Papers Implemented

`Convolutional Networks on Graphs for Learning Molecular Fingerprints <NFP_>`_

David Duvenaud, Dougal Maclaurin, Jorge Aguilera-Iparraguirre, Rafael Gómez-Bombarelli, Timothy Hirzel, Alán Aspuru-Guzik, Ryan P. Adams. NIPS 2015.

:class:`NeuralFingerprintConv <torchdrug.layers.NeuralFingerprintConv>`, :class:`NeuralFingerprint <torchdrug.models.NeuralFingerprint>`

`Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering <ChebNet_>`_

Michaël Defferrard, Xavier Bresson, Pierre Vandergheynst. NIPS 2016.

:class:`ChebyshevConv <torchdrug.layers.ChebyshevConv>`, :class:`ChebyshevConvolutionalNetwork <torchdrug.models.ChebyshevConvolutionalNetwork>`

`Semi-Supervised Classification with Graph Convolutional Networks <GCN_>`_

Thomas N. Kipf, Max Welling. ICLR 2017.

:class:`GraphConv <torchdrug.layers.GraphConv>`, :class:`GraphConvolutionalNetwork <torchdrug.models.GraphConvolutionalNetwork>`

`Neural Message Passing for Quantum Chemistry <ENN-S2S_>`_

Justin Gilmer, Samuel S. Schoenholz, Patrick F. Riley, Oriol Vinyals, George E. Dahl. ICML 2017.

:class:`MessagePassing <torchdrug.layers.MessagePassing>`, :class:`MessagePassingNeuralNetwork <torchdrug.models.MessagePassingNeuralNetwork>`

`SchNet: A continuous-filter convolutional neural network for modeling quantum interactions <SchNet_>`_

Kristof T. Schütt, Pieter-Jan Kindermans, Huziel E. Sauceda, Stefan Chmiela, Alexandre Tkatchenko, Klaus-Robert Müller. NeurIPS 2017.

:class:`ContinuousFilterConv <torchdrug.layers.ContinuousFilterConv>`, :class:`SchNet <torchdrug.models.SchNet>`

`Graph Attention Networks <GAT_>`_

Petar Veličković, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Liò, Yoshua Bengio. ICLR 2018.

:class:`GraphAttentionConv <torchdrug.layers.GraphAttentionConv>`, :class:`GraphAttentionNetwork <torchdrug.models.GraphAttentionNetwork>`

`Modeling Relational Data with Graph Convolutional Networks <RGCN_>`_

Michael Schlichtkrull, Thomas N. Kipf, Peter Bloem, Rianne van den Berg, Ivan Titov, Max Welling. ESWC 2018.

:class:`RelationalGraphConv <torchdrug.layers.RelationalGraphConv>`, :class:`RelationalGraphConvolutionalNetwork <torchdrug.models.RelationalGraphConvolutionalNetwork>`

`How Powerful Are Graph Neural Nerworks? <GIN_>`_

Keyulu Xu, Weihua Hu, Jure Leskovec, Stefanie Jegelka. ICLR 2019.

:class:`GraphIsomorphismConv <torchdrug.layers.GraphIsomorphismConv>`, :class:`GraphIsomorphismNetwork <torchdrug.models.GraphIsomorphismNetwork>`

`Hierarchical Graph Representation Learning with Differentiable Pooling <DiffPool_>`_

Rex Ying, Jiaxuan You, Christopher Morris, Xiang Ren, William L. Hamilton, Jure Leskovec. NeurIPS 2018.

:class:`DiffPool <torchdrug.layers.DiffPool>`

`Spectral Clustering with Graph Neural Networks for Graph Pooling <MinCutPool_>`_

Filippo Maria Bianchi, Daniele Grattarola, Cesare Alippi. ICML 2020.

:class:`MinCutPool <torchdrug.layers.MinCutPool>`

`Order Matters: Sequence to sequence for sets <Set2Set_>`_

Oriol Vinyals, Samy Bengio, Manjunath Kudlur

:class:`Set2Set <torchdrug.layers.Set2Set>`

`PairNorm: Tackling Oversmoothing in GNNs <PairNorm_>`_

Lingxiao Zhao, Leman Akoglu. ICLR 2020.

:class:`PairNorm <torchdrug.layers.PairNorm>`

`InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization <InfoGraph_>`_

Fan-Yun Sun, Jordan Hoffman, Vikas Verma, Jian Tang. ICLR 2020.

:class:`InfoGraph <torchdrug.models.InfoGraph>`

`Strategies for Pre-training Graph Neural Networks <AttrMasking_>`_

Weihua Hu, Bowen Liu, Joseph Gomes, Marinka Zitnik, Percy Liang, Vijay Pande, Jure Leskovec. ICLR 2020.

:class:`EdgePrediction <torchdrug.tasks.EdgePrediction>`, :class:`AttributeMasking <torchdrug.tasks.AttributeMasking>`, :class:`ContextPrediction <torchdrug.tasks.ContextPrediction>`

`Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation. <GCPN_>`_

Jiaxuan You, Bowen Liu, Rex Ying, Vijay Pande, Jure Leskovec. NeurIPS 2018.

