https://github.com/awslabs/dgl-lifesci

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9723c07 Update to 0.2.6 (#106) * Update * Update 28 October 2020, 16:48:10 UTC
e4a8408 Pre-trained Models on MoleculeNet (#104) * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Update * Fix * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Fix * Update * Update * Update * Update * Update * Update * Fix * Fix * Fix * Fix * Fix * Update * Fix * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Fix * Update * Update * Update * Fix * Update * Update * Update * Update * Update * Update * Fix * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Fix * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Fix * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Fix * Update * Update * Update * Fix * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Update * Updateg * Update 28 October 2020, 15:50:44 UTC
ecd95c9 Fiix (#103) 06 October 2020, 08:10:19 UTC
a2c0a80 [Rexgen] Fix for DGL 0.5 (#96) * Fix * Update * Update Co-authored-by: Ubuntu <ubuntu@ip-172-31-48-182.us-west-2.compute.internal> 24 September 2020, 08:22:23 UTC
0550e45 [Release] Update to version 0.2.5 (#94) * Update version * Update 17 September 2020, 19:30:26 UTC
7a910d0 [JTVAE] Update for DGL 0.5 (#91) * Update * Fix * Fix * Fix * Fix * Update * Update * Fix * Fix * Fix * Fix * Fix * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Update * Update * Fix * Update * Update * Fix * Fix * Fix * Update * Update * Update * Fix * Fix * Fix * Update * Update * Fix * Update * Update * Update * Update * Fix * Update * Fix * Update * Fix * Fix * Fix * Update * Update * Fix * Fix * Update * Fix * Fix 14 September 2020, 16:57:24 UTC
b532efe Update splitters.py 01 September 2020, 14:51:38 UTC
bbd1949 Update CONTRIBUTORS.md 01 September 2020, 14:48:04 UTC
4cf3793 MurckoScaffold Fix (#85) * add murcko decompose and assert statements * fix bug * fix test indices * delete debugging print statements * delete includeChirality arg * delete includeChirality in tests and k fold split * delete debug statements * fix linting and delete arg docs Co-authored-by: Mufei Li <mufeili1996@gmail.com> 01 September 2020, 14:30:53 UTC
75acff5 [Dataset] Hot Fix for Invalid Molecules (#87) * Fix * Update * Fix * Add MUV * Add HIV * Add BACE * Update * Fix 30 August 2020, 15:26:56 UTC
32b14bd [Dataset] Add Datasets BBBP, ToxCast, SIDER, ClinTox (#86) * Fix * Update * Fix * Add MUV * Add HIV * Add BACE * Update 30 August 2020, 12:07:06 UTC
b014174 [Dataset] BACE (#83) * Fix * Update * Fix * Add MUV * Add HIV * Add BACE 28 August 2020, 19:10:09 UTC
e3d0c6a [Dataset] Add HIV from MoleculeNet (#82) * Fix * Update * Fix * Add MUV * Add HIV 28 August 2020, 12:46:08 UTC
6759b28 [Dataset] MUV from MoleculeNet (#81) * Fix * Update * Fix * Add MUV 28 August 2020, 10:51:53 UTC
1d51422 [Example] Support PR AUC for Classification on CSV Datasets (#80) * Fix * Update * Fix 28 August 2020, 08:30:47 UTC
833aa58 [Eval] Add Support for PR AUC Metric (#79) * Fix * Update 28 August 2020, 07:47:31 UTC
0fa1162 [Dataset] Fix for Downloading Datasets (#78) * Fix * Trigger CI 27 August 2020, 18:10:45 UTC
dc96092 [Example] Bug Fix for Molecular Property Prediction on A CSV Dataset (#76) * PCBA * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix AttentiveFP 27 August 2020, 09:00:22 UTC
7095532 [Dataset] Add Classification Datasets of MoleculeNet (#61) * PCBA * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix 27 August 2020, 08:57:03 UTC
b27d522 Fix (#75) 24 August 2020, 17:40:51 UTC
da13842 [Data Preprocessing] Support for Virtual Nodes in Graph Construction and Featurization (#74) * Fix * Fix * Support for virtual nodes * Fix 24 August 2020, 16:34:57 UTC
bc1b793 Fix (#73) 24 August 2020, 13:17:07 UTC
6e2d2e6 [Fix] Migrate to 0.5 (#72) * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix 23 August 2020, 20:38:00 UTC
