├── ACNet ├── ACComponents │ ├── ACChemUtils.py │ ├── ACDataset │ │ ├── DataPreprocess.py │ │ ├── DataUtils.py │ │ ├── Dataset.py │ │ └── GenerateACDatasets.py │ ├── ACModels.py │ ├── ACProcessControllers.py │ └── ACSplitter.py ├── ACNetEnviron.yml ├── CMPNNLarge.py ├── CMPNNMedium.py ├── CMPNNSmall.py ├── ChemBERTFew.py ├── FPMLPFew.py ├── FPMLPLarge.py ├── FPMLPMedium.py ├── FPMLPMixRandom.py ├── FPMLPMixTarget.py ├── FPMLPSmall.py ├── GCNLarge.py ├── GCNMedium.py ├── GCNMixRandom.py ├── GCNMixTarget.py ├── GCNSmall.py ├── GINLarge.py ├── GINMedium.py ├── GINSmall.py ├── GROVERFew.py ├── GRULarge.py ├── GRUMedium.py ├── GRUMixRandom.py ├── GRUMixTarget.py ├── GRUSmall.py ├── GraphLoGFew.py ├── GraphormerLarge.py ├── GraphormerMedium.py ├── GraphormerMixRandom.py ├── GraphormerMixTarget.py ├── GraphormerSmall.py ├── LSTMLarge.py ├── LSTMMedium.py ├── LSTMSmall.py ├── MATFew.py ├── Models │ ├── BasicGNNs.py │ ├── CMPNN │ │ ├── CMPNNFeaturizer.py │ │ ├── CMPNNModel.py │ │ └── nn_utils.py │ ├── ClassifierModel.py │ └── Graphormer │ │ ├── Graphormer.py │ │ ├── algos.c │ │ ├── algos.cpython-37m-x86_64-linux-gnu.so │ │ ├── algos.cpython-38-x86_64-linux-gnu.so │ │ ├── algos.pyx │ │ ├── build │ │ ├── temp.linux-x86_64-3.7 │ │ │ └── algos.o │ │ └── temp.linux-x86_64-3.8 │ │ │ └── algos.o │ │ ├── collator.py │ │ ├── data.py │ │ ├── setup.py │ │ └── wrapper.py ├── Pretrain8Few.py ├── PretrainGNNsFew.py ├── SGCLarge.py ├── SGCMedium.py ├── SGCSmall.py ├── SMILESTransformerFew.py └── TrainingFramework │ ├── ChemUtils.py │ ├── Dataset.py │ ├── Evaluator.py │ ├── Featurizer.py │ ├── FileUtils.py │ ├── Initializer.py │ ├── Metrics.py │ ├── ProcessControllers.py │ ├── Scheduler.py │ ├── Splitter.py │ └── Utils.py ├── LICENSE └── README.md /ACNet/ACComponents/ACChemUtils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACChemUtils.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACDataset/DataPreprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACDataset/DataPreprocess.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACDataset/DataUtils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACDataset/DataUtils.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACDataset/Dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACDataset/Dataset.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACDataset/GenerateACDatasets.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACDataset/GenerateACDatasets.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACModels.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACModels.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACProcessControllers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACProcessControllers.py -------------------------------------------------------------------------------- /ACNet/ACComponents/ACSplitter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACComponents/ACSplitter.py -------------------------------------------------------------------------------- /ACNet/ACNetEnviron.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ACNetEnviron.yml -------------------------------------------------------------------------------- /ACNet/CMPNNLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/CMPNNLarge.py -------------------------------------------------------------------------------- /ACNet/CMPNNMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/CMPNNMedium.py -------------------------------------------------------------------------------- /ACNet/CMPNNSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/CMPNNSmall.py -------------------------------------------------------------------------------- /ACNet/ChemBERTFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/ChemBERTFew.py -------------------------------------------------------------------------------- /ACNet/FPMLPFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/FPMLPFew.py -------------------------------------------------------------------------------- /ACNet/FPMLPLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/FPMLPLarge.py -------------------------------------------------------------------------------- /ACNet/FPMLPMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/FPMLPMedium.py -------------------------------------------------------------------------------- /ACNet/FPMLPMixRandom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/FPMLPMixRandom.py -------------------------------------------------------------------------------- /ACNet/FPMLPMixTarget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/FPMLPMixTarget.py -------------------------------------------------------------------------------- /ACNet/FPMLPSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/FPMLPSmall.py -------------------------------------------------------------------------------- /ACNet/GCNLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GCNLarge.py -------------------------------------------------------------------------------- /ACNet/GCNMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GCNMedium.py -------------------------------------------------------------------------------- /ACNet/GCNMixRandom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GCNMixRandom.py -------------------------------------------------------------------------------- /ACNet/GCNMixTarget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GCNMixTarget.py -------------------------------------------------------------------------------- /ACNet/GCNSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GCNSmall.py -------------------------------------------------------------------------------- /ACNet/GINLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GINLarge.py -------------------------------------------------------------------------------- /ACNet/GINMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GINMedium.py -------------------------------------------------------------------------------- /ACNet/GINSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GINSmall.py -------------------------------------------------------------------------------- /ACNet/GROVERFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GROVERFew.py -------------------------------------------------------------------------------- /ACNet/GRULarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GRULarge.py -------------------------------------------------------------------------------- /ACNet/GRUMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GRUMedium.py -------------------------------------------------------------------------------- /ACNet/GRUMixRandom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GRUMixRandom.py -------------------------------------------------------------------------------- /ACNet/GRUMixTarget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GRUMixTarget.py -------------------------------------------------------------------------------- /ACNet/GRUSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GRUSmall.py -------------------------------------------------------------------------------- /ACNet/GraphLoGFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GraphLoGFew.py -------------------------------------------------------------------------------- /ACNet/GraphormerLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GraphormerLarge.py -------------------------------------------------------------------------------- /ACNet/GraphormerMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GraphormerMedium.py -------------------------------------------------------------------------------- /ACNet/GraphormerMixRandom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GraphormerMixRandom.py -------------------------------------------------------------------------------- /ACNet/GraphormerMixTarget.