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Code for paper: "Removing Biases from Molecular Representations via Information Maximization"

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# Removing Biases from Molecular Representations via Information Maximization

The repository contains the code for the `InfoCORE` method presented in the paper ***[Removing Biases from Molecular Representations via Information Maximization](https://arxiv.org/abs/2312.00718)**, Chenyu Wang, Sharut Gupta, Caroline Uhler, Tommi Jaakkola (2023)*. If you have any question, feel free to open an issue or reach out via email: wangchy@mit.edu.

![img](https://raw.githubusercontent.com/uhlerlab/InfoCORE/master/infocore.png)

## Set up the environment

```
conda create -n infocore python=3.10.9
conda activate infocore
bash env.sh
```

## Drug representation experiments
The data used in the drug representation experiments and pretrained models can be downloaded from https://www.dropbox.com/scl/fo/bcj0jf5gacgiapwl33f37/h?rlkey=8eh3v1ilm6r2scgh3mn7syci5&dl=0.

### Gene expression dataset (GE)
1. Data preparation
```
cd GE
mkdir model_save
```
Then add the downloaded data file `GE/data` into the directory `GE`.

2. Model training

The command for `InfoCORE` training can be found in `scripts/script_training.sh`.

3. Model evaluation

The command for the molecule-phenotype retrieval task can be found in `scripts/script_evalacc.sh`; the command for the property prediction task can be found in `scripts/script_finetune.sh`.

### Cell imaging dataset (CP)
1. Data preparation
```
cd CP
mkdir model_save
```
Then add the downloaded data file `CP/data` into the directory `CP`.

2. Model training

The command for `InfoCORE` training can be found in `scripts/script_training.sh`.

3. Model evaluation

The command for the molecule-phenotype retrieval task can be found in `scripts/script_evalacc.sh`; the command for the property prediction task can be found in `scripts/script_finetune.sh`.

## Citation
```
@inproceedings{wang2023removing,
  title={Removing Biases from Molecular Representations via Information Maximization},
  author={Wang, Chenyu and Gupta, Sharut and Uhler, Caroline and Jaakkola, Tommi S},
  booktitle={The Twelfth International Conference on Learning Representations},
  year={2023}
}
``````

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