Recent Releases of deepchem

deepchem - 2.8.0 Initial Release

Initial release of 2.8.0. Human-written release notes to be added soon. We will be doing stability checks over the next few weeks with bugfixes going in 2.8.1

What's Changed

Bug Fix #3086 by @advikavs in https://github.com/deepchem/deepchem/pull/3096
Update by @BalajiAI in https://github.com/deepchem/deepchem/pull/3110
Molnet added example and w matrix explanation by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3143
flake8 configuration update by @arunppsg in https://github.com/deepchem/deepchem/pull/3136
Fixing issue 3090 by @advikavs in https://github.com/deepchem/deepchem/pull/3097
Updating RDKitDescriptors featurizer to support custom descriptors by @arunppsg in https://github.com/deepchem/deepchem/pull/3135
Update hyperlink for "datasets already available in MolNet" in docs by @ARY2260 in https://github.com/deepchem/deepchem/pull/3152
Refactoring DMPNN: removing _MapperDMPNN class by @arunppsg in https://github.com/deepchem/deepchem/pull/3158
Changing indent width to 4 - setup.cfg by @advikavs in https://github.com/deepchem/deepchem/pull/3160
Merge dataset when the dimension of y is 1 by @advikavs in https://github.com/deepchem/deepchem/pull/3163
PEP8 for layers by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3167
Yapf fixes on pytorch_datasets.py by @advikavs in https://github.com/deepchem/deepchem/pull/3165
yapf on datasets.py by @arunppsg in https://github.com/deepchem/deepchem/pull/3166
yapf fixes deepchem/data/data_loader.py by @advikavs in https://github.com/deepchem/deepchem/pull/3171
Feedforward by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3164
yapf fixes to data/tests by @advikavs in https://github.com/deepchem/deepchem/pull/3173
yapf fixes on torch_model.py by @arunppsg in https://github.com/deepchem/deepchem/pull/3172
yapf fixes to trans/tests directory by @maithili232 in https://github.com/deepchem/deepchem/pull/3178
yapf fixes to featurizers by @advikavs in https://github.com/deepchem/deepchem/pull/3177
type fixes for pep 484 compliance by @arunppsg in https://github.com/deepchem/deepchem/pull/3181
yapf fixes deepchem/models by @advikavs in https://github.com/deepchem/deepchem/pull/3186
Adding grover featurizer by @arunppsg in https://github.com/deepchem/deepchem/pull/3138
yapf on deepchem/hyper by @maithili232 in https://github.com/deepchem/deepchem/pull/3188
yapf fixes deepchem keras models by @advikavs in https://github.com/deepchem/deepchem/pull/3192
adding dqc to deepchem by @advikavs in https://github.com/deepchem/deepchem/pull/3196
yapf fixes to deepchem featurizers by @advikavs in https://github.com/deepchem/deepchem/pull/3198
yapf fixes on deepchem/metalearning by @maithili232 in https://github.com/deepchem/deepchem/pull/3197
yapf on deepchem/utils part one by @maithili232 in https://github.com/deepchem/deepchem/pull/3203
yapf on deepchem/utils/test by @maithili232 in https://github.com/deepchem/deepchem/pull/3202
DeepChem package version update in init.py by @arunppsg in https://github.com/deepchem/deepchem/pull/3194
yapf on deepchem/metrics by @maithili232 in https://github.com/deepchem/deepchem/pull/3199
Yapf fixes on molnet directory by @maithili232 in https://github.com/deepchem/deepchem/pull/3169
yapf fixes on deepchem/utils part three by @maithili232 in https://github.com/deepchem/deepchem/pull/3205
changed indentation width to 4 spaces in deepchem/models/layers.py by @brianpzaide in https://github.com/deepchem/deepchem/pull/3210
yapf fixes on deepchem/trans directory by @maithili232 in https://github.com/deepchem/deepchem/pull/3170
Changing indent width to 4 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3207
Yapf fixes on test directories by @arunppsg in https://github.com/deepchem/deepchem/pull/3212
yapf on deepchem/utils part two by @maithili232 in https://github.com/deepchem/deepchem/pull/3204
DQC Pytest by @advikavs in https://github.com/deepchem/deepchem/pull/3220
Changing indent width to 4 spaces on deepchem/models dir by @arunppsg in https://github.com/deepchem/deepchem/pull/3213
Yapf fixes on deepchem.feat module by @arunppsg in https://github.com/deepchem/deepchem/pull/3211
Changing indent to 4 spaces on rl, split, molnet, dock dir by @arunppsg in https://github.com/deepchem/deepchem/pull/3216
DFT initial pr - Adding utilities by @advikavs in https://github.com/deepchem/deepchem/pull/3190
fixing dqc pytest by @advikavs in https://github.com/deepchem/deepchem/pull/3232
Fix flake8 errors by @brianpzaide in https://github.com/deepchem/deepchem/pull/3235
Fixing CI by @arunppsg in https://github.com/deepchem/deepchem/pull/3244
Adding attention layers by @arunppsg in https://github.com/deepchem/deepchem/pull/3183
update quickstart installation procedure by @vsaravind01 in https://github.com/deepchem/deepchem/pull/3249
Adding Usage Examples to Splitters by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3241
ModularTorchModel by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3242
Adding grover layers by @arunppsg in https://github.com/deepchem/deepchem/pull/3179
Refactor MLP by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3257
Infograph by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3254
added base vocabulary builder by @arunppsg in https://github.com/deepchem/deepchem/pull/3265
Adding readout layers for use in grover by @arunppsg in https://github.com/deepchem/deepchem/pull/3269
Fix: flake8 link by @gauthamk02 in https://github.com/deepchem/deepchem/pull/3276
Adding yapf ignore by @advikavs in https://github.com/deepchem/deepchem/pull/3279
Adding hugging-face tokenizer by @arunppsg in https://github.com/deepchem/deepchem/pull/3270
Adding more grover layers by @arunppsg in https://github.com/deepchem/deepchem/pull/3277
ci fix by @advikavs in https://github.com/deepchem/deepchem/pull/3286
Adding DFT data classes by @advikavs in https://github.com/deepchem/deepchem/pull/3284
Graphdata.numpytotorch() by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3283
Grover vocabulary builder by @arunppsg in https://github.com/deepchem/deepchem/pull/3281
Batchgraph edge_index bug fix by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3291
New Code formatting CI by @arunppsg in https://github.com/deepchem/deepchem/pull/3278
Global and Local Mutual Information Loss by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3292
add to device for numpy to torch by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3299
Snap featurizer by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3266
pin torch-sparse to 0.6.16 by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3303
align torch device in MI Loss by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3301
removed embedding output type arg in grover by @arunppsg in https://github.com/deepchem/deepchem/pull/3300
Surpress assignment errors in graph_data by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3304
Rename Infograph to InfoGraphStar, add documentation and fixes by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3282
removing scipy pin by @arunppsg in https://github.com/deepchem/deepchem/pull/3309
PR on nnlda layer by @advikavs in https://github.com/deepchem/deepchem/pull/3237
Batching kwargs in batch graph by @arunppsg in https://github.com/deepchem/deepchem/pull/3294
Infograph and InfographStar by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3280
Wrapper to use hugging face algorithms for building vocabulary by @arunppsg in https://github.com/deepchem/deepchem/pull/3271
Revert pull request 3271 - wrapper to use hugging face algorithms for vocabulary building by @arunppsg in https://github.com/deepchem/deepchem/pull/3314
Docs fix by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3313
DFTYaml Loader by @advikavs in https://github.com/deepchem/deepchem/pull/3295
Added grover loss functions by @arunppsg in https://github.com/deepchem/deepchem/pull/3297
Docs fix remove torch sparse and scatter by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3317
Modular loading from pretrained by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3305
removed torch-scatter and torch-sparse from dependency by @arunppsg in https://github.com/deepchem/deepchem/pull/3319
extracting attributes for grover model from batch graph by @arunppsg in https://github.com/deepchem/deepchem/pull/3312
InfographStar Multitask Classification and Regression by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3318
Cleaning docstring for grover layers by @arunppsg in https://github.com/deepchem/deepchem/pull/3333
Removing duplicate grover test by @arunppsg in https://github.com/deepchem/deepchem/pull/3329
SCF iterations by @advikavs in https://github.com/deepchem/deepchem/pull/3320
adding grover pretrain module by @arunppsg in https://github.com/deepchem/deepchem/pull/3334
adding grover finetune model by @arunppsg in https://github.com/deepchem/deepchem/pull/3335
Infograph test fix by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3340
fixing dqc docs by @advikavs in https://github.com/deepchem/deepchem/pull/3332
update docstring of IRVLayer by @shoaib6174 in https://github.com/deepchem/deepchem/pull/3324
Descriptive names for ci runs by @arunppsg in https://github.com/deepchem/deepchem/pull/3336
adding grover pretrain model as ModularTorchModel by @arunppsg in https://github.com/deepchem/deepchem/pull/3272
remnants of #3336 by @arunppsg in https://github.com/deepchem/deepchem/pull/3348
GNNModular by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3339
Wrapper to use hugging face algorithms for building vocabulary by @arunppsg in https://github.com/deepchem/deepchem/pull/3316
Supervised GNNModular tasks by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3343
fixing dqc workflows by @advikavs in https://github.com/deepchem/deepchem/pull/3361
Adding spin and charge properties to dft data by @advikavs in https://github.com/deepchem/deepchem/pull/3355
Masking tasks for GNN Modular by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3350
DeepGraphInfomax GNNModular pretraining task by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3358
Layers cheatsheet by @anoushka2000 in https://github.com/deepchem/deepchem/pull/3371
add GraphData subgraph, shortest length by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3373
MoleculeNet Cheatsheet by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3368
Context pred GNN Modular by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3369
DFT XC Model by @advikavs in https://github.com/deepchem/deepchem/pull/3363
DeepGraphInfomaxLoss docs fix by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3375
Adding DFT layers to docs table by @advikavs in https://github.com/deepchem/deepchem/pull/3377
Modifying calculations for polyatomic molecules by @advikavs in https://github.com/deepchem/deepchem/pull/3376
Integrating Huggingface models in Deepchem by @arunppsg in https://github.com/deepchem/deepchem/pull/3362
density profile loss function by @advikavs in https://github.com/deepchem/deepchem/pull/3381
Adding weights to DFT datasets by @advikavs in https://github.com/deepchem/deepchem/pull/3380
Tutorial render order by @Yukino2002 in https://github.com/deepchem/deepchem/pull/3384
RdkitConformerFeaturizer by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3378
GNN Modular encoder layers by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3372
Added support for Multitask regression task in HuggingFace models by @arunppsg in https://github.com/deepchem/deepchem/pull/3389
Fixing load from pretrained for huggingFace Models by @arunppsg in https://github.com/deepchem/deepchem/pull/3390