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GraphormerMixTarget.py -------------------------------------------------------------------------------- /ACNet/GraphormerSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/GraphormerSmall.py -------------------------------------------------------------------------------- /ACNet/LSTMLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/LSTMLarge.py -------------------------------------------------------------------------------- /ACNet/LSTMMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/LSTMMedium.py -------------------------------------------------------------------------------- /ACNet/LSTMSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/LSTMSmall.py -------------------------------------------------------------------------------- /ACNet/MATFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/MATFew.py -------------------------------------------------------------------------------- /ACNet/Models/BasicGNNs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/BasicGNNs.py -------------------------------------------------------------------------------- /ACNet/Models/CMPNN/CMPNNFeaturizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/CMPNN/CMPNNFeaturizer.py -------------------------------------------------------------------------------- /ACNet/Models/CMPNN/CMPNNModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/CMPNN/CMPNNModel.py -------------------------------------------------------------------------------- /ACNet/Models/CMPNN/nn_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/CMPNN/nn_utils.py -------------------------------------------------------------------------------- /ACNet/Models/ClassifierModel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/ClassifierModel.py -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/Graphormer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/Graphormer.py -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/algos.c: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/algos.c -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/algos.cpython-37m-x86_64-linux-gnu.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/algos.cpython-37m-x86_64-linux-gnu.so -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/algos.cpython-38-x86_64-linux-gnu.so: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/algos.cpython-38-x86_64-linux-gnu.so -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/algos.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/algos.pyx -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/build/temp.linux-x86_64-3.7/algos.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/build/temp.linux-x86_64-3.7/algos.o -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/build/temp.linux-x86_64-3.8/algos.o: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/build/temp.linux-x86_64-3.8/algos.o -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/collator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/collator.py -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/data.py -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/setup.py -------------------------------------------------------------------------------- /ACNet/Models/Graphormer/wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Models/Graphormer/wrapper.py -------------------------------------------------------------------------------- /ACNet/Pretrain8Few.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/Pretrain8Few.py -------------------------------------------------------------------------------- /ACNet/PretrainGNNsFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/PretrainGNNsFew.py -------------------------------------------------------------------------------- /ACNet/SGCLarge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/SGCLarge.py -------------------------------------------------------------------------------- /ACNet/SGCMedium.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/SGCMedium.py -------------------------------------------------------------------------------- /ACNet/SGCSmall.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/SGCSmall.py -------------------------------------------------------------------------------- /ACNet/SMILESTransformerFew.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/SMILESTransformerFew.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/ChemUtils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/ChemUtils.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Dataset.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Evaluator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Evaluator.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Featurizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Featurizer.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/FileUtils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/FileUtils.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Initializer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Initializer.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Metrics.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/ProcessControllers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/ProcessControllers.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Scheduler.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Scheduler.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Splitter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Splitter.py -------------------------------------------------------------------------------- /ACNet/TrainingFramework/Utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/ACNet/TrainingFramework/Utils.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DrugAI/ACNet/HEAD/README.md --------------------------------------------------------------------------------