0d27271 Add self_loop to mol_to_bigraph in UnlabeledSMILES if any model from GIN is used for inference (#66) * self loop fix for UnlabeledSMILES * delete print statement Co-authored-by: Mufei Li <mufeili1996@gmail.com> 23 August 2020, 12:45:44 UTC
e0563ac Migrate to DGL 0.5 (#71) * Update * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix 22 August 2020, 20:04:36 UTC
56f4bd3 Add parallel processing to MoleculeCSVDataset using joblib (#67) Co-authored-by: Mufei Li <mufeili1996@gmail.com> 21 August 2020, 08:17:45 UTC
a28f6db Support For GuacaMol (#69) * Support For GuacaMol * Support For GuacaMol UPDATE 20 August 2020, 16:50:13 UTC
152ccd3 minor fix (#68) * bug fix * Update * UPDATE * minor fix Co-authored-by: mufeili <mufeili1996@gmail.com> 18 August 2020, 02:46:45 UTC
e874d2e Support Vocabulary of GuacaMol for JTNN (#62) * bug fix * Update * UPDATE Co-authored-by: mufeili <mufeili1996@gmail.com> 05 August 2020, 05:55:25 UTC
82ae3cf Update README.md 30 July 2020, 03:39:42 UTC
2b6b583 Update for Conda Release (#60) * Update * Update 28 July 2020, 15:01:08 UTC
bba4370 Update (#59) 28 July 2020, 14:03:21 UTC
fd73efa [Molecular Property Prediction on CSV Datasets] Add Support for Random Split (#56) * Update * Update * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Update * Update * Fix * Update * Add random split 23 July 2020, 08:10:43 UTC
6ba0c55 Update README.md 22 July 2020, 06:04:35 UTC
47c7fdd Update README.md 22 July 2020, 06:04:22 UTC
7367db3 [Molecular Property Prediction on CSV Dataset] Hot Fix (#55) * Update * Update * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix 16 July 2020, 14:24:14 UTC
5fb0150 [Molecular Property Prediction on CSV Dataset] Add Support for Fine-tuning Pre-trained GINs (#54) * Update * Update * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix 16 July 2020, 09:07:18 UTC
dec60f4 [Molecular Property Prediction on CSV Dataset] Add Support for AttentiveFP (#53) * Update * Update 15 July 2020, 06:49:19 UTC
ad936b0 [Molecular Property Prediction on CSV] Add Support for MPNN (#52) * Update * Update * Update * Fix * Update * Fix * Update * Update * Support GAT * Fix * Fix * Fix * Fix * Update * Update * Update * Update * Fix * Fix * Update * Support MPNN * Fix * Fix * Update * Fix * Update * Fix * Fix * Fix * Fix * Use DGL latest stable for the time being * Fix * Fix 15 July 2020, 04:24:48 UTC
94322a8 [Molecular Property Prediction on CSV Dataset] Add Support for Weave (#51) * Update * Update * Update * Fix * Update * Fix * Update * Update * Support GAT * Fix * Fix * Fix * Fix * Update * Update * Update * Update * Fix * Fix 13 July 2020, 14:06:39 UTC
a9a79b7 Hot Fix for Molecular Property Prediction on CSV Datasets (#50) * Update * Update * Update * Fix * Update * Fix * Update * Update * Support GAT * Fix * Fix * Fix * Fix 12 July 2020, 18:15:42 UTC
94fb0fd [Utils] Atom/Bond Featurizers for AttentiveFP (#49) * Update * Update * Update * Fix 12 July 2020, 14:36:33 UTC
8e7ce53 Create readthedocs.yml (#48) * Create readthedocs.yml * Update readthedocs.yml 09 July 2020, 08:37:16 UTC
96895f2 [Bug fix] Fix the scripts for property prediction on CSV datasets (#47) * Update * Update * Udpate * Update * Add dataset analysos * Update * Fix lint * Fix lint * Update * Update * Update * Update * Update * Update * Update * Update * Update * Updatee * Fix * Fix * Update * Update * Fix * Fix * Fix * Add new dataset * Update * Update * Update * Fix bug 07 July 2020, 19:21:05 UTC
895d942 [CSV Property Prediction] Allow Taking the Logarithm of Labels in Regression (#46) * Update * Update * Udpate * Update * Add dataset analysos * Update * Fix lint * Fix lint * Update * Update * Update * Update * Update * Update * Update * Update * Update * Updatee * Fix * Fix * Update * Update * Fix * Fix * Fix * Add new dataset * Update * Update * Update 07 July 2020, 17:41:39 UTC
