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Empowering biomedical discovery with AI agents
Open accessAbstract
We envision "AI scientists" as systems capable of skeptical learning and reasoning that empower biomedical research through collaborative agents that integrate AI models and biomedical tools with experimental platforms. Rather than taking humans out of the discovery process, biomedical AI agents combine human creativity and expertise with AI's ability to analyze large datasets, navigate hypothesis spaces, and execute repetitive tasks. AI agents are poised to be proficient in various tasks, planning discovery workflows and performing self-assessment to identify and mitigate gaps in their knowledge. These agents use large language models and generative models to feature structured memory for continual learning and use machine learning tools to incorporate scientific knowledge, biological principles, and theories. AI agents can impact areas ranging from virtual cell simulation, programmable control of phenotypes, and the design of cellular circuits to developing new therapies.
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“collaborative agent teams have produced superior results on complex bioinformatics analyses and clinical decision support challenges where no single model excels [1,4].”
From A Review of Multi-Agent AI Systems for Biological and Clinical Data Analysis (2026) · cites this paper as [4]
In the citing paper
“In various domains, genomics, electronic health records, imaging, and beyond, MAS approaches have already demonstrated improved performance, reliability, and explainability compared to single-agent methods.”
From A Review of Multi-Agent AI Systems for Biological and Clinical Data Analysis (2026) · cites this paper as [4]
In the citing paper
“Furthermore, another critical feature of LLMs is their capability to use tools for automated online search, task design, and experiment execution [203–205], which exhibits their further capabilities in automatically collecting and preprocessing biomedical datasets, designing bioinformatic analyses to identify disease-related molecular regulations, conducting literature reviews for result inte”
From Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis (2025) · cites this paper as [205]
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Self-citationTALM: Tool Augmented Language Models
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Promptbreeder: Self-Referential Self-Improvement via Prompt Evolution
Fernando, C., Banarse, D., Michalewski, H., Osindero, S., & Rocktäschel, T. (2023) · arXiv · doi:10.48550/arxiv.2309.16797 · Cited by 31
Active learning for optimal intervention design in causal models
Zhang, J., Cammarata, L. V., Squires, C., Sapsis, T. P., & Uhler, C. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00719-0 · Cited by 29
Digital pipette: open hardware for liquid transfer in self-driving laboratories
Yoshikawa, N., Darvish, K., Vakili, M. G., Garg, A., & Aspuru‐Guzik, A. (2023) · Digital Discovery · doi:10.1039/d3dd00115f · Cited by 29
Confounding by linkage disequilibrium
Aı̈ssani, B. (2013) · Journal of Human Genetics · doi:10.1038/jhg.2013.130 · Cited by 26
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Epidemic Modeling with Generative Agents
Williams, R., Hosseinichimeh, N., Majumdar, A., & Ghaffarzadegan, N. (2023) · arXiv · doi:10.48550/arxiv.2307.04986 · Cited by 19
The Ethics of Interaction: Mitigating Security Threats in LLMsPreprint
Kumar, A., Murthy, S. V., Singh, S., & Ragupathy, S. (2024) · arXiv (Cornell University) · doi:10.48550/arxiv.2401.12273 · Cited by 19
De novo Drug Design using Reinforcement Learning with Multiple GPT Agents
Hu, X., Liu, G., Zhao, Y., & Zhang, H. (2023) · neural information processing systems · doi:10.52202/075280-0325 · Cited by 14
ChatDB: Augmenting LLMs with Databases as Their Symbolic Memory
Hu, C., Fu, J., Du, C., Luo, S., Zhao, J., & Zhao, H. (2023) · arXiv · doi:10.48550/arxiv.2306.03901 · Cited by 13
