- hetgnn_main.py
- Main script for HetGNN. Layer configurations can be modified in
gat_dependency/GAT_model.py
.
- Main script for HetGNN. Layer configurations can be modified in
- DLP_main.py
- Implements DLP with the Whole split method.
- DLP_cellsplit.py
- Implements DLP with the Cell Only split method.
- construct_heterogeneous_graph_jihwan.py
- Script for constructing a heterogeneous graph.
- construct_heterogeneous_graph_pyG_jihwan.py
- Script for constructing a heterogeneous graph with biological features using Pytorch Geometric.
- Conda list
- Conda environment settings required for running the project.
- Final_Result
- Contains code for generating figures, tables, and lists of reprioritized genes. (See Jupyter Notebook in folder)
- Contains generated figures by pptxm can be checked in
Final_Result/Fugures made.pptx
.
You can run the scripts with the following format, adjusting arguments using --arg
:
python hetgnn_main.py --epochs 30 --lr 0.0001 --batch_size 256 --emb_dim 512 --seed 42 --exp_name example_test
All resources and data sources mentioned in this thesis are publicly accessible.
- Protein-protein network: Download FIsInGene with annotations
- DepMap Public 23Q2 Files: View all data
- DepMap Score: CRISPRGeneEffect.csv
- Cell Line Name: Model.csv
- Expression: OmicsExpressionProteinCodingGenesTPMLogp1.csv
- Copy Number Variation: OmicsCNGene.csv
- Control: AchillesCommonEssentialControls.csv
- CGP: Download CGP Symbols (GMT)
- CP: Download CP Symbols (GMT)
- GO: Download GO Symbols (GMT)
- BP: Download BP Symbols (GMT)
All results can be found in WandB and check comments in overview first!
- DLP: View DLP Project
- HetGNN: View HetGNN Project
- HetGNN-Lin: View HetGNN-Lin Project