# Empowering Biomedical Discovery with AI Agents

arXiv: https://arxiv.org/abs/2404.02831 · HTML: https://mlsanity.com/paper/2404.02831/

## Key facts

- Cited by 118 papers in the map (data through 14 Oct 2026).
- Builds on 108 of its 220 references that are in the map.
- First posted on arXiv 3 Apr 2024.

## Builds on (most cited first, 30 of 108)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [ReAct: Synergizing Reasoning and Acting in Language Models](https://mlsanity.com/paper/2210.03629/) (2022)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Direct Preference Optimization: Your Language Model is Secretly a Reward Model](https://mlsanity.com/paper/2305.18290/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Flamingo: a Visual Language Model for Few-Shot Learning](https://mlsanity.com/paper/2204.14198/) (2022)
- [Large Language Models are Zero-Shot Reasoners](https://mlsanity.com/paper/2205.11916/) (2022)
- [Zero-Shot Text-to-Image Generation](https://mlsanity.com/paper/2102.12092/) (2021)
- [Reflexion: Language Agents with Verbal Reinforcement Learning](https://mlsanity.com/paper/2303.11366/) (2023)
- [Toolformer: Language Models Can Teach Themselves to Use Tools](https://mlsanity.com/paper/2302.04761/) (2023)
- [Finetuned Language Models Are Zero-Shot Learners](https://mlsanity.com/paper/2109.01652/) (2021)
- [Generative Agents: Interactive Simulacra of Human Behavior](https://mlsanity.com/paper/2304.03442/) (2023)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [QLoRA: Efficient Finetuning of Quantized LLMs](https://mlsanity.com/paper/2305.14314/) (2023)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [InstructBLIP: Towards General-purpose Vision-Language Models with Instruction Tuning](https://mlsanity.com/paper/2305.06500/) (2023)
- [MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models](https://mlsanity.com/paper/2304.10592/) (2023)
- [Locating and Editing Factual Associations in GPT](https://mlsanity.com/paper/2202.05262/) (2022)
- [Do As I Can, Not As I Say: Grounding Language in Robotic Affordances](https://mlsanity.com/paper/2204.01691/) (2022)
- [A Survey on Large Language Model based Autonomous Agents](https://mlsanity.com/paper/2308.11432/) (2023)
- [Voyager: An Open-Ended Embodied Agent with Large Language Models](https://mlsanity.com/paper/2305.16291/) (2023)
- [PaLM-E: An Embodied Multimodal Language Model](https://mlsanity.com/paper/2303.03378/) (2023)

## Built on by (most cited first, 30 of 118)

- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [Towards Scientific Intelligence: A Survey of LLM-based Scientific Agents](https://mlsanity.com/paper/2503.24047/) (2025)
- [From Automation to Autonomy: A Survey on Large Language Models in Scientific Discovery](https://mlsanity.com/paper/2505.13259/) (2025)
- [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://mlsanity.com/paper/2503.00096/) (2025)
- [Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions](https://mlsanity.com/paper/2503.08979/) (2025)
- [LLM Agents for Education: Advances and Applications](https://mlsanity.com/paper/2503.11733/) (2025)
- [How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities](https://mlsanity.com/paper/2409.11654/) (2024)
- [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://mlsanity.com/paper/2405.17631/) (2024)
- [LLM Agents Making Agent Tools](https://mlsanity.com/paper/2502.11705/) (2025)
- [MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks](https://mlsanity.com/paper/2503.07459/) (2025)
- [Agent Design Pattern Catalogue: A Collection of Architectural Patterns for Foundation Model based Agents](https://mlsanity.com/paper/2405.10467/) (2024)
- [MicroVQA: A Multimodal Reasoning Benchmark for Microscopy-Based Scientific Research](https://mlsanity.com/paper/2503.13399/) (2025)
- [Hypothesis Generation for Materials Discovery and Design Using Goal-Driven and Constraint-Guided LLM Agents](https://mlsanity.com/paper/2501.13299/) (2025)
- [CPathAgent: An Agent-based Foundation Model for Interpretable High-Resolution Pathology Image Analysis Mimicking Pathologists' Diagnostic Logic](https://mlsanity.com/paper/2505.20510/) (2025)
- [MLRC-Bench: Can Language Agents Solve Machine Learning Research Challenges?](https://mlsanity.com/paper/2504.09702/) (2025)
- [Agentic AI Security: Threats, Defenses, Evaluation, and Open Challenges](https://mlsanity.com/paper/2510.23883/) (2025)
- [Evidence-based diagnostic reasoning with multi-agent copilot for human pathology](https://mlsanity.com/paper/2506.20964/) (2025)
- [LIDDIA: Language-based Intelligent Drug Discovery Agent](https://mlsanity.com/paper/2502.13959/) (2025)
- [ToolUniverse: An open platform for democratizing AI scientists](https://mlsanity.com/paper/2509.23426/) (2025)
- [MDCrow: Automating Molecular Dynamics Workflows with Large Language Models](https://mlsanity.com/paper/2502.09565/) (2025)
- [KGARevion: An AI Agent for Knowledge-Intensive Biomedical QA](https://mlsanity.com/paper/2410.04660/) (2024)
- [RAG-Enhanced Collaborative LLM Agents for Drug Discovery](https://mlsanity.com/paper/2502.17506/) (2025)
- [Empowering Scientific Workflows with Federated Agents](https://mlsanity.com/paper/2505.05428/) (2025)
- [μ-Bench: A Vision-Language Benchmark for Microscopy Understanding](https://mlsanity.com/paper/2407.01791/) (2024)
- [AutoElicit: Using Large Language Models for Expert Prior Elicitation in Predictive Modelling](https://mlsanity.com/paper/2411.17284/) (2024)
- [L-MTP: Leap Multi-Token Prediction Beyond Adjacent Context for Large Language Models](https://mlsanity.com/paper/2505.17505/) (2025)
- [SOP-Agent: Empower General Purpose AI Agent with Domain-Specific SOPs](https://mlsanity.com/paper/2501.09316/) (2025)
- [Episodic memory in AI agents poses risks that should be studied and mitigated](https://mlsanity.com/paper/2501.11739/) (2025)
- [Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics](https://mlsanity.com/paper/2510.09901/) (2025)
- [BioKGBench: A Knowledge Graph Checking Benchmark of AI Agent for Biomedical Science](https://mlsanity.com/paper/2407.00466/) (2024)

## Abstract (arXiv)

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.