--- a +++ b/doc/source/api/models.rst @@ -0,0 +1,174 @@ +torchdrug.models +================ + +.. currentmodule:: torchdrug.models + +Knowledge Graph Reasoning Models +-------------------------------- + +TransE +^^^^^^ +.. autoclass:: TransE + :members: + +DistMult +^^^^^^^^ +.. autoclass:: DistMult + :members: + +ComplEx +^^^^^^^ +.. autoclass:: ComplEx + :members: + +SimplE +^^^^^^ +.. autoclass:: SimplE + :members: + +RotatE +^^^^^^ +.. autoclass:: RotatE + :members: + +NeuralLP +^^^^^^^^ +.. autoclass:: NeuralLogicProgramming + :members: + +.. autoclass:: NeuralLP + +KBGAT +^^^^^ +.. autoclass:: KnowledgeBaseGraphAttentionNetwork + :members: + +.. autoclass:: KBGAT + +Graph Neural Networks +--------------------- + +ChebNet +^^^^^^^ +.. autoclass:: ChebyshevConvolutionalNetwork + :members: + +.. autoclass:: ChebNet + +GCN +^^^ +.. autoclass:: GraphConvolutionalNetwork + :members: + +.. autoclass:: GCN + +GAT +^^^ +.. autoclass:: GraphAttentionNetwork + :members: + +.. autoclass:: GAT + +GIN +^^^ +.. autoclass:: GraphIsomorphismNetwork + :members: + +.. autoclass:: GIN + +MPNN +^^^^ +.. autoclass:: MessagePassingNeuralNetwork + :members: + +.. autoclass:: MPNN + +NFP +^^^ +.. autoclass:: NeuralFingerprint + :members: + +.. autoclass:: NFP + +RGCN +^^^^ +.. autoclass:: RelationalGraphConvolutionalNetwork + :members: + +.. autoclass:: RGCN + +GearNet +^^^^^^^ +.. autoclass:: GeometryAwareRelationalGraphNeuralNetwork + :members: + +.. autoclass:: GearNet + +SchNet +^^^^^^ +.. autoclass:: SchNet + :members: + + +Protein Sequence Encoders +------------------------- + +ESM +^^^ +.. autoclass:: EvolutionaryScaleModeling + :members: + +ProteinCNN +^^^^^^^^^^ +.. autoclass:: ProteinConvolutionalNetwork + :members: + +ProteinResNet +^^^^^^^^^^^^^ +.. autoclass:: ProteinResNet + :members: + +ProteinLSTM +^^^^^^^^^^^ +.. autoclass:: ProteinLSTM + :members: + +ProteinBERT +^^^^^^^^^^^ +.. autoclass:: ProteinBERT + :members: + +Statistic Feature Engineering +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: Statistic + :members: + +Physicochemical Feature Engineering +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: Physicochemical + :members: + + +Normalizing Flows +----------------- + +GraphAutoregressiveFlow +^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: GraphAutoregressiveFlow + :members: + +.. autoclass:: GraphAF + + +Self-supervised Models +---------------------- + +InfoGraph +^^^^^^^^^ +.. autoclass:: InfoGraph + :members: + +MultiviewContrast +^^^^^^^^^^^^^^^^^ +.. autoclass:: MultiviewContrast + :members: