ajayago/cs6208_project

Code base for CS6208 project

CS6208_project

Code base for CS6208 project

Raw Data:

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The raw data used for creating our graphs is made available in this repo.

• 9606.protein.info.v11.5.txt for gene-gene interactions
• DrugSimDB_v1_0_0.csv for drug-drug similarity
• GDSC2_fitted_dose_response_24Jul22.xlsx for cell line response to drugs
• Model.csv for metadata on cell lines, used to create cell line node features
• chemBL_drugs.csv for constructing drug node features using SMILES
• drugbank_vocabulary.csv for drug metadata
• gene_pathways.txt for constructing gene node features from the pathways each gene belongs to
• interactions.tsv for information on the gene each drug targets
• OmicsSomaticMutations.csv to get the list of genes mutated in each cell line

Graph Construction:

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To construct the heterogeneous graph please refer to the folder "Graph Construction". The final version of the graph can be downloaded from https://drive.google.com/drive/folders/1vEqd-ghoeO31bjzBHrMXK_QqCeiwZhqQ?usp=share_link

Benchmarks:

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We compare our method against existing methods for (1) heterogeneous graphs - RGCN and HGT as well as (2) existing cell line drug response prediction models (GraphCDR). These can be found in the folder benchmarks