GitHub / DeepGraphLearning/torchdrug / commits
A powerful and flexible machine learning platform for drug discovery
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| 6066fbd8 | v0.2.1 | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| 17ab229f | support customized edge feature in graph construction | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| 91e9bd9f | change chain id to accept lowercase and digits | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| c8155f40 | update md5s for alphafolddb and handle unknown residue types in esm | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| 5d21a5f6 | fix broken nvidia apt keys (#207) |
Cody Scandore <c****e@g****m>
Committed by: GitHub <n****y@g****m> |
about 3 years ago | |
| e3e659d4 |
Apple Silicon installation instructions (#176)
Co-authored-by: Zhaocheng Zhu <h****l@1****m> |
Michael Galkin <m****n@g****m>
Committed by: GitHub <n****y@g****m> |
about 3 years ago | |
| 323ed656 | clean up | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| 8a07e53e | fix multiview contrast & graph construction | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| a56f2c5f | make data.Graph compatible with load_state_dict() in PyTorch 1.11+ | Zhaocheng Zhu <h****l@1****m> | about 3 years ago | |
| a959f68f | Include ESM-2 models in esm.py |
Zuobai Zhang <1****5@f****n>
Committed by: GitHub <n****y@g****m> |
over 3 years ago | |
| ed176106 | Fix a bug in the call of layers.Set2Set in MPNN |
Zuobai Zhang <1****5@f****n>
Committed by: GitHub <n****y@g****m> |
over 3 years ago | |
| 01f4eaf6 | add full batch eval for knowledge graph completion | Zhaocheng Zhu <h****l@1****m> | over 3 years ago | |
| 87c1d589 | compatibility with python3.10 and torch2.0 | Zhaocheng Zhu <h****l@1****m> | over 3 years ago | |
| 60bf0afa | compact the log of config dict | Zhaocheng Zhu <h****l@1****m> | over 3 years ago | |
| dec42a94 | deprecate _size_to_index() implementation | Zhaocheng Zhu <h****l@1****m> | over 3 years ago | |
| 97858c6c | fix a bug in config_dict() |
Zuobai Zhang <1****5@f****n>
Committed by: Zhaocheng Zhu <h****l@1****m> |
over 3 years ago | |
| 115ca157 | add batch_norm & dropout in mlp of property prediction | oxer <1****5@f****n> | over 3 years ago | |
| 4e76c309 | fix bugs in SubsequenceNode & GraphConstruction | oxer <1****5@f****n> | almost 4 years ago | |
| 4ea99a04 | fix a bug on reloading scheduler | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| f92f8621 | remove deprecated floor div for PyTorch >= 1.10 | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| 28a677d2 |
handling case where all molecules are invalid in property optimization (#125)
Co-authored-by: Zhaocheng Zhu <h****l@1****m> |
Jannis Born <j****b@z****m>
Committed by: GitHub <n****y@g****m> |
almost 4 years ago | |
| cc2c1ca9 | depend on matplotlib-base conda package (#141) |
James Myatt <j****s@j****k>
Committed by: GitHub <n****y@g****m> |
almost 4 years ago | |
| 597f43ba | fix num_class in property prediction | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| cf2222e0 | avoid in-place RDKit operations in molecule construction | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| b41a7647 | fix bugs in layers.conv when using edge_linear | oxer <1****5@f****n> | almost 4 years ago | |
| c873e0e9 |
fix: Un-standardization of predict method in PropertyPrediction #109 (#111)
Co-authored-by: Saurav Maheshkar <s****r@g****m>, oxer <1****5@f****n> |
Hiroshi Kajino <h****9@g****m>
Committed by: GitHub <n****y@g****m> |
almost 4 years ago | |
| 02fb1e8a | update AlphaFold links (#137) |
Shoufa Chen <s****n@1****m>
Committed by: GitHub <n****y@g****m> |
almost 4 years ago | |
| 180a9a8b | align esm with the latest fair-esm interface | oxer <1****5@f****n> | almost 4 years ago | |
| c277640b | fix num_entity in NeuralLP | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| b834f40f | v0.2.0 | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| 09ffe181 | add papers implemented | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| 186aef28 | update doc | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| cd45518e | clean up | Zhaocheng Zhu <h****l@1****m> | almost 4 years ago | |
| cf1a62c3 | add protein transforms | oxer <1****5@f****n> | almost 4 years ago | |
| 921f3f38 | add protein tasks | oxer <1****5@f****n> | almost 4 years ago | |
| 786d2387 | add protein models | oxer <1****5@f****n> | almost 4 years ago | |
| 2be5c851 | add protein datasets | oxer <1****5@f****n> | almost 4 years ago | |
| 462fd860 | add the dataset class and data structure for proteins | oxer <1****5@f****n> | almost 4 years ago | |
| 9fac9129 | fix feature padding in GCPN | Zhaocheng Zhu <h****l@1****m> | about 4 years ago | |
| 342c87e7 | fix feature padding in G2Gs | Zhaocheng Zhu <h****l@1****m> | about 4 years ago | |
| 5e07dd36 | fix a typo in data.Graph.split() | oxer <1****5@f****n> | about 4 years ago | |
| a1df0a20 | update signature & docs for deprecated_alias | Zhaocheng Zhu <h****l@1****m> | about 4 years ago | |
| d2823133 | add setter functions for molecule features | Zhaocheng Zhu <h****l@1****m> | about 4 years ago | |
| 518a699b | fix utils.cached | Zhaocheng Zhu <h****l@1****m> | about 4 years ago | |
| dbf6f4e9 | Add opencontainers image-spec to `Dockerfile` |
Saurav Maheshkar <s****r@g****m>
Committed by: Zhaocheng Zhu <h****l@1****m> |
about 4 years ago | |
