├── 1. Data_preprocessing ├── 1-1-1.prepare_molecular_label.py ├── 1-2-1.segment_tiles.py ├── 1-2-2.tumor_detection.py ├── 1-2-3.tumor_prediction.py ├── 1-3-1.tile_normalization.py ├── 1-3-2.feature_extraction.py ├── 1-4-1.generate_adj_similar.py └── readme.md ├── 2. Prediction_on_TCGA_dataset ├── 2-1.coad_cross_validation_all_task.py ├── 2-2.read_validation_all_task.py └── readme.md ├── 3. Validation_on_CPTAC_dataset ├── 3-1.cptac_coad_validation_all_task.py └── readme.md ├── Figure ├── readme.md └── the pipeline and data statistics.png ├── README.md └── functions ├── model_architecture.py └── utils.py /1. Data_preprocessing/1-1-1.prepare_molecular_label.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-1-1.prepare_molecular_label.py -------------------------------------------------------------------------------- /1. Data_preprocessing/1-2-1.segment_tiles.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-2-1.segment_tiles.py -------------------------------------------------------------------------------- /1. Data_preprocessing/1-2-2.tumor_detection.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-2-2.tumor_detection.py -------------------------------------------------------------------------------- /1. Data_preprocessing/1-2-3.tumor_prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-2-3.tumor_prediction.py -------------------------------------------------------------------------------- /1. Data_preprocessing/1-3-1.tile_normalization.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-3-1.tile_normalization.py -------------------------------------------------------------------------------- /1. Data_preprocessing/1-3-2.feature_extraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-3-2.feature_extraction.py -------------------------------------------------------------------------------- /1. Data_preprocessing/1-4-1.generate_adj_similar.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/1-4-1.generate_adj_similar.py -------------------------------------------------------------------------------- /1. Data_preprocessing/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/1. Data_preprocessing/readme.md -------------------------------------------------------------------------------- /2. Prediction_on_TCGA_dataset/2-1.coad_cross_validation_all_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/2. Prediction_on_TCGA_dataset/2-1.coad_cross_validation_all_task.py -------------------------------------------------------------------------------- /2. Prediction_on_TCGA_dataset/2-2.read_validation_all_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/2. Prediction_on_TCGA_dataset/2-2.read_validation_all_task.py -------------------------------------------------------------------------------- /2. Prediction_on_TCGA_dataset/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/2. Prediction_on_TCGA_dataset/readme.md -------------------------------------------------------------------------------- /3. Validation_on_CPTAC_dataset/3-1.cptac_coad_validation_all_task.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/3. Validation_on_CPTAC_dataset/3-1.cptac_coad_validation_all_task.py -------------------------------------------------------------------------------- /3. Validation_on_CPTAC_dataset/readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/3. Validation_on_CPTAC_dataset/readme.md -------------------------------------------------------------------------------- /Figure/readme.md: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /Figure/the pipeline and data statistics.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/Figure/the pipeline and data statistics.png -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/README.md -------------------------------------------------------------------------------- /functions/model_architecture.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/functions/model_architecture.py -------------------------------------------------------------------------------- /functions/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Cassie07/Review_Molecular_profile_prediction_GNN/HEAD/functions/utils.py --------------------------------------------------------------------------------