diff --git a/README.md b/README.md index 878a1de..d92a416 100644 --- a/README.md +++ b/README.md @@ -57,11 +57,14 @@ The pipeline is configured to run on task 1 with the `mae_ps_enet` model across If you use LEAP in your research, please cite our paper: ```bibtex -@article{bodinier2025predicting, - title={Predicting gene essentiality and drug response from perturbation screens in preclinical cancer models with LEAP: Layered Ensemble of Autoencoders and Predictors}, - author={Bodinier, Barbara and Dissez, Gaetan and Bleistein, Linus and Dauvin, Antonin}, - journal={arXiv preprint arXiv:2502.15646}, - year={2025} +@misc{bodinier2025predictinggeneessentialitydrug, + title={Predicting gene essentiality and drug response from perturbation screens in preclinical cancer models with LEAP: Layered Ensemble of Autoencoders and Predictors}, + author={Barbara Bodinier and Gaetan Dissez and Lucile Ter-Minassian and Linus Bleistein and Roberta Codato and John Klein and Eric Durand and Antonin Dauvin}, + year={2025}, + eprint={2502.15646}, + archivePrefix={arXiv}, + primaryClass={cs.LG}, + url={https://arxiv.org/abs/2502.15646}, } ``` diff --git a/configs/get_config_data.py b/configs/get_config_data.py index b8cb2fb..8964551 100644 --- a/configs/get_config_data.py +++ b/configs/get_config_data.py @@ -146,7 +146,7 @@ def _get_path_list_of_genes_rnaseq(list_of_genes: str) -> Path | None: if list_of_genes not in possible_gene_lists: raise ValueError( - f"{list_of_genes} does not exis. Please provide a valid `list_of_genes` in {possible_gene_lists}." + f"{list_of_genes} does not exist. Please provide a valid `list_of_genes` in {possible_gene_lists}." ) if list_of_genes == "all": @@ -172,7 +172,7 @@ def _get_path_list_of_perturbations(list_of_perturbations: str) -> Path | None: } if list_of_perturbations not in possible_perturbations: raise ValueError( - f"{list_of_perturbations} does not exis. Please provide a valid " + f"{list_of_perturbations} does not exist. Please provide a valid " f"`list_of_perturbations` in {possible_perturbations}." ) diff --git a/data/README.md b/data/README.md index 9a06ed5..6bef9fc 100644 --- a/data/README.md +++ b/data/README.md @@ -1,6 +1,15 @@ # Data -Directory for storing datasets. +Directory for storing the data required to run models. + +> [!NOTE] +> Added data files are gitignored. Only this README and the pre-existing lists of genes, perturbations and tissues are tracked. + +## Existing Files + +The files traked here are lists of genes, perturbation and tissues that are useful to reproduce the different tasks described in the paper. + +## Files to download To run experiments, please download the following files from [DepMap](https://depmap.org/portal/data_page/?tab=allData): - CRISPRGeneDependency.csv @@ -9,6 +18,4 @@ To run experiments, please download the following files from [DepMap](https://de And [this file](https://www.gsea-msigdb.org/gsea/msigdb/download_file.jsp?filePath=/msigdb/release/2025.1.Hs/c2.all.v2025.1.Hs.json) from MsigDB. This file is the JSON bundle associated with the GCP (chemical and genetic perturbations) gene set. -Save all those file in this directory. - -**Note:** Data files are gitignored. Only this README is tracked. +Save all those files in this directory. diff --git a/models/README.md b/models/README.md index d97462e..6c99918 100644 --- a/models/README.md +++ b/models/README.md @@ -2,4 +2,5 @@ Directory for storing trained models. -**Note:** Model files are gitignored. Only this README is tracked. +> [!NOTE] +> Model files are gitignored. Only this README is tracked. diff --git a/results/README.md b/results/README.md index 1d0bbc1..b72ad58 100644 --- a/results/README.md +++ b/results/README.md @@ -2,4 +2,5 @@ Directory for experiment outputs and results. -**Note:** Result files are gitignored. Only this README is tracked. +> [!NOTE] +> Result files are gitignored. Only this README is tracked.