928057a [Dataset] AstraZeneca Solubility Dataset from ChEMBL (#45) * Update * Update * Udpate * Update * Add dataset analysos * Update * Fix lint * Fix lint * Update * Update * Update * Update * Update * Update * Update * Update * Update * Updatee * Fix * Fix * Update * Update * Fix * Fix * Fix * Add new dataset * Update * Update 07 July 2020, 17:23:46 UTC
e81ad78 Update Command Line Interface (#44) * Update * Update * Udpate * Update * Add dataset analysos * Update * Fix lint * Fix lint * Update * Update * Update * Update * Update * Update * Update * Update * Update * Updatee * Fix * Fix * Update * Update * Fix * Fix * Fix 07 July 2020, 14:02:05 UTC
4c85ad4 [Data] Add Datasets for ESOL, FreeSolv, Lipophilicity (#43) * Check if RDKit is installed * Check if RDKit is installed * Allow RDKit not installed * Fix * Allow RDKit not installed * Update * Update * Fix * Update * Finish ESOL * Add FreeSolv * Add doc * Add lipophilicity 02 July 2020, 19:33:33 UTC
6a0f05e Remove the Requirement for RDKit in Importing dgllife (#42) * Check if RDKit is installed * Check if RDKit is installed * Allow RDKit not installed * Fix * Allow RDKit not installed * Update * Update * Fix * Update 02 July 2020, 07:27:51 UTC
2f48064 Update CONTRIBUTORS.md 01 July 2020, 04:22:59 UTC
ec36fcb add notice for the atom map id in the rxn. (#36) * add notice for the atom map id in the rxn. The map ids in the rxn should be consecutive! * Update README.md * Update README.md * Update README.md Co-authored-by: Mufei Li <mufeili1996@gmail.com> 01 July 2020, 04:20:16 UTC
d3aa61e [Utils] Allow Representing Hydrogen Atoms as Explicit Nodes (#39) * Update * Fix * Update * Allow explicit hydrogens * Update 30 June 2020, 15:04:51 UTC
e837ee7 [Reaction Prediction] Handle Invalid Input Reactions (#38) * Update * Fix * Update 30 June 2020, 11:47:44 UTC
e834ec6 Original GCN combined with Ogbg-ppa's GCN. (#26) * GCN combined with ogbg-ppa's GCN * GCN combined with ogbg-ppa's GCN * Update * Fix lint * Fix * Fix * Update * Fixgit status * Update * Fix * Update * Fix * Update * Fix * Update * Update * Update test_property_prediction.py Co-authored-by: mufeili <mufeili1996@gmail.com> 30 June 2020, 03:59:36 UTC
be40342 Fix (#35) 28 June 2020, 06:09:13 UTC
889be12 [Reaction Prediction] Fix for rexgen_direct (#32) * Update * Fix 25 June 2020, 05:47:38 UTC
1e08671 Link predictor (#24) * full_graph_link_predictor * Create gcn_link_predictor.py * Create sage_link_predictor.py * Create test_link_prediction.py * Create full_graph_link_predictor.py * Create logger.py * Add files via upload * Add files via upload * Update README.md * Update README.md * Update README.md * Delete full_graph_link_predictor.py * Update * Update * Fix * Update (#5) * Remove outdated code * Update * Fix (#6) * Remove outdated code * Update * Fix * Try CI (#7) * Remove outdated code * Update * Fix * Hotfix (#30) * Reset parameters * Update * Update * Update * Update * Fix * Fix * Test * CI (#8) * Remove outdated code * Update * Fix * Test * CI Co-authored-by: zhongyue <37361694+seqRep@users.noreply.github.com> Co-authored-by: Mufei Li <mufeili1996@gmail.com> 24 June 2020, 08:46:49 UTC
8e3721a Hotfix (#30) * Reset parameters * Update * Update * Update * Update * Fix * Fix 23 June 2020, 10:46:57 UTC
08fc317 [Examples] Hotfix (#28) * Reset parameters * Update * Update * Update * Update * hotfix 20 June 2020, 19:47:50 UTC
b7be8c8 [Model] Allow Reseting Model Parameters (#27) * Reset parameters * Update * Update * Update * Update 18 June 2020, 18:44:04 UTC
448fbd0 [Reaction Prediction] Fix the Multiprocessing Issue (#22) * Update * Fix * Fix * Fix * Update * Fix * Update * Update * Fix the multiprocessing issue for candidate ranking 15 June 2020, 06:17:29 UTC
268a033 [Molecule Embedding] Hot fix (#21) * Update * Fix * Fix * Fix * Update * Fix * Update * Update 14 June 2020, 20:12:53 UTC
961e27e [Molecule Embedding] Compute Molecule Embeddings with Pre-trained GNNs (#20) * Update * Fix * Fix * Fix * Update 14 June 2020, 19:11:46 UTC
4871299 Update README for Reaction Prediction and Conda Channel for RDKit (#19) * Update README.md * Update torch_gpu.yml * Update torch_cpu.yml 13 June 2020, 17:41:23 UTC