Hypothesis Search: Inductive Reasoning with Language ModelsPreprint
Wang, R., Zelikman, E., Poesia, G., Pu, Y., Haber, N., & Goodman, N. D. (2023) · arXiv (Cornell University) · doi:10.48550/arxiv.2309.05660 · Cited by 13
Enhancing Trust in LLM-Based AI Automation Agents: New Considerations and Future ChallengesPreprint
Schwartz, S., Yaeli, A., & Shlomov, S. (2023) · arXiv (Cornell University) · doi:10.48550/arxiv.2308.05391 · Cited by 13
Recruitment strategies and lessons learned from a large genetic study of African Americans
Salowe, R., Lee, R., Zenebe-Gete, S., Vaughn, M., Gudiseva, H. V., Pistilli, M., Kikut, A., Becker, E. M., Collins, D. W., He, J., et al. (2022) · PLOS Global Public Health · doi:10.1371/journal.pgph.0000416 · Cited by 12
Unreliable LLM bioethics assistants: Ethical and pedagogical risks
Goetz, L., Trengove, M., Trotsyuk, A., & Federico, C. A. (2023) · The American Journal of Bioethics · doi:10.1080/15265161.2023.2249843 · Cited by 12
GAIA: a benchmark for General AI Assistants
Mialon, G., Fourrier, C., Swift, C., Wolf, T., LeCun, Y., & Scialom, T. (2023) · arXiv · doi:10.48550/arxiv.2311.12983 · Cited by 12
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Self-citation
Flagged first, then by citations
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Sorted by citations
Agentic AI: Autonomous intelligence for complex goals–a comprehensive survey
Acharya, D. B., Kuppan, K., & Divya, B. (2025) · IEEE Access · doi:10.1109/access.2025.3532853 · Cited by 717
How to build the virtual cell with artificial intelligence: Priorities and opportunities
Bunne, C., Roohani, Y., Rosen, Y., Gupta, A., Zhang, X., Roed, M., Alexandrov, T., AlQuraishi, M., Brennan, P., Burkhardt, D. B., et al. (2024) · Cell · doi:10.1016/j.cell.2024.11.015 · Cited by 393
A review of large language models and autonomous agents in chemistry
Ramos, M. C., Collison, C. J., & White, A. D. (2025) · Chemical Science · doi:10.1039/d4sc03921a · Cited by 274
From text to insight: large language models for chemical data extraction
Schilling-Wilhelmi, M., Ríos-García, M., Shabih, S., Gil, M. V., Miret, S., Koch, C. T., Marquez, J. A., & Jablonka, K. M. (2024) · Chemical Society Reviews · doi:10.1039/d4cs00913d · Cited by 178
The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies
Swanson, K., Wu, W., Bulaong, N. L., Pak, J. E., & Zou, J. (2025) · Nature · doi:10.1038/s41586-025-09442-9 · Cited by 169
Metadata
- Authors
- Gao, S., Fang, A., Huang, Y., Giunchiglia, V., Noori, A., Schwarz, J. R., Ektefaie, Y., Kondic, J., & Zitnik, M.
- Affiliations
- Harvard University (US)
- Massachusetts Institute of Technology (US)
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2024-10
- Volume
- 187
- Issue
- 22
- Pages
- 6125-6151
- ISSN
- 0092-8674 (ISSN-L)
- OpenAlex
- W4403925918
- Cited by
- 315
- References
- 199
- Citations by year
- 2026: 168 · 2025: 135 · 2024: 12
- FWCI
- 7.19
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion, cc-by)
- arXiv (Cornell University) (cc-by)
- Funders
- Medical Research Council (T32 HG002295, MR/W00710X/1)
- National Institutes of Health (R01-HD108794)
- Harvard Medical School
- National Science Foundation (2339524, FA8702-15-D-0001)
- Aligning Science Across Parkinson's
- Harvard Data Science Initiative, Harvard University
- The Chan Zuckerberg Initiative
- National Human Genome Research Institute
- Milken Institute
- Topics
- Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
- Physical Sciences › Computer Science › Artificial Intelligence › Artificial Intelligence Applications
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Keywords
- AI agents, AI scientists, biomedical discovery, large language models, generative models, continual learning, structured memory, hypothesis generation, therapy design, human-AI collaboration
- MeSH terms
- Machine Learning, Artificial Intelligence, Humans, Biomedical Research
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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