MLP batchnorm by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3385
Encoder layers for 3D infomax by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3391
Graph utils for 3dinfomax by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3394
PNA layers by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3392
Fix Tutorial 13 on Molecular Docking by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3387
chemberta in deepchem by @arunppsg in https://github.com/deepchem/deepchem/pull/3382
Allow loading only specific tasks in zinc15 dataset by @arunppsg in https://github.com/deepchem/deepchem/pull/3399
PNA GNN by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3395
Porting SetGather by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3255
Principal Neighborhood Aggregnation model by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3405
3d GNN layer by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3397
fix featurization freesolv by @ARY2260 in https://github.com/deepchem/deepchem/pull/3407
Net3D network by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3401
NTXent loss by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3409
fix docker build issues by @ARY2260 in https://github.com/deepchem/deepchem/pull/3422
Load from pretrained test for chemberta model by @arunppsg in https://github.com/deepchem/deepchem/pull/3413
fix 'gilbrat' scipy.stats error by @ARY2260 in https://github.com/deepchem/deepchem/pull/3424
InfoMax3DModular by @tonydavis629 in https://github.com/deepchem/deepchem/pull/3406
Porting DTNNEmbedding Layer by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3415
Unsortedsegmentsum and unittest by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3430
Update documentation of BasicMolGANModel by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3331
Sorted segment sum by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3431
Add EdgeNetwork Layer by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3439
Adding gpu training support for chemberta and grover by @arunppsg in https://github.com/deepchem/deepchem/pull/3443
add copy button to code blocks by @arunppsg in https://github.com/deepchem/deepchem/pull/3432
Porting Weave Layer to Torch by @NimishaDey in https://github.com/deepchem/deepchem/pull/3428
Adding NNPBE by @advikavs in https://github.com/deepchem/deepchem/pull/3418
Porting DTNNStep Layer by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3436
[DOCS] note on using deepchem data dir env variable by @arunppsg in https://github.com/deepchem/deepchem/pull/3453
Fix grover vocabulary builder by @arunppsg in https://github.com/deepchem/deepchem/pull/3450
fixes in chemberta docstring by @arunppsg in https://github.com/deepchem/deepchem/pull/3442
Porting of MolGANConvolutionLayer from tensorflow to pytorch by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3444
DTNNEmbedding Layer Parameter Error Fix by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3455
Add mxmnet_featurizer and tests by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3426
changes to electron sampler for ferminet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3447
DTNNStep Parameter error Fix by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3454
Minor Patches by @arunppsg in https://github.com/deepchem/deepchem/pull/3461
Porting of MolGANAggregationLayer from TF to Torch by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3460
Added logging utils to grover vocabulary builder by @arunppsg in https://github.com/deepchem/deepchem/pull/3472
Porting DTNNGather Layer by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3446
Adding XC model tutorial by @advikavs in https://github.com/deepchem/deepchem/pull/3465
Adding pyscf to CI tests for ferminet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3471
Weavegather torch by @NimishaDey in https://github.com/deepchem/deepchem/pull/3448
Fix in RDKitDescriptors by @arunppsg in https://github.com/deepchem/deepchem/pull/3484
Fix typo in pytest markers of infomax by @arunppsg in https://github.com/deepchem/deepchem/pull/3487
MolGANMultiConvolutionLayer Porting by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3470
Adding Equivariance Tutorial by @mgyigit in https://github.com/deepchem/deepchem/pull/3477
fix dockerfile v2 by @ARY2260 in https://github.com/deepchem/deepchem/pull/3425
Adding function to calculate HF orbitals and made minor reformat - Ferminet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3466
Adding weighted_skip parameter to MutilayerPerceptron layer by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3494
MolGANEncoderLayer Porting by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3493
Adding _MXMNetEnvelope layer by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3496
Added infograph model finetuning support by @arunppsg in https://github.com/deepchem/deepchem/pull/3491
Grover finetuning fix on mps/cuda devices by @arunppsg in https://github.com/deepchem/deepchem/pull/3507
Updated Tutorial doc by @Ash-29 in https://github.com/deepchem/deepchem/pull/3519
Tutorial IntroductiontoBioinformatics.ipynb updated and fixed a Bug in the code by @piyushkanadje in https://github.com/deepchem/deepchem/pull/3481
Update type test to satisfy new flake8 by @arunppsg in https://github.com/deepchem/deepchem/pull/3521
Global Message Passing Layer for MXMNet Model by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3479
MXMNetBesselBasis Layer by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3497
Added additional user argument to load subset of tasks in tox21 dataset by @arunppsg in https://github.com/deepchem/deepchem/pull/3515
Skip scaffold generation on invalid molecules by @arunppsg in https://github.com/deepchem/deepchem/pull/3520
Feature function - Batch Utils by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3523
Added assertion for task, mode in infograph model by @arunppsg in https://github.com/deepchem/deepchem/pull/3525
Ensure built during modular model restore by @arunppsg in https://github.com/deepchem/deepchem/pull/3528
Porting DTNN Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3513
adding ferminet electron feature layer by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3538
chemberta set problem type in config by @arunppsg in https://github.com/deepchem/deepchem/pull/3540
Porting encoder rnn by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3536
Porting DTNNModel Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3514
Integrated dqc.grid.base_grid.BaseGrid dependency into DeepChem by @vmm221313 in https://github.com/deepchem/deepchem/pull/3531
Adding ferminet envelope layer and dqc test fix by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3541
Fix restoring PyTorch trained model on different device by @vsaravind01 in https://github.com/deepchem/deepchem/pull/3542
Fix restoring HuggingFaceModel model trained on different device by @vsaravind01 in https://github.com/deepchem/deepchem/pull/3547
Local Message Passing layer for MXMNet Model by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3480
Integrating DQC: SpinParam + BaseQCCalc by @vmm221313 in https://github.com/deepchem/deepchem/pull/3549
fix optimizer bug in TF tests by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3563
Making InfoMax3D similar to original implementation by @arunppsg in https://github.com/deepchem/deepchem/pull/3560
add wigner D by @mgyigit in https://github.com/deepchem/deepchem/pull/3558
Porting decoder rnn by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3537
minor api changes for ferminet layers by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3551
Typos by @CurtisColwell in https://github.com/deepchem/deepchem/pull/3570
Utilities for SeqToSeq Model. by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3569
Update to infomax3d model by @arunppsg in https://github.com/deepchem/deepchem/pull/3561
MXMNetSphericalBasis Layer by @riya-singh28 in https://github.com/deepchem/deepchem/pull/3499
Porting variational by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3546
Ferminet forward pass complete by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3552
Infomax3D support for finetuning by @arunppsg in https://github.com/deepchem/deepchem/pull/3564
Porting seqtoseq Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3576
Added support for classification in infograph model by @arunppsg in https://github.com/deepchem/deepchem/pull/3575
Update classification pred computation in infomax model by @arunppsg in https://github.com/deepchem/deepchem/pull/3581
DFT Utilities [PR-1] [Config | Ztypes] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3588
adding complete forward and backward pass for ferminet pretraining by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3553
Memory Utilities [DFT] [PR-2] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3590
periodic table Utilities [DFT] [PR-3] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3591
Revert "periodic table Utilities [DFT] [PR-3]" by @rbharath in https://github.com/deepchem/deepchem/pull/3598
adding energy function for ferminet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3596
Gan by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3586
Deep dft periodic table Utils by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3600
Added Weave class and WeaveModel class by @NimishaDey in https://github.com/deepchem/deepchem/pull/3529
Seq to seq model by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3583
Correction in docs by @NimishaDey in https://github.com/deepchem/deepchem/pull/3611
doc fix on keras models by @KitVB in https://github.com/deepchem/deepchem/pull/3585
Atomic Convolution Module with Pytorch by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3617
Attrribute Utilities for EditableModule by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3612
added documentation tutorials by @KitVB in https://github.com/deepchem/deepchem/pull/3619
Scscore docs fixes and added References by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3595
Tokenizer Fix by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3628
Lattice [DFT] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3627
Fix Mac Build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3629
Fix PR for acnn test by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3638
Editable module by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3618
Utility to build grover vocab from csv by @arunppsg in https://github.com/deepchem/deepchem/pull/3621
Improvements to grover runtime by @arunppsg in https://github.com/deepchem/deepchem/pull/3615
Parse Molecule Description by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3641
Atomic Contributions bug fix by @MarcS18 in https://github.com/deepchem/deepchem/pull/3632
Orbparams by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3626
Spin Param and Val Grad by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3646
bumping torch to 2.1.0 for CI by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3633
mypy fix by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3656
Broadcast Utils [LinearOperator] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3648
Jax Test Fix by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3658
GANModel Porting by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3601
BaseXC by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3649
Fixes test on ci by @arunppsg in https://github.com/deepchem/deepchem/pull/3654
