├── LICENSE ├── MCM_for_molecule_benchmarks ├── README.md ├── batch.py ├── dataloader.py ├── finetune.py ├── finetune_extend.py ├── loader.py ├── model.py ├── model_extend.py ├── ogb_dataset.py ├── splitters.py └── util.py ├── MCM_for_qm9 ├── MCM_tsne_visual.png ├── README.md ├── excludedMolecules_MG.txt ├── layers.py ├── main.py ├── model.py ├── qm9_dataset.py ├── requirements.txt └── utils.py ├── MCM_for_syn ├── README.md ├── __pycache__ │ ├── dataset.cpython-39.pyc │ ├── gcn.cpython-39.pyc │ └── gin_model.cpython-39.pyc ├── dataset.py ├── extended_syn-data-500.pt ├── gcn.py ├── gcn_main.py ├── gcn_model.py ├── gin_main.py ├── gin_model.py ├── mcm_main.py ├── syn-data-500.pt └── syn_data.py ├── README.md ├── graph_match ├── Graph.py ├── KHopChemMotif.py ├── README.md ├── __pycache__ │ ├── Graph.cpython-37.pyc │ ├── Graph.cpython-38.pyc │ ├── KHopChemMotif.cpython-38.pyc │ ├── preprocess.cpython-37.pyc │ └── preprocess.cpython-38.pyc ├── clustering.py ├── cuda │ ├── __pycache__ │ │ └── kernels.cpython-38.pyc │ ├── helper.h │ ├── kernels.py │ ├── matchScore │ │ ├── build.ninja │ │ ├── matchScore.cpp │ │ ├── matchScore.cu │ │ ├── matchScore.cuda.o │ │ ├── matchScore.h │ │ └── matchScore.o │ ├── nodeSim │ │ ├── build.ninja │ │ ├── nodeSim.cpp │ │ ├── nodeSim.cu │ │ ├── nodeSim.cuda.o │ │ ├── nodeSim.h │ │ └── nodeSim.o │ ├── similarity.h │ ├── toHardAssign │ │ ├── build.ninja │ │ ├── toHardAssign.cpp │ │ ├── toHardAssign.cu │ │ ├── toHardAssign.cuda.o │ │ ├── toHardAssign.h │ │ └── toHardAssign.o │ └── updateM │ │ ├── build.ninja │ │ ├── updateM.cpp │ │ ├── updateM.cu │ │ ├── updateM.cuda.o │ │ ├── updateM.h │ │ └── updateM.o ├── extend.py ├── extend_pyg.py ├── gmatch.yaml ├── preprocess.py ├── qm9_motifs_100.pt └── run_gm.py └── pipeline.png /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/LICENSE -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/README.md -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/batch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/batch.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/dataloader.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/finetune.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/finetune.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/finetune_extend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/finetune_extend.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/loader.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/model.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/model_extend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/model_extend.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/ogb_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/ogb_dataset.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/splitters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/splitters.py -------------------------------------------------------------------------------- /MCM_for_molecule_benchmarks/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_molecule_benchmarks/util.py -------------------------------------------------------------------------------- /MCM_for_qm9/MCM_tsne_visual.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/MCM_tsne_visual.png -------------------------------------------------------------------------------- /MCM_for_qm9/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/README.md -------------------------------------------------------------------------------- /MCM_for_qm9/excludedMolecules_MG.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/excludedMolecules_MG.txt -------------------------------------------------------------------------------- /MCM_for_qm9/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/layers.py -------------------------------------------------------------------------------- /MCM_for_qm9/main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/main.py -------------------------------------------------------------------------------- /MCM_for_qm9/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/model.py -------------------------------------------------------------------------------- /MCM_for_qm9/qm9_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/qm9_dataset.py -------------------------------------------------------------------------------- /MCM_for_qm9/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/requirements.txt -------------------------------------------------------------------------------- /MCM_for_qm9/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_qm9/utils.py -------------------------------------------------------------------------------- /MCM_for_syn/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/README.md -------------------------------------------------------------------------------- /MCM_for_syn/__pycache__/dataset.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/__pycache__/dataset.cpython-39.pyc -------------------------------------------------------------------------------- /MCM_for_syn/__pycache__/gcn.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/__pycache__/gcn.cpython-39.pyc -------------------------------------------------------------------------------- /MCM_for_syn/__pycache__/gin_model.cpython-39.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/__pycache__/gin_model.cpython-39.pyc -------------------------------------------------------------------------------- /MCM_for_syn/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/dataset.py -------------------------------------------------------------------------------- /MCM_for_syn/extended_syn-data-500.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/extended_syn-data-500.pt -------------------------------------------------------------------------------- /MCM_for_syn/gcn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/gcn.py -------------------------------------------------------------------------------- /MCM_for_syn/gcn_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/gcn_main.py -------------------------------------------------------------------------------- /MCM_for_syn/gcn_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/gcn_model.py -------------------------------------------------------------------------------- /MCM_for_syn/gin_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/gin_main.py -------------------------------------------------------------------------------- /MCM_for_syn/gin_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/gin_model.py -------------------------------------------------------------------------------- /MCM_for_syn/mcm_main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/mcm_main.py -------------------------------------------------------------------------------- /MCM_for_syn/syn-data-500.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/syn-data-500.pt -------------------------------------------------------------------------------- /MCM_for_syn/syn_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/MCM_for_syn/syn_data.py -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/README.md -------------------------------------------------------------------------------- /graph_match/Graph.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/Graph.py -------------------------------------------------------------------------------- /graph_match/KHopChemMotif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/KHopChemMotif.py -------------------------------------------------------------------------------- /graph_match/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/README.md -------------------------------------------------------------------------------- /graph_match/__pycache__/Graph.