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Benchmarking code for Benchmarking Transcriptomics Foundation Models for Perturbation Analysis

Associated paper link : Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all

Usage

Installation

This code is currently tested with Python 3.9 and 3.10. No other Python version have been tested yet.

Current code is run with Pytorch 2.0.1 for CUDA 11.7. Other versions not tested yet.

Install pytorch using :

conda install pytorch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2 pytorch-cuda=11.7 -c pytorch -c nvidia
# Or 
pip install torch==2.0.1 torchvision==0.15.2 torchaudio==2.0.2

Except for pytorch, please install all dependencies using poetry.

Use poetry install on the root of repository.

Quickstart

Download data

All datasets are available through the following links : Part 1, Part 2, Part 3

replogle_2022 dataset has been split into 3 parts, it would need to be merged first through the following python code :

import anndata as ad

# Read the three split AnnData files
adata_part1 = ad.read_h5ad('replogle_2022_part1.h5ad')
adata_part2 = ad.read_h5ad('replogle_2022_part2.h5ad')
adata_part3 = ad.read_h5ad('replogle_2022_part3.h5ad')

# Concatenate the AnnData objects in the original order
adata_full = ad.concat([adata_part1, adata_part2, adata_part3], axis=0, join='outer')

# Save the concatenated AnnData object
adata_full.write_h5ad('replogle_2022.h5ad')

Prepare data

Create a datasets folder in the root of repository.

Run :

mkdir datasets/eval
mkdir datasets/train
mkdir datasets/test1
mkdir datasets/test2

Put full data anndata h5ad file in datasets/eval. You can use replogle_2022 or l1000_crispr, or use your own perturbation data for evaluation.

Prepare embeddings to evaluate

Extract the embeddings of your adata in datasets/eval using the models you want to evaluate.

Save the embeddings in adata.obsm['your_model_key'] of the datasets/eval adata. Shape and order should be the same as original data in adata.X and adata.obs.

Optional : Post-process embeddings to be evaluated

Post process the embeddings saved in the anndata file, if you want to explore post processing effect.

Three post processing approaches are handled : Centering, Center Scaling, and TVN.

In ./biomodalities/data/post_process.py, modify the following values to fit your data :

folder_path = './datasets/eval'
file_name = 'your_anndata_file.h5ad' # File to post-process

pert_col = "is_control" # Perturbation column in .obs
batch_col = "dataset_batch_num" # Batch column in .obs
control_key = True # Control value in perturbation column
obsm_keys = ["your_model_key"] # List of embedding obsm keys to post-process

Run post processing with the following command from root :

python -m biomodalities.data.post_process

Split data into train and test

We split data into train and test. We will have two test sets : test1 is for linear probing and knn, it shares the same perturbations as training, but has distinct batches. test2 is for reconstruction, it has distinct perturbations and distinct batches from training.

In ./biomodalities/data/data_split.py, modify the following to fit your data :

file_path = "./datasets/eval/crispr_l1000.h5ad" # your file path
batch = "gem_group" # Batch column
perturbation = "gene_id" # Perturbation column
control_column = "is_control" # Control column, can be the same as perturbation column
control_key = True # Control samples key

You can split your adata with the following command from root :

python -m biomodalities.data.data_split

Optional : Create config file

If you are using an evaluation dataset separate from replogle_2022 and l1000_cripr of the article, you will have to create a new configuration file for the evaluation dataset. Please refer to ./cfg/config/replogle_eval.yaml and ./cfg/config/replogle_eval_reconstruct.yaml for a template for creating your config file.

Wandb

You need to have wandb setup properly on your terminal and machine. Specify in your config yaml file the wandb project name and entity.

Running code

Run from root :

python main_eval.py --config ./cfg/config/replogle_eval.yaml --seed {{SEED}} --run_name {{JOB_NAME}} --eval_method {{JOB_TYPE}} --obsm_key {{OBSM_KEY}}

Replace {{JOB_TYPE}} with the evaluation of choice (bmdb, bmdb_precision, reconstruct, linear, knn, ilisi)

If you use SLURM for job management, run from root :

bash cfg/schedulers/submit_jobs.sh
# OR 
bash cfg/schedulers/submit_arrays.sh

Cite the work :

If this has been useful to you, cite us through :

@inproceedings{bendidi2024benchmarkingtranscriptomicsfoundationmodels,
      title={Benchmarking Transcriptomics Foundation Models for Perturbation Analysis : one PCA still rules them all}, 
      author={Ihab Bendidi and Shawn Whitfield and Kian Kenyon-Dean and Hanene Ben Yedder and Yassir El Mesbahi and Emmanuel Noutahi and Alisandra K. Denton},
      year={2024},
      booktitle={NeurIPS AIDrugX Workshop}, 
}