Bumping torch 2.1.0 for dqc by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3661
Added output_types in grover by @arunppsg in https://github.com/deepchem/deepchem/pull/3644
LightGBM - GBDT model earlystop bug fix by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3614
CI Unit tests fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3662
Miscellaneous methods for differentiation_utils. by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3665
Ferminet: adding torch.func and changes to model input type by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3623
mypy fix for ferminet energy function by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3671
AddXC [Basexc Helper class] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3670
LinearOperator Base Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3659
Jax Tests fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3680
Mypy Fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3681
Adding DeepChemXAlphafold tutorial by @soulpower007 in https://github.com/deepchem/deepchem/pull/3574
Dmpnn test fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3677
BaseGrid by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3669
ADD tutorial: openpom for olfaction by @ARY2260 in https://github.com/deepchem/deepchem/pull/3684
MolNet BBBC Load Function fix by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3676
Add attention mask for chemberta by @arunppsg in https://github.com/deepchem/deepchem/pull/3667
mamba warning fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3688
FermiNet Training Complete (Bacward pass + Forward) by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3689
AddLinearOperator [Linear Operator Helper Class] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3679
Mulbasexc by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3678
Wgan Porting by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3666
Bump up pytorch-lightning to 2.1.2 by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3687
Update requirements.rst to current req by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3690
Added Links for wishlists by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3691
Fix classification in infomax3d by @arunppsg in https://github.com/deepchem/deepchem/pull/3696
BaseDF Main Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3699
Add Atomic Convolution Model in Pytorch by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3698
Fix Atomic Convolution Model (ACNN) tests in Pytorch and Tensorflow by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3702
Update models init.py by @P-Kelley in https://github.com/deepchem/deepchem/pull/3705
BaseHamilton Main Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3701
MulLinearOperator LinearOperator Helper Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3708
Safe Operations by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3712
Fix Transformers Pin and Docs by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3693
add vina to python 3.10 by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3713
remove mypy pin by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3697
Fixed missing comma that broke notebook and switched glitter to discord by @P-Kelley in https://github.com/deepchem/deepchem/pull/3711
error fix in safeops by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3718
fix read the docs build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3720
OrbParam Shift to deep_dft by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3721
read the docs fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3724
Added weight decay argument to adam optimizer by @arunppsg in https://github.com/deepchem/deepchem/pull/3703
Missing Modules fix by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3725
Matmul linear operator by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3727
Modifications to Image Loader by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3695
FermiNet changes for weight initialization and minor type fix by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3736
MatrixLinearOperator Support Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3734
AdjointLinearOperator LinearOperator Support class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3735
DOC test fix - add to env by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3731
DFT example fixes by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3738
Added distributed loading of PyTorch DiskDataset by @arunppsg in https://github.com/deepchem/deepchem/pull/3704
CGTOBasis and AtomCGTOBasis by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3740
Change folder to DFT by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3732
Base System. Parent Class of Mol Object Class by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3742
Update AnIntroductionTo_MoleculeNet.ipynb by @naseehasalam in https://github.com/deepchem/deepchem/pull/3723
Update Link in Profile AboutnODEUsingTorchdiffeqin_Deepchem.ipynb by @shivance in https://github.com/deepchem/deepchem/pull/3743
Porting MetaLearning to PyTorch by @NimishaDey in https://github.com/deepchem/deepchem/pull/3653
Changed the deprecated usage of torch.Tensor.grad.data by @HridayM25 in https://github.com/deepchem/deepchem/pull/3726
Documentation Fixes by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3714
Tensor Non tensor separator and Uniquifier by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3748
fix pytorch geometric dependency by @P-Kelley in https://github.com/deepchem/deepchem/pull/3767
Layers Patches by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3760
symeig utility functions - 1 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3756
Minor fixes to PyTorch Lightning by @arunppsg in https://github.com/deepchem/deepchem/pull/3766
Distributed Trainer by @arunppsg in https://github.com/deepchem/deepchem/pull/3745
symeig utility functions - 2 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3773
Adding output logging for fermient by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3775
Fixed ImageLoader mypy issues by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3780
Fixing inconsistency in docstring by @HridayM25 in https://github.com/deepchem/deepchem/pull/3779
Doctest Ci error fixes by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3781
Purefunction-1 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3777
Docs Build Fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3789
Ci fixes by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3792
Ci fixes by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3794
Fix pypi build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3795
Dft Part - 1 [Current Open Pulls] by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3793
Doctest fix FermiNet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3791
Fix pypi build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3806
Addition of BBBC004 image set by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3706
rebased samloader by @KitVB in https://github.com/deepchem/deepchem/pull/3799
CI Fixes by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3800
CI fix - MordredFeat assertion error by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3802
Wgan fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3787
CI Fix by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3811
Dft part-2 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3807
BBBC0003 Loader Addition by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3788
Highway layer torch by @Shiva-sankaran in https://github.com/deepchem/deepchem/pull/3801
BBBC5 Cell Counting Loader Addition by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3798
port: base ProgressiveMultitask model to torch by @gauthamk02 in https://github.com/deepchem/deepchem/pull/3782
MolGAN Torch Model by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3814
adding ionic charge initialization using Hartree-Fock for FermiNet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3776
Ci fixes by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3815
Fix IndexError #3810 by @quincylin1 in https://github.com/deepchem/deepchem/pull/3820
adding FermiNet tutorial by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3819
Bamloader by @KitVB in https://github.com/deepchem/deepchem/pull/3825
Ci Fix - Storage issues on github runners by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3826
Update tutorials to discord by @P-Kelley in https://github.com/deepchem/deepchem/pull/3835
cramloader by @KitVB in https://github.com/deepchem/deepchem/pull/3830
Updating tutorials from glitter to discord by @P-Kelley in https://github.com/deepchem/deepchem/pull/3839
Improved energy calculation of FermiNet using vectorized hessian and jacobian by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/3829
Update homepage glitter to discord by @P-Kelley in https://github.com/deepchem/deepchem/pull/3844
Fix examples.rst doc for better reproducibility by @P-Kelley in https://github.com/deepchem/deepchem/pull/3871
Fixes - Torch Tests and CI storage by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3849
update: ProgresiveMultitask by @gauthamk02 in https://github.com/deepchem/deepchem/pull/3827
Porting TextCNN base model to Torch by @Shiva-sankaran in https://github.com/deepchem/deepchem/pull/3841
Porting TextCNN model from Tensorflow to Torch by @Shiva-sankaran in https://github.com/deepchem/deepchem/pull/3828
Pytest Fix (temporary) by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3880
Add Python 3.11 Support by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3686
DFT Part-3 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3817
Added Cell counting Tutorial by @aaronrockmenezes in https://github.com/deepchem/deepchem/pull/3845
Reduce import warnings by @arunppsg in https://github.com/deepchem/deepchem/pull/3846
Remove invalid line in hf_models.py by @arunppsg in https://github.com/deepchem/deepchem/pull/3866
Fix failing torch tests due to missing pydantic package by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3883
Fix bugs on ligand handling and pdbqt ligand support by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3881
Molgan GPU Support by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3816
Doctest Fix for SAMLoader, BAMLoader, CRAMLoader by @KitVB in https://github.com/deepchem/deepchem/pull/3890
port: ProgressiveMultitask Regressor and Classifier by @gauthamk02 in https://github.com/deepchem/deepchem/pull/3822
Updating deepchem's splitters tutorial by @Dragonwagon18 in https://github.com/deepchem/deepchem/pull/3837
Dft dev 4 by @GreatRSingh in https://github.com/deepchem/deepchem/pull/3876
CI fixes: add flaky to some tests, fix deprecation warnings by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3885
Update tutorials by @karannb in https://github.com/deepchem/deepchem/pull/3832
CI Fixes: patch fix for tfp, docker build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3896
Added TextCNN wrapper TorchModel by @Shiva-sankaran in https://github.com/deepchem/deepchem/pull/3877
Fix Docker Build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3907
bump up torch version to 2.2.1 by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3887
Bump torch cuda version to 11.8 by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3917
bump up deepchem version to 2.8.0 by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3936
V2.8.0 minor fixes for release by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3937

