592-024-02370-y)
- [2024.09 Preprint] [Simplifying bioinformatics data analysis through conversation](https://www.biorxiv.org/content/10.1101/2023.10.29.564479v2.abstract)
- [2024.10 Preprint] [Multimodal learning of transcriptomes and text enables interactive single-cell RNA-seq data exploration with natural-language chats](https://www.biorxiv.org/content/10.1101/2024.10.15.618501v1)
- [2024.10 Preprint] [MMedAgent: Learning to Use Medical Tools with Multi-modal Agent](https://arxiv.org/abs/2407.02483)
- [2024.10 Preprint] [RNA-GPT: Multimodal Generative System for RNA Sequence Understanding](https://arxiv.org/abs/2411.08900)
- [2024.11 Preprint] [The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation](https://www.biorxiv.org/content/10.1101/2024.11.11.623004v1)
- [2024.11 Advanced Science] [An AI Agent for Fully Automated Multi-Omic Analyses](https://onlinelibrary.wiley.com/doi/10.1002/advs.202407094)
- [2024.11 Nature Medicine] [Collaboration between clinicians and vision–language models in radiology report generation](https://www.nature.com/articles/s41591-024-03302-1)
- [2024.11 eBioMedicine] [Generative AI agents are transforming biology research: high resolution functional genome annotation for multiscale understanding of life](https://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(24)00482-1/fulltext)
- [2024.11 Preprint] [DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration](https://arxiv.org/abs/2411.15692v1)
- [2024.11 Preprint] [PIORS: Personalized Intelligent Outpatient Reception based on Large Language Model with Multi-Agents Medical Scenario Simulation](https://arxiv.org/abs/2411.13902)
- [2024.12 Advanced Materials] [SciAgents: Automating Scientific Discovery Through Bioinspired Multi-Agent Intelligent Graph Reasoning](https://onlinelibrary.wiley.com/doi/full/10.1002/adma.202413523)
- [2024.12 Nature Machine Intelligence] [LLM-based agentic systems in medicine and healthcare](https://www.nature.com/articles/s42256-024-00944-1)
- [2024.12 Preprint] [AI-HOPE: An AI-Driven conversational agent for enhanced clinical and genomic data integration in precision medicine research](https://www.medrxiv.org/content/10.1101/2024.11.27.24318113v4)
- [2025.01 Preprint] [KG4Diagnosis: A Hierarchical Multi-Agent LLM Framework with Knowledge Graph Enhancement for Medical Diagnosis](https://arxiv.org/abs/2412.16833)
- [2025.01 Preprint] [Agent Laboratory: Using LLM Agents as Research Assistants](https://arxiv.org/abs/2501.04227)
- [2025.01 Preprint] [A Multi-Modal AI Copilot for Single-Cell Analysis with Instruction Following](https://arxiv.org/abs/2501.08187)
- [2025.01 Preprint] [BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems](https://arxiv.org/abs/2501.06314)
- [2025.01 Preprint] [BioMaster: Multi-agent System for Automated Bioinformatics Analysis Workflow](https://www.biorxiv.org/content/10.1101/2025.01.23.634608v1)
- [2025.02 Preprint] [scBaseCamp: an AI agent-curated, uniformly processed, and continually expanding single cell data repository](https://arcinstitute.org/manuscripts/scBaseCamp)
- [2025.02 Preprint] [Towards an AI co-scientist](https://arxiv.org/abs/2502.18864)
- [2025.02 Preprint] [Spike sorting AI agent](https://www.biorxiv.org/content/10.1101/2025.02.11.637754v1)
- [2025.03 Nature communications] [DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis](https://www.nature.com/articles/s41467-025-57430-4)
- [2025.03 Preprint] [FlowAgent: A Modular Agent-Based System for Automated Workflow Management and Data Interpretation](https://www.biorxiv.org/content/10.1101/2025.03.06.641728v1)
- [2025.03 Preprint] [TxAgent: An AI Agent for Therapeutic Reasoning Across a Universe of Tools](https://arxiv.org/abs/2503.10970)
- [2025.03 Preprint] [IAN: An Intelligent System for Omics Data Analysis and Discovery](https://www.biorxiv.org/content/10.1101/2025.03.06.640921v1)
- [2025.03 Preprint] [PharmAgents: Building a Virtual Pharma with Large Language Model Agents](https://arxiv.org/abs/2503.22164)
- [2025.03 Preprint] [CompBioAgent: An LLM-powered agent for single-cell RNA-seq data exploration](https://www.biorxiv.org/content/10.1101/2025.03.17.643771v1)
- [2025.07 Preprint] [GenoMAS: A Multi-Agent Framework for Scientific Discovery via Code-Driven Gene Expression Analysis](https://arxiv.org/abs/2507.21035) [[code]](https://github.com/Liu-Hy/GenoMAS) [[website]](https://liu-hy.github.io/GenoMAS/)

