BioDiscoveryAgent is an AI agent for closed loop design of biological experiments. BioDiscoveryAgent designs genetic perturbation experiments using only an LLM (Claude v1) paired with a suite of tools (literature search, gene search, AI critique).
Install required packages using the following command:
pip install -r requirements.txt
Claude API key is required for running the code. Please visit the Anthropic website for more information
- IFNG
- IL2
- Carnevale
- Scharenberg
To run BioDiscoveryAgent with all tools on the IFNG dataset:
python research_assistant.py --task perturb-genes-brief --model claude-1 --run_name test --data_name IFNG --steps 5 --num_genes 128 --log_dir v1
To preprocess your own dataset, please follow the instructions in the preprocessing notebook
Please cite our preprint if you use this code in your research:
@article{roohani2024,
title={BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments},
author={Roohani, Yusuf and Vora, Jian and Huang, Qian and Steinhart,
Zachary and Marson, Alexander, Liang, Percy and Leskovec, Jure},
journal={arXiv preprint},
year={2024},
}