New Contributors

@maithili232 made their first contribution in https://github.com/deepchem/deepchem/pull/3178
@brianpzaide made their first contribution in https://github.com/deepchem/deepchem/pull/3210
@GreatRSingh made their first contribution in https://github.com/deepchem/deepchem/pull/3207
@vsaravind01 made their first contribution in https://github.com/deepchem/deepchem/pull/3249
@gauthamk02 made their first contribution in https://github.com/deepchem/deepchem/pull/3276
@shoaib6174 made their first contribution in https://github.com/deepchem/deepchem/pull/3324
@anoushka2000 made their first contribution in https://github.com/deepchem/deepchem/pull/3371
@Yukino2002 made their first contribution in https://github.com/deepchem/deepchem/pull/3384
@riya-singh28 made their first contribution in https://github.com/deepchem/deepchem/pull/3430
@shreyasvinaya made their first contribution in https://github.com/deepchem/deepchem/pull/3331
@NimishaDey made their first contribution in https://github.com/deepchem/deepchem/pull/3428
@mgyigit made their first contribution in https://github.com/deepchem/deepchem/pull/3477
@Ash-29 made their first contribution in https://github.com/deepchem/deepchem/pull/3519
@piyushkanadje made their first contribution in https://github.com/deepchem/deepchem/pull/3481
@vmm221313 made their first contribution in https://github.com/deepchem/deepchem/pull/3531
@CurtisColwell made their first contribution in https://github.com/deepchem/deepchem/pull/3570
@KitVB made their first contribution in https://github.com/deepchem/deepchem/pull/3585
@aaronrockmenezes made their first contribution in https://github.com/deepchem/deepchem/pull/3595
@MarcS18 made their first contribution in https://github.com/deepchem/deepchem/pull/3632
@soulpower007 made their first contribution in https://github.com/deepchem/deepchem/pull/3574
@P-Kelley made their first contribution in https://github.com/deepchem/deepchem/pull/3705
@naseehasalam made their first contribution in https://github.com/deepchem/deepchem/pull/3723
@HridayM25 made their first contribution in https://github.com/deepchem/deepchem/pull/3726
@Shiva-sankaran made their first contribution in https://github.com/deepchem/deepchem/pull/3801
@quincylin1 made their first contribution in https://github.com/deepchem/deepchem/pull/3820
@Dragonwagon18 made their first contribution in https://github.com/deepchem/deepchem/pull/3837
@karannb made their first contribution in https://github.com/deepchem/deepchem/pull/3832

Full Changelog: https://github.com/deepchem/deepchem/compare/2.7.1...2.8.0

- Python
Published by rbharath almost 2 years ago

deepchem - 2.8.0.pre

Pre-release for 2.8.0. If tests look stable, will release 2.8.0 shortly

- Python
Published by rbharath almost 2 years ago

deepchem - 2.7.1

Update to release workflow for publishing package in pypi

- Python
Published by arunppsg about 3 years ago

Highlights

DeepChem adds support for new models including DMPNNs, and MEGNet
We have ported NormalizingFlows to PyTorch
Added support for multi-gpu training via pytorch lightning.
Utilities to run hhsearch multisequence alignment search on a dataset
We have ported several layers to pytorch

Porting Models to PyTorch

The following models/layers have been ported to pytorch: GRU, InterAtomicL2Distance, WeightedLinearCombo, CombineMeanStd, AtomicConvolution layer, NeighborList, CNN, LSTMStep

New Features

Fake graph data generator to generate random graphs
FASTQ Loader to load biological sequences of data
Added topkaccuracy_score metric for evaluating model performances
Extracting molecular coordinates from QM9 dataset
Support for Random hyperparameter tuning

Featurizers

DMPNN Featurizer
Sparse matrix one hot featurizer
Position Frequency Matrix Featurizer implements a featurizer for position frequency matrices on a list of multisequence alignments to return a list of position frequency matrices.

