AI for Antibiotics (AI4AB)

Deep learning recognises antibiotic mode of action from brightfield images

Overview

This repository contains the source code to reproduce the analysis from "Deep learning recognises antibiotic mode of action from brightfield images".

Installation

1. Clone the repository with git clone https://github.com/krentzd/ai4ab.git
2. Create a conda environment with python=3.9
3. Navigate to the direcotry containing the cloned repository and install the necessary packages in your conda environment with pip install -r requirements.txt

Usage

1. Download embedding data here
2. Unzip file and move embedding data to directory DATA in ai4ab
3. Run analysis notebooks

How to cite

@article{krentzel2025deep,
  title={Deep learning recognises antibiotic modes of action from brightfield images},
  author={Krentzel, Daniel and Kho, Kelvin and Petit, Julienne and Mahtal, Nassim and Chiaravalli, Jeanne and Shorte, Spencer L and Wehenkel, Anne Marie and Boneca, Ivo G and Zimmer, Christophe},
  journal={bioRxiv},
  pages={2025--03},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}