b8fec00 add links of installing pytorch and dgl (#14) add links of installing pytorch and dgl Co-authored-by: Mufei Li <mufeili1996@gmail.com> 12 June 2020, 10:50:05 UTC
bfd4d5c Update CONTRIBUTORS.md (#16) 12 June 2020, 05:49:59 UTC
546e26a update rdkit channel (#15) update rdkit channel 12 June 2020, 05:27:12 UTC
abafa5d [Example] Refactor and Improve Interface (#13) * Refactor * Update * Update * Fix * Update * Update * Update * Fix * Fix * Fix * Update * Update * Fix * Fix * Update * Fix * Update * Update * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Fix * Update * Update * Update * Update Link * Update * Update conda * Update * Update * Fix 09 June 2020, 20:28:04 UTC
3dea423 [Examples] Migration (#11) * AttentiveFP * Add file header * Fix import * GAT Predictor * Fix import * GCN Predictor * Fix import * GIN Predictor * Fix lint * MGCN Predictor * MPNN Predictor * SchNet * Weave predictor * Reaction prediction * Fix test * DGMG * JTNN * Fix test * Pretrain * Doc * Protein-ligand binding * DGMG * JTNN * Final 05 June 2020, 12:54:53 UTC
4743c41 [Doc] Migration (#10) * AttentiveFP * Add file header * Fix import * GAT Predictor * Fix import * GCN Predictor * Fix import * GIN Predictor * Fix lint * MGCN Predictor * MPNN Predictor * SchNet * Weave predictor * Reaction prediction * Fix test * DGMG * JTNN * Fix test * Pretrain * Doc 05 June 2020, 11:35:28 UTC
ebc1294 [Model] Migration2 (#9) * AttentiveFP * Add file header * Fix import * GAT Predictor * Fix import * GCN Predictor * Fix import * GIN Predictor * Fix lint * MGCN Predictor * MPNN Predictor * SchNet * Weave predictor * Reaction prediction * Fix test * DGMG * JTNN * Fix test * Pretrain 05 June 2020, 10:39:09 UTC
8011fa7 [Model] Migration1 (#8) * MLP Readout * Fix * Weighted sum and max * Update * Weave * GNN for AttentiveFP * GAT * GCN for GNN * GNN for GIN * GNN for MGCN * GNN for SchNet * GNN for MPNN * GNN for Weave * GNN for WLN * ACNN 04 June 2020, 18:23:47 UTC
f8ce4d8 [Doc] Shorter File Headers (#7) * Alchemy * Update * PDBBind * Pubchem aromaticity * Tox21 * Tox21 * USPTO * Update * Fix for test * Shorter file headers 04 June 2020, 08:40:07 UTC
bc718dc [Data] Migration (#6) * Alchemy * Update * PDBBind * Pubchem aromaticity * Tox21 * Tox21 * USPTO * Update * Fix for test 04 June 2020, 03:45:53 UTC
9bacb42 Merge pull request #5 from mufeili/master [Utils] Migration 03 June 2020, 10:45:24 UTC
18baed2 Fix 03 June 2020, 10:44:07 UTC
b1f6972 Fix eval 03 June 2020, 10:38:16 UTC
8965e03 Fix test 03 June 2020, 10:32:50 UTC
3490019 Requires python 3.6+ 03 June 2020, 10:30:34 UTC
b50b5af Eval & Early Stop 03 June 2020, 10:27:52 UTC
c512e8f Fix test 03 June 2020, 10:19:50 UTC
1a8b427 Import order 03 June 2020, 10:14:46 UTC
8ec5180 Import order 03 June 2020, 10:13:49 UTC
3ee7682 Change import order 03 June 2020, 10:04:40 UTC
7e0dcd5 CI Lint 03 June 2020, 10:01:33 UTC
b75032b grouped import 03 June 2020, 09:55:44 UTC
c8c7745 Add splitters 03 June 2020, 09:52:56 UTC
d13419d Splitters 03 June 2020, 09:51:08 UTC
5ab50d4 Disable pytest warnings 03 June 2020, 09:44:55 UTC
4ef1c82 RDKit utils 03 June 2020, 09:36:02 UTC
0b9ec38 Merge branch 'master' of https://github.com/mufeili/dgl-lifesci 03 June 2020, 08:38:56 UTC
8178d07 CI 03 June 2020, 08:38:46 UTC
7f7f676 Merge branch 'master' into master 03 June 2020, 08:33:47 UTC
f781117 Complex to graph 03 June 2020, 08:31:52 UTC
af17f8f Merge pull request #3 from mufeili/master [Utils] Featurization and Graph Construction for Molecules 31 May 2020, 20:19:48 UTC
d818d54 Merge branch 'master' of https://github.com/mufeili/dgl-lifesci 31 May 2020, 20:18:39 UTC
3b642c4 Fix deprecation 31 May 2020, 20:18:29 UTC
15fc112 Merge branch 'master' into master 31 May 2020, 20:16:48 UTC
ebd9fa6 Fix deprecation 31 May 2020, 20:16:16 UTC
6af2564 Fix 31 May 2020, 20:09:40 UTC
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