New Layers

MEGNet Layer

Deprecations

dc.evaluate.utils.relative_difference is being deprecated. A deprecation warning to use math.isclose, np.isclose, np.allclose has been put in place.

Examples and Tutorials

Using hydra config system with pytorch-lightning system
New tutorial have been added to DeepQMC, SCVI and ScanPy, HierVAE, molGAN, hyper-parameter optimization, neural ODE, gaussian process, pytorch lightning, training a normalising flow on qm9 model, grover.

Documentation

Documentation has been improved with wider examples, using deepchem with docker, model cheat sheets.
Citations have been added to some of the tutorials to make them citable.

Improvements

Speed up in atomic convolution model
Utilities in deepchem disk dataset to convert it to a csv file.
Added file storage of validation and train scores during hyperparameter optimization.
Modified GraphData to support kwargs for storing additional attributes
Made it possible to run DeepChem in offline mode by removing default download call from CGCNN

Refactors

Mol2vec_fingerprints to directly use method from gensim library rather than mol2vec sub-package.

Bug Fixes

Retrieving shape of disk dataset when task names are not specified
Improvements in k-fold split when the number of data points is not exactly divisible by k
Fix a bug in SmilesToSeq featurizer when the padding length is 0.
A bug in which LogTransformer fails on data without an explicit task dimension has been fixed.