| e73d2c93 | release v0.1.3 | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| ce75ce43 | add some documentation | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 957cec70 | small change to neurallp | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 5f9ce1c1 | add metrics | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 4b4b30a2 | add variadic functions & fix rspmm small bug | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 36832c6f | small documentation modification | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| cd2d10f2 | add smart_open | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| f8d2de6f | add node/edge/graph reference & change node/edge to atom/bond | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 20f84170 | add wandb demo |
Chence Shi <c****i@p****n>
Committed by: GitHub <n****y@g****m> |
over 4 years ago | |
| f5d9689c | fix: RuntimeError in GraphIsomorphismNetwork #92 (#93) |
Hiroshi Kajino <h****9@g****m>
Committed by: GitHub <n****y@g****m> |
over 4 years ago | |
| 26f15f63 |
fix: RuntimeError if batch has only invalid mols (#84)
Co-authored-by: Zhaocheng Zhu <z****u@p****n> |
Jannis Born <j****n@g****e>
Committed by: GitHub <n****y@g****m> |
over 4 years ago | |
| b411837f | make register_buffer consistent with PyTorch 1.6.0+ | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| f29dc555 | fix patch for torch.utils.data.Dataset | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 119002a4 | add silent option in core.Meter.log() | oxer <1****5@f****n> | over 4 years ago | |
| 1cfb186e |
add documentation for W&B logger (#74)
Co-authored-by: Zhaocheng Zhu <h****l@1****m> |
Manan Goel <m****9@g****m>
Committed by: Zhaocheng Zhu <h****l@1****m> |
over 4 years ago | |
| eeee1918 | update citation | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 29e18eed | integrate wandb logger (#72) |
Manan Goel <m****9@g****m>
Committed by: GitHub <n****y@g****m> |
over 4 years ago | |
| 17477caa |
Implement `PackedGraph.to()` (#70)
Co-authored-by: Zhaocheng Zhu <h****l@1****m> |
Charles Tapley Hoyt <c****t@g****m>
Committed by: GitHub <n****y@g****m> |
over 4 years ago | |
| a93356e8 | extend SynthonCompletion for arbitrary node features | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 04746980 | speed up spmm & rspmm | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 70a70915 | add Dockerfile | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| c067129e | add CITATION.cff | Zhaocheng Zhu <h****l@1****m> | over 4 years ago | |
| 278bcc8c | avoid rdkit mol creation if lazy load |
Will Connell <w****3@g****m>
Committed by: Zhaocheng Zhu <h****l@1****m> |
over 4 years ago | |
| a710097c | update dependency to torch 1.8.0 | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 909dd2d3 | support Windows installation | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 5bf0a505 | add Twitter link and update Colab link | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 13550185 | add doc for variadic_sample | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| e30e2b0a | fix synthon for USPTO50k | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 489677cb | release v0.1.2 | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 3ab63a77 | cache atom types & bond types once computed | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| e9c02e1d | simplify KnowledgeGraphCompletion implementation | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 98c855a3 | add data.Dictionary & data.Graph.match | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 6f92bc31 | add variadic_sample, multi_slice & add more instances for spmm/rspmm | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| fef62bc3 | update some figures | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| c06d61fd | add graphaf figure | chenceshi <c****i@p****n> | almost 5 years ago | |
| 7fed9a51 | add figure for ContextPred | oxer <1****5@f****n> | almost 5 years ago | |
| 46b7df5d | Fix https://github.com/DeepGraphLearning/torchdrug/issues/35 (#47) |
juntae <k****9@n****m>
Committed by: GitHub <n****y@g****m> |
almost 5 years ago | |
| cda8e8b0 | fix retrosynthesis tutorial | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 588d5d29 | fix bugs in loading chembl filtered |
Oxer11 <1****5@f****n>
Committed by: Zhaocheng Zhu <h****l@1****m> |
almost 5 years ago | |
| 6687d1be | fix a bug in loading zinc2m | Oxer11 <1****5@f****n> | almost 5 years ago | |
| d1428a03 | merge Merge branch 'master' of github.com:DeepGraphLearning/torchdrug | Oxer11 <1****5@f****n> | almost 5 years ago | |
| 300189e7 | small fix on retrosynthesis | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| d4b78839 | remove bond stereo in USPTO50k & speed up USPTO50k loading | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 227e42f0 | add Colab link | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| f14caf76 | release v0.1.1 | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 10ca2ed9 | include sascorer from RDKit | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 461ba1a3 | fix to_molecule for stereo atoms | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 81596851 | fix JIT compilation for macOS | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| bf8be52b | add pip support | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 953acab0 | small fix on PackedMolecule.from_smiles and plot.echarts | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 24eb73ff | add variadic_randperm | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| a12bbd32 | fix issues in docs and add tutorial for finetuning | Zhaocheng Zhu <h****l@1****m> | almost 5 years ago | |
| 39015cde | fix a bug in _Configurable.config_dict |
Oxer11 <1****5@f****n>
Committed by: Zhaocheng Zhu <h****l@1****m> |
almost 5 years ago | |
| d5700830 | fix a bug in _Configurable.config_dict | Oxer11 <1****5@f****n> | almost 5 years ago | |
| 5c4607ea | fix bugs in SchNet and add test code |
Oxer11 <1****5@f****n>
Committed by: Zhaocheng Zhu <h****l@1****m> |
almost 5 years ago |