--- a +++ b/doc/source/bibliography.rst @@ -0,0 +1,73 @@ +.. Dataset +.. _QM8: https://arxiv.org/pdf/1703.00564.pdf +.. _QM9: https://arxiv.org/pdf/1703.00564.pdf +.. _BBBP: https://arxiv.org/pdf/1703.00564.pdf +.. _Tox21: https://arxiv.org/pdf/1703.00564.pdf +.. _ToxCast: https://arxiv.org/pdf/1703.00564.pdf +.. _SIDER: https://arxiv.org/pdf/1703.00564.pdf +.. _ClinTox: https://arxiv.org/pdf/1703.00564.pdf +.. _MUV: https://arxiv.org/pdf/1703.00564.pdf +.. _HIV: https://arxiv.org/pdf/1703.00564.pdf +.. _BACE: https://arxiv.org/pdf/1703.00564.pdf +.. _ChEMBL: https://pubmed.ncbi.nlm.nih.gov/30155234/ +.. _ZINC250k: https://pubs.acs.org/doi/pdfplus/10.1021/ci3001277 +.. _ZINC2M: https://pubs.acs.org/doi/10.1021/acs.jcim.5b00559 +.. _ZINC15: https://pubs.acs.org/doi/10.1021/acs.jcim.5b00559 +.. _USPTO50k: https://aspace.repository.cam.ac.uk/bitstream/handle/1810/244727/lowethesis.pdf +.. _FB15k: http://papers.nips.cc/paper/5071-translating-embeddings-for-modeling-multi-relational-data.pdf +.. _FB15k-237: https://www.aclweb.org/anthology/W15-4007 +.. _WN18: http://papers.nips.cc/paper/5071-translating-embeddings-for-modeling-multi-relational-data.pdf +.. _WN18RR: https://www.aaai.org/ocs/index.php/AAAI/AAAI18/paper/download/17366/15884 + +.. Graph Neural Networks +.. _NFP: https://papers.nips.cc/paper/5954-convolutional-networks-on-graphs-for-learning-molecular-fingerprints.pdf +.. _GCN: https://arxiv.org/pdf/1609.02907.pdf +.. _GAT: https://arxiv.org/pdf/1710.10903.pdf +.. _ENN-S2S: https://arxiv.org/pdf/1704.01212.pdf +.. _SchNet: https://aip.scitation.org/doi/pdf/10.1063/1.5019779 +.. _GIN: https://arxiv.org/pdf/1810.00826.pdf +.. _RGCN: https://arxiv.org/abs/1703.06103.pdf +.. _ChebNet: https://arxiv.org/pdf/1606.09375.pdf + +.. Differentiable Graph Pooling +.. _DiffPool: https://papers.nips.cc/paper/2018/file/e77dbaf6759253c7c6d0efc5690369c7-Paper.pdf +.. _MinCutPool: http://proceedings.mlr.press/v119/bianchi20a/bianchi20a.pdf +.. Readout Layers +.. _Set2Set: https://arxiv.org/pdf/1511.06391.pdf + +.. Normalization Layers +.. _PairNorm: https://openreview.net/pdf?id=rkecl1rtwB + +.. Readout Layers +.. _Set2Set: https://arxiv.org/pdf/1511.06391.pdf + +.. Normalization Layers +.. _PairNorm: https://openreview.net/pdf?id=rkecl1rtwB + +.. Pretrained molecular representations +.. _EdgePred: https://arxiv.org/pdf/1706.02216.pdf +.. _InfoGraph: https://arxiv.org/pdf/1908.01000.pdf +.. _AttrMasking: https://arxiv.org/pdf/1905.12265.pdf +.. _ContextPred: https://arxiv.org/pdf/1905.12265.pdf + +.. De Novo Molecule Design +.. _GCPN: https://papers.nips.cc/paper/7877-graph-convolutional-policy-network-for-goal-directed-molecular-graph-generation.pdf +.. _GraphAF: https://arxiv.org/pdf/2001.09382.pdf + +.. Retrosynthesis +.. _G2Gs: https://arxiv.org/pdf/2003.12725.pdf + +.. Protein Representation Learning +.. _TAPE: https://proceedings.neurips.cc/paper/2019/file/37f65c068b7723cd7809ee2d31d7861c-Paper.pdf +.. _ProteinCNN: https://arxiv.org/pdf/2011.03443.pdf +.. _ESM: https://www.biorxiv.org/content/10.1101/622803v1.full.pdf +.. _GearNet: https://arxiv.org/pdf/2203.06125.pdf + +.. Knowledge Graph Reasoning +.. _TransE: http://papers.nips.cc/paper/5071-translating-embeddings-for-modeling-multi-relational-data.pdf +.. _DistMult: https://arxiv.org/pdf/1412.6575.pdf +.. _ComplEx: http://proceedings.mlr.press/v48/trouillon16.pdf +.. _SimplE: https://papers.nips.cc/paper/7682-simple-embedding-for-link-prediction-in-knowledge-graphs.pdf +.. _RotatE: https://arxiv.org/pdf/1902.10197.pdf +.. _KBGAT: https://www.aclweb.org/anthology/P19-1466.pdf +.. _NeuralLP: https://papers.nips.cc/paper/2017/file/0e55666a4ad822e0e34299df3591d979-Paper.pdf \ No newline at end of file