Maintenance

Adding type hints.
CI pipeline to consume less time

What's Changed

Bump to dev version by @rbharath in https://github.com/deepchem/deepchem/pull/2825
add topkaccuracy metric by @tonydavis629 in https://github.com/deepchem/deepchem/pull/2818
Update models.rst by @neerajanand321 in https://github.com/deepchem/deepchem/pull/2828
adding Docker tutorial by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2814
Added Graph Networks by @arunppsg in https://github.com/deepchem/deepchem/pull/2843
added molGAN tutorial by @saithat in https://github.com/deepchem/deepchem/pull/2773
adding hyperopt tutorials by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2851
Improvements to GraphData by @arunppsg in https://github.com/deepchem/deepchem/pull/2860
Update to Documentation for Using DeepChem in Jupyter Notebook by @iherath in https://github.com/deepchem/deepchem/pull/2856
Removing some obsolete code by @arunppsg in https://github.com/deepchem/deepchem/pull/2855
Removing package pins by @arunppsg in https://github.com/deepchem/deepchem/pull/2783
Fake graph data generator by @arunppsg in https://github.com/deepchem/deepchem/pull/2865
removing package pin by @arunppsg in https://github.com/deepchem/deepchem/pull/2873
adding jax dependencies by @arunppsg in https://github.com/deepchem/deepchem/pull/2877
Sparse matrix one hot featurizer by @davidRFB in https://github.com/deepchem/deepchem/pull/2870
added neural ode tutorial :books: by @shivance in https://github.com/deepchem/deepchem/pull/2859
Fixing Colab Links by @rbharath in https://github.com/deepchem/deepchem/pull/2883
Adding batch processing to GraphNet layer by @arunppsg in https://github.com/deepchem/deepchem/pull/2874
MEGNet layer implementation by @arunppsg in https://github.com/deepchem/deepchem/pull/2837
Fixing broken CI on windows - Jax and Vina by @arunppsg in https://github.com/deepchem/deepchem/pull/2886
Fresh gp tutorial by @TheRealSalmon in https://github.com/deepchem/deepchem/pull/2864
Fix to log transformer by @rbharath in https://github.com/deepchem/deepchem/pull/2887
Best score callback by @TheRealSalmon in https://github.com/deepchem/deepchem/pull/2866
fix for bug(issue #2106) by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2857
deepchem pytorch lightning tutorial by @Chahalprincy in https://github.com/deepchem/deepchem/pull/2826
sequence_utils for sequence homology search by @tonydavis629 in https://github.com/deepchem/deepchem/pull/2890
Speed up AtomicConv model, improvements to AtomicConv tutorial by @juliusgeo in https://github.com/deepchem/deepchem/pull/2888
Update TrainingaNormalizingFlowon_QM9.ipynb by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2885
Resolve the bug issue of loading the .sdf files by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2795
Position Frequency Matrix Featurizer by @tonydavis629 in https://github.com/deepchem/deepchem/pull/2896
Adding a tutorial for GROVER. by @atreyamaj in https://github.com/deepchem/deepchem/pull/2901
Update tutorials.rst by @BalajiAI in https://github.com/deepchem/deepchem/pull/2902
Adding FutureWarning to depreciate deepchem.utils.evaluate.relative_difference by @arunppsg in https://github.com/deepchem/deepchem/pull/2909
Module dl dependancies by @Nozziel in https://github.com/deepchem/deepchem/pull/2908
Extracting molecular coordinates for QM9 dataset from sdf files by @arunppsg in https://github.com/deepchem/deepchem/pull/2903
Add bibtex citation to first tutorial by @paupaiz in https://github.com/deepchem/deepchem/pull/2912
Update torchvision version requirement by @Matthew-Hostetler in https://github.com/deepchem/deepchem/pull/2916
add citation tutorial 4 by @paupaiz in https://github.com/deepchem/deepchem/pull/2921
add citation tutorial 5 by @paupaiz in https://github.com/deepchem/deepchem/pull/2922
Fixing CI errors by @arunppsg in https://github.com/deepchem/deepchem/pull/2931
Update scientists.rst by @shivance in https://github.com/deepchem/deepchem/pull/2932
resolved deprecation warning by @ARY2260 in https://github.com/deepchem/deepchem/pull/2937
atom features function and helper functions for DMPNN Featurizer by @ARY2260 in https://github.com/deepchem/deepchem/pull/2929
NormalizingFlow class and Affine transformation created using Pytorch by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2918
add bond_features and reaction mapping with suitable tests for DMPNN by @ARY2260 in https://github.com/deepchem/deepchem/pull/2942
Adding DeepQMC tutorial by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2914
Intro8 bibtex by @paupaiz in https://github.com/deepchem/deepchem/pull/2925
add bibtex tutorial 7 by @paupaiz in https://github.com/deepchem/deepchem/pull/2924
Update model cheatsheet by @j-frie in https://github.com/deepchem/deepchem/pull/2947
first steps in fixing docker build by @Nozziel in https://github.com/deepchem/deepchem/pull/2949
Added torch equivalent of InterAtomicL2Distances in torch_layers.py + YAPF changes by @atreyamaj in https://github.com/deepchem/deepchem/pull/2934
added HierVAE tutorial by @saithat in https://github.com/deepchem/deepchem/pull/2904
modify molecular featurizer base class and suitable tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/2960
added _MapperDMPNN class and suitable tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/2962
implement DCLightningModule by @Chahalprincy in https://github.com/deepchem/deepchem/pull/2945
Normalizing Flow Torch Model by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2944
Adding Metropolis Hasting sampler by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2935
Minor fix for utils.rst by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2973
add global feature generator and suitable unit tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/2971
Updated Tutorial File with TorchModel example by @allesrebel in https://github.com/deepchem/deepchem/pull/2977
:octocat: Fixed potential bug in deepchem's CNN implementation by @shivance in https://github.com/deepchem/deepchem/pull/2964
fix bug in GraphData class and add suitable unit test by @ARY2260 in https://github.com/deepchem/deepchem/pull/2979
Gcn by @Chahalprincy in https://github.com/deepchem/deepchem/pull/2958
python v3.8 in readthedocs.yml by @arunppsg in https://github.com/deepchem/deepchem/pull/2984
Pinning sphinx version in docs/requirements.txt by @arunppsg in https://github.com/deepchem/deepchem/pull/2985
Fixing #2986 by @shivance in https://github.com/deepchem/deepchem/pull/2988
PEP-008 style corrections for electron sampler by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2987
add count-based morgan fingerprint featurizer and suitable unit tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/2980
removed css theme by @arunppsg in https://github.com/deepchem/deepchem/pull/2991
modify RDKitDescriptors class for normalized features by @ARY2260 in https://github.com/deepchem/deepchem/pull/2983
Add Trident Chemwidgets tutorial to `examples/tutorials by @TShimko126 in https://github.com/deepchem/deepchem/pull/2965
add DMPNN featurizer class and suitable unit tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/2995
add new global feature generators and units tests for DMPNN featurizer by @ARY2260 in https://github.com/deepchem/deepchem/pull/3005
bibtex tutorial 9 by @paupaiz in https://github.com/deepchem/deepchem/pull/2926
implement dc lightning dataset module by @Chahalprincy in https://github.com/deepchem/deepchem/pull/2993
update unit tests with DC Lightning dataset module by @Chahalprincy in https://github.com/deepchem/deepchem/pull/2994
Added pytorch-lightning in mac requirements by @ojeda-e in https://github.com/deepchem/deepchem/pull/3008
modify PositionwiseFeedForward class and add unit tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/3009
add mapper class for dmpnn model and suitable unit tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/3001
:octocat: Porting CNN, TF ➡️ PyTorch by @shivance in https://github.com/deepchem/deepchem/pull/2963
Adding KFAC by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2972
ScanPy tutorial by @paupaiz in https://github.com/deepchem/deepchem/pull/3018
Adding to_csv method to DiskDataset by @arunppsg in https://github.com/deepchem/deepchem/pull/3007
bibtex tutorial 10 by @paupaiz in https://github.com/deepchem/deepchem/pull/2927
Port of WeightedLinearCombo from Keras to Torch by @subzjee in https://github.com/deepchem/deepchem/pull/3022
add dmpnn encoder layer and suitable unit test by @ARY2260 in https://github.com/deepchem/deepchem/pull/3023
Port of CombineMeanStd from Keras to Torch by @subzjee in https://github.com/deepchem/deepchem/pull/3021
Port of AtomicConvolution to Torch by @subzjee in https://github.com/deepchem/deepchem/pull/3026
Port of NeighborList from Keras to Torch by @subzjee in https://github.com/deepchem/deepchem/pull/3020
add dmpnn class and suitable unit tests by @ARY2260 in https://github.com/deepchem/deepchem/pull/3028
Scvi tools tutorial by @paupaiz in https://github.com/deepchem/deepchem/pull/3025
Adding electron input streams for Ferminet by @shaipranesh2 in https://github.com/deepchem/deepchem/pull/2997
add torch model wrapper for DMPNN model class by @ARY2260 in https://github.com/deepchem/deepchem/pull/3034
Real NVP Transformation Layer for Normalizing Flows by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/2996
Fixes to k-fold fingerprint splitting by @chertianser in https://github.com/deepchem/deepchem/pull/3038
GCNModel benchmark script for gpu by @Chahalprincy in https://github.com/deepchem/deepchem/pull/3016
Update pytorch-lightning version by @Chahalprincy in https://github.com/deepchem/deepchem/pull/3042
FASTQ loader by @paupaiz in https://github.com/deepchem/deepchem/pull/3036
pinning scipy to fix torch build in ci by @arunppsg in https://github.com/deepchem/deepchem/pull/3051
Using github actions v3 in workflows by @arunppsg in https://github.com/deepchem/deepchem/pull/3053
Removing mol2vec dependency by @arunppsg in https://github.com/deepchem/deepchem/pull/3052
Refactoring CI by @arunppsg in https://github.com/deepchem/deepchem/pull/3055
Fix issue #3057 (update _Mapper class for dmpnn) by @ARY2260 in https://github.com/deepchem/deepchem/pull/3058
Hydra by @Chahalprincy in https://github.com/deepchem/deepchem/pull/3030
Improving CI by @arunppsg in https://github.com/deepchem/deepchem/pull/3056
Assigning task names when they are not specified by @arunppsg in https://github.com/deepchem/deepchem/pull/3047
Update init.py by @ARY2260 in https://github.com/deepchem/deepchem/pull/3063
Correctly import lightning to avoid import errors by @abhiskk in https://github.com/deepchem/deepchem/pull/3065
Ported Tensorflow LSTMStep to PyTorch by @vinay-hebb in https://github.com/deepchem/deepchem/pull/3072
Add random hyperparameter search by @Manas2030 in https://github.com/deepchem/deepchem/pull/2897
added file output of validation and train scores by @arunppsg in https://github.com/deepchem/deepchem/pull/3073
Adding CI tests for python 3.10 by @arunppsg in https://github.com/deepchem/deepchem/pull/2846
Fix broken typehint in SparseMatrixOneHotFeaturizer.untransform by @AcylSilane in https://github.com/deepchem/deepchem/pull/3080
Substract padding from list length when slicing by @xerus in https://github.com/deepchem/deepchem/pull/3079
Ported Tensorflow GRU to PyTorch by @vinay-hebb in https://github.com/deepchem/deepchem/pull/3076
implementation of batching for DMPNN model by @ARY2260 in https://github.com/deepchem/deepchem/pull/3040
Minor Patch by @arunppsg in https://github.com/deepchem/deepchem/pull/3101
Minor patches by @arunppsg in https://github.com/deepchem/deepchem/pull/3105
adding batch size argument to lightning module by @arunppsg in https://github.com/deepchem/deepchem/pull/3106
updated mdtraj requirement by @arunppsg in https://github.com/deepchem/deepchem/pull/3112
Deepchem 2.7.0 by @arunppsg in https://github.com/deepchem/deepchem/pull/3099

New Contributors

@shaipranesh2 made their first contribution in https://github.com/deepchem/deepchem/pull/2814
@saithat made their first contribution in https://github.com/deepchem/deepchem/pull/2773
@iherath made their first contribution in https://github.com/deepchem/deepchem/pull/2856
@shivance made their first contribution in https://github.com/deepchem/deepchem/pull/2859
@TheRealSalmon made their first contribution in https://github.com/deepchem/deepchem/pull/2864
@juliusgeo made their first contribution in https://github.com/deepchem/deepchem/pull/2888
@JoseAntonioSiguenza made their first contribution in https://github.com/deepchem/deepchem/pull/2885
@BalajiAI made their first contribution in https://github.com/deepchem/deepchem/pull/2902
@Nozziel made their first contribution in https://github.com/deepchem/deepchem/pull/2908
@paupaiz made their first contribution in https://github.com/deepchem/deepchem/pull/2912
@Matthew-Hostetler made their first contribution in https://github.com/deepchem/deepchem/pull/2916
@ARY2260 made their first contribution in https://github.com/deepchem/deepchem/pull/2937
@j-frie made their first contribution in https://github.com/deepchem/deepchem/pull/2947
@allesrebel made their first contribution in https://github.com/deepchem/deepchem/pull/2977
@TShimko126 made their first contribution in https://github.com/deepchem/deepchem/pull/2965
@ojeda-e made their first contribution in https://github.com/deepchem/deepchem/pull/3008
@subzjee made their first contribution in https://github.com/deepchem/deepchem/pull/3022
@chertianser made their first contribution in https://github.com/deepchem/deepchem/pull/3038
@abhiskk made their first contribution in https://github.com/deepchem/deepchem/pull/3065
@vinay-hebb made their first contribution in https://github.com/deepchem/deepchem/pull/3072
@Manas2030 made their first contribution in https://github.com/deepchem/deepchem/pull/2897
@AcylSilane made their first contribution in https://github.com/deepchem/deepchem/pull/3080
@xerus made their first contribution in https://github.com/deepchem/deepchem/pull/3079

Full Changelog: https://github.com/deepchem/deepchem/compare/2.6.1...2.7.0

- Python
Published by arunppsg about 3 years ago

deepchem - Minor version bump for numpy

This release is a minor version bump that increases the required version of numpy.

