Key Datasets

Key datasets

Only the files that the notebooks actually read or write are listed here, grouped by stage in the pipeline.

1 Raw source files

File	Location in Drive	First used in	Purpose
CCLE_expression.csv	CCLE-DepMap22Q2_geneexp/	CCLE_expression.ipynb	Full CCLE 22Q2 expression matrix (1,406 cell lines × 19,221 genes).
GDSC2_fitted_dose_response_27Oct23.xlsx	GDSC2_drugsens/	01_data_prep.ipynb	IC₅₀ values for 228 drugs across 987 cell lines.
screened_compounds_rel_8.5.csv	GDSC2_drugsens/	01_data_prep.ipynb	Drug metadata, including SMILES strings used for fingerprints.

---

2 Cleaned & aligned tables

File	Location	First used in	What changed
CCLE_expression_cleaned.csv	CCLE-DepMap22Q2_geneexp/	01_data_prep.ipynb	Reduced to 735 cancer-associated genes, renamed headers to gene symbols.
drug_info.csv	GDSC2_drugsens/datasets/	01_data_prep.ipynb	228 compounds with validated SMILES only.
cell_line_info.csv	GDSC2_drugsens/datasets/	01_data_prep.ipynb	CCLE ↔ DepMap–aligned cell-line metadata (676 lines).
ic50_cleaned.csv	GDSC2_drugsens/datasets/	01_data_prep.ipynb	Long-format ln(IC₅₀) table ready for labelling.
GeneExp.csv	GDSC2_drugsens/datasets/features/	02_gen_dataset.ipynb	Expression matrix trimmed to the 676 aligned cell lines.

---

3 Labelled & split datasets

Files	Location	Notebook	Role
DrugSens_clas_pivot_train/val/test.csv	…/pivot/clas/	02_gen_dataset.ipynb	Binary sensitivity matrices, stratified 60 / 20 / 20.
DrugSens_regr_pivot_train/val/test.csv	…/pivot/regr/	02_gen_dataset.ipynb	Continuous ln(IC₅₀) matrices for regression experiments.

---

4 Final multimodal feature set

File	Location	Notebook	Contents
multimodal_dataset_final.csv	processed_datasets/	Data Integration & Preparation.ipynb	108,696 rows × 2,783 features (735 genes + 2,048 fingerprints).
multimodal_dataset_final.pkl	processed_datasets/	same as above	Same data as a 6.8 GB Pickle for faster loading in Colab.

---

All datasets and the trained model checkpoint live exclusively in the shared Google Drive folder, keeping the GitHub repository lightweight.