## Benchmarks

- [2024.06 MLCB 2025 Oral] [GenoTEX: An LLM Agent Benchmark for Automated Gene Expression Data Analysis](https://arxiv.org/abs/2406.15341) [[code]](https://github.com/Liu-Hy/GenoTEX) [[website]](https://liu-hy.github.io/GenoTEX/)
- [2025.03 Preprint] [BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning](https://arxiv.org/abs/2502.16660)
- [2025.03 Preprint] [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://arxiv.org/abs/2503.00096)
- [2025.03 Preprint] [MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research](https://arxiv.org/abs/2503.13399)

## Reviews

- [2023.05 Arquivos Brasileiros de Cirurgia Digestiva] [Future of the Language Models in Healthcare: The Role of ChatGPT](https://pmc.ncbi.nlm.nih.gov/articles/PMC10168663/)
- [2023.11 Preprint] [A Survey of Large Language Models in Medicine: Progress, Application, and Challenge](https://arxiv.org/abs/2311.05112)
- [2023.07 Lancet] [The promise of large language models in health care](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(23)00216-7/fulltext)
- [2024.04 npj Digital Medicine] [Evaluating large language models as agents in the clinic](https://www.nature.com/articles/s41746-024-01083-y)
- [2024.05 iScience] [The application of large language models in medicine: A scoping review](https://www.sciencedirect.com/science/article/pii/S2589004224009350)
- [2024.06 Preprint] [Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review](https://arxiv.org/abs/2403.15274)
- [2024.07 Preprint] [Empowering Biomedical Discovery with AI Agents](https://arxiv.org/abs/2404.02831v1)
- [2024.07 Nature Medicine] [Evaluating the clinical benefits of LLMs](https://doi.org/10.1038/s41591-024-03181-6)
- [2024.07 arXiv] [Large Language Models in Healthcare and Medical Domain: A Review](https://arxiv.org/abs/2401.06775v2)
- [2024.10 Cell] [Empowering biomedical discovery with AI agents](https://www.sciencedirect.com/science/article/pii/S0092867424010705)
- [2024.10 JCO Precision Oncology] [Expert-Guided Large Language Models for Clinical Decision Support in Precision Oncology](https://ascopubs.org/doi/10.1200/PO-24-00478)
- [2024.11 Preprint] [A Review of Large Language Models and Autonomous Agents in Chemistry](https://arxiv.org/abs/2407.01603)
- [2024.11 PLOS Digital Health] [Large language models in medicine: A review of current clinical trials across healthcare applications](https://doi.org/10.1371/journal.pdig.0000662)
- [2024.12 Computational and Structural Biotechnology Journal] [Large language models and their applications in bioinformatics](https://doi.org/10.1016/j.csbj.2024.09.031)
- [2024.12 Springer] [Large language models in medical and healthcare fields: applications, advances, and challenges](https://link.springer.com/article/10.1007/s10462-024-10921-0)
- [2024.08 Springer Link] [Large models for genomics](https://doi.org/10.1038/s41592-023-02105-5)
- [2024.05 PMC] [Clinical and Surgical Applications of Large Language Models: A Systematic Review](https://pmc.ncbi.nlm.nih.gov/articles/PMC11172607/)
- [2024.09 Artificial Intelligence Review] [Large language models in medical and healthcare fields: applications, advances, and challenges](https://link.springer.com/article/10.1007/s10462-024-10921-0)
- [2024.12 Nature Cancer] [How AI agents will change cancer research and oncology](https://www.nature.com/articles/s43018-024-00861-7)
- [2025.02 The Lancet] [The rise of agentic AI teammates in medicine](https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(25)00202-8/abstract)
- [2025.03 Trends in Biotechnology] [Large language model for knowledge synthesis and AI-enhanced biomanufacturing](https://www.cell.com/trends/biotechnology/fulltext/S0167-7799(25)00045-9#:~:text=LLMs%20empower%20metabolic%20models%20to,gain%20new%20insights%20and%20predictions)

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