What's Changed

fix gpu installation by @Chahalprincy in https://github.com/deepchem/deepchem/pull/2806
Release 2.6.0 by @arunppsg in https://github.com/deepchem/deepchem/pull/2812
Dependecy version fixes by @arunppsg in https://github.com/deepchem/deepchem/pull/2815
tighten testregressionoverfit bound by @austereantelope in https://github.com/deepchem/deepchem/pull/2796
Update uv_datasets.py by @neerajanand-coder in https://github.com/deepchem/deepchem/pull/2817
Minor Release 2.6.1 by @arunppsg in https://github.com/deepchem/deepchem/pull/2821

New Contributors

@Chahalprincy made their first contribution in https://github.com/deepchem/deepchem/pull/2806
@austereantelope made their first contribution in https://github.com/deepchem/deepchem/pull/2796
@neerajanand-coder made their first contribution in https://github.com/deepchem/deepchem/pull/2817

Full Changelog: https://github.com/deepchem/deepchem/compare/2.6.0...2.6.1

- Python
Published by rbharath about 4 years ago

deepchem - DeepChem 2.6.0

DeepChem 2.6.0 adds a range of new features (detailed below) along with significant improvements to the robustness of our testing infrastructure.

What's Changed

Version bump to 2.6.0.dev by @rbharath in https://github.com/deepchem/deepchem/pull/2447
Revised first tutorial by @Suzukazole in https://github.com/deepchem/deepchem/pull/2435
Add save reload to atomicconv by @ncfrey in https://github.com/deepchem/deepchem/pull/2450
Fix import issue in 22:Chemberta tutorial by @seyonechithrananda in https://github.com/deepchem/deepchem/pull/2445
Fixed error in computing Pearson correlation coefficient by @peastman in https://github.com/deepchem/deepchem/pull/2463
[WIP] Generalize OneHotFeaturizer to Support Arbitrary Strings by @alat-rights in https://github.com/deepchem/deepchem/pull/2458
Run all tests even if some fail by @peastman in https://github.com/deepchem/deepchem/pull/2461
Adds zip handling to SDFLoader by @NinadBhat in https://github.com/deepchem/deepchem/pull/2446
Use Log Transform for Clearance and HPPB by @mufeili in https://github.com/deepchem/deepchem/pull/2462
Improve SmilesToImage Error Message for long molecules by @PascalIversen in https://github.com/deepchem/deepchem/pull/2442
Added updating website to release instructions by @alat-rights in https://github.com/deepchem/deepchem/pull/2469
Fix pymatgen subclasses import error by @JainSamyak8840 in https://github.com/deepchem/deepchem/pull/2460
Update issues.rst by @alat-rights in https://github.com/deepchem/deepchem/pull/2471
Fixed Documentation for Graph Convolution Featurizers - MolGanFeaturizer by @atreyamaj in https://github.com/deepchem/deepchem/pull/2473
Add img_size parameter to ChemCeption by @PascalIversen in https://github.com/deepchem/deepchem/pull/2466
Fixing the failing test case - testmol2vecfingerprint by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2486
MEGNET model and evaluate the design by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2485
Update infra.rst by @alat-rights in https://github.com/deepchem/deepchem/pull/2491
Update release.md to reflect migration of deepchem.io repo by @alat-rights in https://github.com/deepchem/deepchem/pull/2492
Fix String Comparison to use POSIX standard #2481 by @peterskipper in https://github.com/deepchem/deepchem/pull/2482
Adding essential Molecular Utils by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2484
Basic MolGAN model by @MiloszGrabski in https://github.com/deepchem/deepchem/pull/2426
Adding the Huber Loss function by @atreyamaj in https://github.com/deepchem/deepchem/pull/2479
Update moleculenet.rst by @ncfrey in https://github.com/deepchem/deepchem/pull/2503
PAGTN featurisation support for Molecular Graph Conv by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2496
Added Sparse/Lazy Adam optimizer by @atreyamaj in https://github.com/deepchem/deepchem/pull/2493
Adding the AdamW optimizer by @atreyamaj in https://github.com/deepchem/deepchem/pull/2488
n_classes made variable(fixed to 2 classes) by @OmerOzgur271 in https://github.com/deepchem/deepchem/pull/2506
Added Squared Hinge loss by @atreyamaj in https://github.com/deepchem/deepchem/pull/2497
Fix DGL Dependency by @mufeili in https://github.com/deepchem/deepchem/pull/2516
Wrapper function for Pagtn Model by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2508
Tokenizer fix by @schithranandanurix in https://github.com/deepchem/deepchem/pull/2524
Adding Pytorch dependency into deepchem by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2541
added paper reference to tutorial 28 by @MariBerry in https://github.com/deepchem/deepchem/pull/2535
Fix typo in class name by @alat-rights in https://github.com/deepchem/deepchem/pull/2539
correct link of flake8 by @autodataming in https://github.com/deepchem/deepchem/pull/2522
Converted MultitaskRegressor and MultitaskClassifier to PyTorch by @peastman in https://github.com/deepchem/deepchem/pull/2559
Fixed errors in training models with uncertainty by @peastman in https://github.com/deepchem/deepchem/pull/2538
Setup for Jax dependency by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2560
[WIP] Adding the MAT Featurizer by @atreyamaj in https://github.com/deepchem/deepchem/pull/2544
Weights & Biases Basic Integration by @kshen3778 in https://github.com/deepchem/deepchem/pull/2520
Fix failing test cases by @peastman in https://github.com/deepchem/deepchem/pull/2568
Fix: Tokenizer is not able to encode triple bonds by @niklashoelter in https://github.com/deepchem/deepchem/pull/2566
Flake8 fix for molnet directory by @Suzukazole in https://github.com/deepchem/deepchem/pull/2525
Tensorflow independent environment by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2567
deepchem-Torch environment by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2563
Add DummyFeaturizer by @Suzukazole in https://github.com/deepchem/deepchem/pull/2570
Corrected Test Case for Smiles Tokenizer (adding to #2572) by @seyonechithrananda in https://github.com/deepchem/deepchem/pull/2578
Update FASTA Loader to accept arbitrary featurizers by @alat-rights in https://github.com/deepchem/deepchem/pull/2565
[WIP] Added examples for featurizers in documentation by @arunppsg in https://github.com/deepchem/deepchem/pull/2571
Fix full CI by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2573
Add section on setting up symbolic link by @Suzukazole in https://github.com/deepchem/deepchem/pull/2587
Added 'transformers' argument to ValidationCallback by @kshen3778 in https://github.com/deepchem/deepchem/pull/2584
USPTO Loader by @Suzukazole in https://github.com/deepchem/deepchem/pull/2546
Updates docs to Material Featurizers by @arunppsg in https://github.com/deepchem/deepchem/pull/2585
Adding the Freesolv dataset by @atreyamaj in https://github.com/deepchem/deepchem/pull/2576
Remove pin for matminer by @peastman in https://github.com/deepchem/deepchem/pull/2590
JaxModel (For integerating Jax into deepchem) by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2549
Adding Docs for New CI by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2591