:class:`GCPNGeneration <torchdrug.tasks.GCPNGeneration>`

`GraphAF: A Flow-based Autoregressive Model for Molecular Graph Generation. <GraphAF_>`_

Chence Shi, Minkai Xu, Zhaocheng Zhu, Weinan Zhang, Ming Zhang, Jian Tang. ICLR 2020.

:class:`GraphAutoregressiveFlow <torchdrug.models.GraphAutoregressiveFlow>`, :class:`AutoregressiveGeneration <torchdrug.tasks.AutoregressiveGeneration>`

`A Graph to Graphs Framework for Retrosynthesis Prediction. <G2Gs_>`_

Chence Shi, Minkai Xu, Hongyu Guo, Ming Zhang, Jian Tang. ICML 2020.

:class:`CenterIdentification <torchdrug.tasks.CenterIdentification>`, :class:`SynthonCompletion <torchdrug.tasks.SynthonCompletion>`, :class:`Retrosynthesis <torchdrug.tasks.Retrosynthesis>`

`Evaluating Protein Transfer Learning with TAPE <TAPE_>`_

Roshan Rao, Nicholas Bhattacharya, Neil Thomas, Yan Duan, Xi Chen, John Canny, Pieter Abbeel, Yun S Song. NeurIPS 2019.

:class:`SinusoidalPositionEmbedding <torchdrug.layers.SinusoidalPositionEmbedding>` :class:`SelfAttentionBlock <torchdrug.layers.SelfAttentionBlock>` :class:`ProteinResNetBlock <torchdrug.layers.ProteinResNetBlock>` :class:`ProteinBERTBlock <torchdrug.layers.ProteinBERTBlock>` :class:`ProteinResNet <torchdrug.models.ProteinResNet>` :class:`ProteinLSTM <torchdrug.models.ProteinLSTM>` :class:`ProteinBERT <torchdrug.models.ProteinBERT>`

`Is Transfer Learning Necessary for Protein Landscape Prediction? <ProteinCNN_>`_

Amir Shanehsazzadeh, David Belanger, David Dohan. arXiv 2020.

:class:`ProteinCNN <torchdrug.models.ProteinCNN>`

`Biological Structure and Function Emerge from Scaling Unsupervised Learning to 250 Million Protein Sequences <ESM_>`_

Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, Rob Fergus. PNAS 2021.

:class:`EvolutionaryScaleModeling <torchdrug.models.EvolutionaryScaleModeling>`

`Protein Representation Learning by Geometric Structure Pretraining <GearNet_>`_

Zuobai Zhang, Minghao Xu, Arian Jamasb, Vijil Chenthamarakshan, Aurélie Lozano, Payel Das, Jian Tang. arXiv 2022.

:class:`GeometricRelationalGraphConv <torchdrug.layers.GeometricRelationalGraphConv>` :class:`GeometryAwareRelationalGraphNeuralNetwork <torchdrug.models.GeometryAwareRelationalGraphNeuralNetwork>` :mod:`torchdrug.layers.geometry`

`Translating Embeddings for Modeling Multi-relational Data <TransE_>`_

Antoine Bordes, Nicolas Usunier, Alberto García-Durán. NIPS 2013.

:func:`transe_score <torchdrug.layers.functional.transe_score>`, :class:`TransE <torchdrug.models.DistMult>`

`Embedding Entities and Relations for Learning and Inference in Knowledge Bases <DistMult_>`_

Bishan Yang, Wen-tau Yih, Xiaodong He, Jianfeng Gao, Li Deng. ICLR 2015.

:func:`distmult_score <torchdrug.layers.functional.distmult_score>`, :class:`DistMult <torchdrug.models.DistMult>`

`Complex Embeddings for Simple Link Prediction <ComplEx_>`_

Théo Trouillon, Johannes Welbl, Sebastian Riedel, Éric Gaussier, Guillaume Bouchard. ICML 2016.

:func:`complex_score <torchdrug.layers.functional.complex_score>`, :class:`ComplEx <torchdrug.models.DistMult>`

`Differentiable Learning of Logical Rules for Knowledge Base Reasoning <NeuralLP_>`_

Fan Yang, Zhilin Yang, William W. Cohen. NIPS 2017.

:class:`NeuralLogicProgramming <torchdrug.models.NeuralLogicProgramming>`

`SimplE Embedding for Link Prediction in Knowledge Graphs <SimplE_>`_

Seyed Mehran Kazemi, David Poole. NeurIPS 2018.

:func:`simple_score <torchdrug.layers.functional.simple_score>`, :class:`SimplE <torchdrug.models.SimplE>`

`RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space <RotatE_>`_

Zhiqing Sun, Zhi-Hong Deng, Jian-Yun Nie, Jian Tang. ICLR 2019.

:func:`rotate_score <torchdrug.layers.functional.rotate_score>`, :class:`RotatE <torchdrug.models.RotatE>`

`Learning Attention-based Embeddings for Relation Prediction in Knowledge Graphs <KBGAT_>`_

Deepak Nathani, Jatin Chauhan, Charu Sharma, Manohar Kaul. ACL 2019.

:class:`KnowledgeBaseGraphAttentionNetwork <torchdrug.models.KnowledgeBaseGraphAttentionNetwork>`