├── .idea ├── PGCL.iml ├── deployment.xml ├── inspectionProfiles │ ├── Project_Default.xml │ └── profiles_settings.xml ├── misc.xml ├── modules.xml ├── webServers.xml └── workspace.xml ├── readme.md ├── transferLearning_MoleculeNet_PPI ├── README.md ├── chem │ ├── batch.py │ ├── dataloader.py │ ├── finetune.py │ ├── finetune.sh │ ├── finetune_all.sh │ ├── finetune_tune.sh │ ├── loader.py │ ├── model.py │ ├── parse_result.py │ ├── pgcl.py │ ├── pgcl_sr.py │ ├── pretrain_contextpred.py │ ├── pretrain_deepgraphinfomax.py │ ├── pretrain_edgepred.py │ ├── pretrain_graphcl.py │ ├── pretrain_masking.py │ ├── pretrain_masking_virtual.py │ ├── pretrain_supervised.py │ ├── run.sh │ ├── splitters.py │ └── util.py └── install.sh └── unsupervised_TU ├── Logistic_regression.py ├── README.md ├── __init__.py ├── arguments.py ├── aug.py ├── cortex_DIM ├── __init__.py ├── configs │ ├── __init__.py │ ├── convnets.py │ └── resnets.py ├── functions │ ├── __init__.py │ ├── dim_losses.py │ ├── gan_losses.py │ └── misc.py └── nn_modules │ ├── __init__.py │ ├── convnet.py │ ├── encoder.py │ ├── mi_networks.py │ ├── misc.py │ └── resnet.py ├── dgl.py ├── evaluate_embedding.py ├── gin.py ├── go_PGCL.sh ├── gsimclr_PGCL_tsne.py ├── losses.py ├── model.py ├── pgcl_main.py ├── pgcl_sr.py ├── pretrain_graphcl.py ├── src ├── __init__.py ├── logger.py └── utils.py └── tsne.py /.idea/PGCL.iml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/PGCL.iml -------------------------------------------------------------------------------- /.idea/deployment.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/deployment.xml -------------------------------------------------------------------------------- /.idea/inspectionProfiles/Project_Default.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/inspectionProfiles/Project_Default.xml -------------------------------------------------------------------------------- /.idea/inspectionProfiles/profiles_settings.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/inspectionProfiles/profiles_settings.xml -------------------------------------------------------------------------------- /.idea/misc.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/misc.xml -------------------------------------------------------------------------------- /.idea/modules.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/modules.xml -------------------------------------------------------------------------------- /.idea/webServers.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/webServers.xml -------------------------------------------------------------------------------- /.idea/workspace.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/.idea/workspace.xml -------------------------------------------------------------------------------- /readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/readme.md -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/README.md -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/batch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/batch.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/dataloader.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/finetune.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/finetune.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/finetune.sh -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/finetune_all.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/finetune_all.sh -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/finetune_tune.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/finetune_tune.sh -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/loader.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/model.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/parse_result.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/parse_result.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pgcl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pgcl.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pgcl_sr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pgcl_sr.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_contextpred.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_contextpred.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_deepgraphinfomax.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_deepgraphinfomax.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_edgepred.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_edgepred.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_graphcl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_graphcl.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_masking.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_masking.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_masking_virtual.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_masking_virtual.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/pretrain_supervised.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/pretrain_supervised.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/run.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/run.sh -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/splitters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/splitters.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/chem/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/chem/util.py -------------------------------------------------------------------------------- /transferLearning_MoleculeNet_PPI/install.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/transferLearning_MoleculeNet_PPI/install.sh -------------------------------------------------------------------------------- /unsupervised_TU/Logistic_regression.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/README.md -------------------------------------------------------------------------------- /unsupervised_TU/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/arguments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/arguments.py -------------------------------------------------------------------------------- /unsupervised_TU/aug.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/aug.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/configs/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/configs/convnets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/configs/convnets.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/configs/resnets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/configs/resnets.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/functions/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/functions/dim_losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/functions/dim_losses.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/functions/gan_losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/functions/gan_losses.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/functions/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/functions/misc.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/nn_modules/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/nn_modules/convnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/nn_modules/convnet.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/nn_modules/encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/nn_modules/encoder.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/nn_modules/mi_networks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/nn_modules/mi_networks.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/nn_modules/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/nn_modules/misc.py -------------------------------------------------------------------------------- /unsupervised_TU/cortex_DIM/nn_modules/resnet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/cortex_DIM/nn_modules/resnet.py -------------------------------------------------------------------------------- /unsupervised_TU/dgl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/dgl.py -------------------------------------------------------------------------------- /unsupervised_TU/evaluate_embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/evaluate_embedding.py -------------------------------------------------------------------------------- /unsupervised_TU/gin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/gin.py -------------------------------------------------------------------------------- /unsupervised_TU/go_PGCL.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/go_PGCL.sh -------------------------------------------------------------------------------- /unsupervised_TU/gsimclr_PGCL_tsne.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/gsimclr_PGCL_tsne.py -------------------------------------------------------------------------------- /unsupervised_TU/losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/losses.py -------------------------------------------------------------------------------- /unsupervised_TU/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/model.py -------------------------------------------------------------------------------- /unsupervised_TU/pgcl_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/pgcl_main.py -------------------------------------------------------------------------------- /unsupervised_TU/pgcl_sr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/pgcl_sr.py -------------------------------------------------------------------------------- /unsupervised_TU/pretrain_graphcl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/pretrain_graphcl.py -------------------------------------------------------------------------------- /unsupervised_TU/src/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /unsupervised_TU/src/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/src/logger.py -------------------------------------------------------------------------------- /unsupervised_TU/src/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/src/utils.py -------------------------------------------------------------------------------- /unsupervised_TU/tsne.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ha-lins/PGCL/HEAD/unsupervised_TU/tsne.py --------------------------------------------------------------------------------