feat: improve readme and typos

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},
 }
 ```
 

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}."
         )
 

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.

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.

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.