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/__pycache__/Graph.cpython-37.pyc -------------------------------------------------------------------------------- /graph_match/__pycache__/Graph.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/__pycache__/Graph.cpython-38.pyc -------------------------------------------------------------------------------- /graph_match/__pycache__/KHopChemMotif.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/__pycache__/KHopChemMotif.cpython-38.pyc -------------------------------------------------------------------------------- /graph_match/__pycache__/preprocess.cpython-37.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/__pycache__/preprocess.cpython-37.pyc -------------------------------------------------------------------------------- /graph_match/__pycache__/preprocess.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/__pycache__/preprocess.cpython-38.pyc -------------------------------------------------------------------------------- /graph_match/clustering.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/clustering.py -------------------------------------------------------------------------------- /graph_match/cuda/__pycache__/kernels.cpython-38.pyc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/__pycache__/kernels.cpython-38.pyc -------------------------------------------------------------------------------- /graph_match/cuda/helper.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/helper.h -------------------------------------------------------------------------------- /graph_match/cuda/kernels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/kernels.py -------------------------------------------------------------------------------- /graph_match/cuda/matchScore/build.ninja: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/matchScore/build.ninja -------------------------------------------------------------------------------- /graph_match/cuda/matchScore/matchScore.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/matchScore/matchScore.cpp -------------------------------------------------------------------------------- /graph_match/cuda/matchScore/matchScore.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/matchScore/matchScore.cu -------------------------------------------------------------------------------- /graph_match/cuda/matchScore/matchScore.cuda.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/matchScore/matchScore.cuda.o -------------------------------------------------------------------------------- /graph_match/cuda/matchScore/matchScore.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/matchScore/matchScore.h -------------------------------------------------------------------------------- /graph_match/cuda/matchScore/matchScore.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/matchScore/matchScore.o -------------------------------------------------------------------------------- /graph_match/cuda/nodeSim/build.ninja: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/nodeSim/build.ninja -------------------------------------------------------------------------------- /graph_match/cuda/nodeSim/nodeSim.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/nodeSim/nodeSim.cpp -------------------------------------------------------------------------------- /graph_match/cuda/nodeSim/nodeSim.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/nodeSim/nodeSim.cu -------------------------------------------------------------------------------- /graph_match/cuda/nodeSim/nodeSim.cuda.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/nodeSim/nodeSim.cuda.o -------------------------------------------------------------------------------- /graph_match/cuda/nodeSim/nodeSim.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/nodeSim/nodeSim.h -------------------------------------------------------------------------------- /graph_match/cuda/nodeSim/nodeSim.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/nodeSim/nodeSim.o -------------------------------------------------------------------------------- /graph_match/cuda/similarity.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/similarity.h -------------------------------------------------------------------------------- /graph_match/cuda/toHardAssign/build.ninja: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/toHardAssign/build.ninja -------------------------------------------------------------------------------- /graph_match/cuda/toHardAssign/toHardAssign.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/toHardAssign/toHardAssign.cpp -------------------------------------------------------------------------------- /graph_match/cuda/toHardAssign/toHardAssign.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/toHardAssign/toHardAssign.cu -------------------------------------------------------------------------------- /graph_match/cuda/toHardAssign/toHardAssign.cuda.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/toHardAssign/toHardAssign.cuda.o -------------------------------------------------------------------------------- /graph_match/cuda/toHardAssign/toHardAssign.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/toHardAssign/toHardAssign.h -------------------------------------------------------------------------------- /graph_match/cuda/toHardAssign/toHardAssign.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/toHardAssign/toHardAssign.o -------------------------------------------------------------------------------- /graph_match/cuda/updateM/build.ninja: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/updateM/build.ninja -------------------------------------------------------------------------------- /graph_match/cuda/updateM/updateM.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/updateM/updateM.cpp -------------------------------------------------------------------------------- /graph_match/cuda/updateM/updateM.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/updateM/updateM.cu -------------------------------------------------------------------------------- /graph_match/cuda/updateM/updateM.cuda.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/updateM/updateM.cuda.o -------------------------------------------------------------------------------- /graph_match/cuda/updateM/updateM.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/updateM/updateM.h -------------------------------------------------------------------------------- /graph_match/cuda/updateM/updateM.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/cuda/updateM/updateM.o -------------------------------------------------------------------------------- /graph_match/extend.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/extend.py -------------------------------------------------------------------------------- /graph_match/extend_pyg.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/extend_pyg.py -------------------------------------------------------------------------------- /graph_match/gmatch.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/gmatch.yaml -------------------------------------------------------------------------------- /graph_match/preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/preprocess.py -------------------------------------------------------------------------------- /graph_match/qm9_motifs_100.pt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/qm9_motifs_100.pt -------------------------------------------------------------------------------- /graph_match/run_gm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/graph_match/run_gm.py -------------------------------------------------------------------------------- /pipeline.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yifeiwang15/MotifConv/HEAD/pipeline.png --------------------------------------------------------------------------------