Improved handling of classificationhandlingmode in Metric by @peastman in https://github.com/deepchem/deepchem/pull/2595
Added MATFeaturizer to website by @atreyamaj in https://github.com/deepchem/deepchem/pull/2599
Fixed errors caused by new Pandas version by @peastman in https://github.com/deepchem/deepchem/pull/2605
WandbLogger fixes: removed finish() from Model fit(), ValidationCallbacks fixes by @kshen3778 in https://github.com/deepchem/deepchem/pull/2586
Added ScaleNorm as the first MAT layer by @atreyamaj in https://github.com/deepchem/deepchem/pull/2601
Fixed ScaleNorm Test by @atreyamaj in https://github.com/deepchem/deepchem/pull/2610
Added ToC and Getting Started section in CONTRIBUTING.md by @arunppsg in https://github.com/deepchem/deepchem/pull/2592
Changed return type to np.ndarray in a few files by @atreyamaj in https://github.com/deepchem/deepchem/pull/2607
Made behavior of GaussianProcessHyperparamOpt more consistent by @peastman in https://github.com/deepchem/deepchem/pull/2620
Added defaults for precisionrecallcurve by @peastman in https://github.com/deepchem/deepchem/pull/2614
FirstDraftTutorial30 by @davidRFB in https://github.com/deepchem/deepchem/pull/2483
Fixed examples for loading perovskite dataset by @arunppsg in https://github.com/deepchem/deepchem/pull/2621
Reaction Split Transformer by @Suzukazole in https://github.com/deepchem/deepchem/pull/2597
Update loader to include transformer by @Suzukazole in https://github.com/deepchem/deepchem/pull/2628
Evaluation stage of JaxModel by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2604
Tutorial 31 - Introduction to material science by @arunppsg in https://github.com/deepchem/deepchem/pull/2626
[WIP] MAT: Attention Module by @atreyamaj in https://github.com/deepchem/deepchem/pull/2622
Adding bash-script for lightweight installs by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2618
Fixes to robertafeaturizer by @seyonechithrananda in https://github.com/deepchem/deepchem/pull/2581
pass featurizer kwargs by @walid0925 in https://github.com/deepchem/deepchem/pull/2507
RobertaFeaturizer by @walid0925 in https://github.com/deepchem/deepchem/pull/2523
First linear layer from AlphaFold by @rbharath in https://github.com/deepchem/deepchem/pull/2634
Minor fixes to examples in torch models by @arunppsg in https://github.com/deepchem/deepchem/pull/2630
[WIP] MAT Layers: Encoder by @atreyamaj in https://github.com/deepchem/deepchem/pull/2623
Fix doctest error in RxnSplitTransform by @Suzukazole in https://github.com/deepchem/deepchem/pull/2643
Made a test less flaky by @peastman in https://github.com/deepchem/deepchem/pull/2645
[WIP] MAT Layers: Embedding + Generator by @atreyamaj in https://github.com/deepchem/deepchem/pull/2624
Add integrations section to README by @kshen3778 in https://github.com/deepchem/deepchem/pull/2649
Init parameter modifications for WandbLogger by @kshen3778 in https://github.com/deepchem/deepchem/pull/2648
Update PR template and docs with doctest, pytest by @Suzukazole in https://github.com/deepchem/deepchem/pull/2651
Fix splitter errors for datasets without labels by @Suzukazole in https://github.com/deepchem/deepchem/pull/2641
installation clarification for zsh [skip ci] by @arunppsg in https://github.com/deepchem/deepchem/pull/2664
fixes attribute error from sklearn in print model by @arunppsg in https://github.com/deepchem/deepchem/pull/2671
BertFeaturizer (Replaces #2608) by @alat-rights in https://github.com/deepchem/deepchem/pull/2642
Fixes to tutorial section by @arunppsg in https://github.com/deepchem/deepchem/pull/2637
Fixes to MATFeaturizer and Tests by @atreyamaj in https://github.com/deepchem/deepchem/pull/2652
Reaction Featurizer by @Suzukazole in https://github.com/deepchem/deepchem/pull/2656
adding PINNs class by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2658
Adding Optimizers in Jax by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2695
Fix doctest - assign featurize to variable by @seyonechithrananda in https://github.com/deepchem/deepchem/pull/2696
Pinns Tutorial using PINNModel/JaxModel by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2682
MATModel: Wrapper MATModel class by @atreyamaj in https://github.com/deepchem/deepchem/pull/2691
Docs ScaffoldSplitter by @davidRFB in https://github.com/deepchem/deepchem/pull/2698
Bug fix to_json method by @arunppsg in https://github.com/deepchem/deepchem/pull/2694
Merge datasets preserves shard sizes by @EvanKomp in https://github.com/deepchem/deepchem/pull/2654
Updates to documentation by @arunppsg in https://github.com/deepchem/deepchem/pull/2712
Changes to CI by @arunppsg in https://github.com/deepchem/deepchem/pull/2715
Documenting CI by @arunppsg in https://github.com/deepchem/deepchem/pull/2713
Mypy fix by @arunppsg in https://github.com/deepchem/deepchem/pull/2720
Diffrential Physics in Deepchem with Jax by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2711
Tutorial Notebook for MAT by @atreyamaj in https://github.com/deepchem/deepchem/pull/2708
Minor fix to CI template by @arunppsg in https://github.com/deepchem/deepchem/pull/2722
modify tutorial 1 text to include log(solubility) by @deloragaskins in https://github.com/deepchem/deepchem/pull/2729
Remove omnia channel when installing dependencies by @peastman in https://github.com/deepchem/deepchem/pull/2732
Improvements to Grid Hyperparameter logging by @arunppsg in https://github.com/deepchem/deepchem/pull/2725
Pinned torch scatter to 2.0.8 by @arunppsg in https://github.com/deepchem/deepchem/pull/2733
Added rdkit-pypi to install requires in setup.py by @arunppsg in https://github.com/deepchem/deepchem/pull/2740
Reshard with no labels. by @davidRFB in https://github.com/deepchem/deepchem/pull/2707
Integrating with Autodock Vina's Python API by @arunppsg in https://github.com/deepchem/deepchem/pull/2741
Minor fixes by @arunppsg in https://github.com/deepchem/deepchem/pull/2742
Recommendations Ext File by @davidRFB in https://github.com/deepchem/deepchem/pull/2752
Fixed documentation by @tonydavis629 in https://github.com/deepchem/deepchem/pull/2751
PAINS filtering for LargeScaleChemical_Screens.ipynb#1355 by @puaykaipoh in https://github.com/deepchem/deepchem/pull/2746
Very small quick fix by @VIGNESHinZONE in https://github.com/deepchem/deepchem/pull/2759
Fixes to MAT model testing by @arunppsg in https://github.com/deepchem/deepchem/pull/2757
added assertion for number of atoms in MolGraphConvFeaturizer by @arunppsg in https://github.com/deepchem/deepchem/pull/2766
Removal of dc.feat.graph_features.AtomicConvFeaturizer by @arunppsg in https://github.com/deepchem/deepchem/pull/2769
Doc fixes by @arunppsg in https://github.com/deepchem/deepchem/pull/2768
Changes to removemissingentries by @arunppsg in https://github.com/deepchem/deepchem/pull/2774
Temporary fix to low r2-scores on benchmarking QM7 dataset by @arunppsg in https://github.com/deepchem/deepchem/pull/2777
Minor fixes by @arunppsg in https://github.com/deepchem/deepchem/pull/2767
updated tensorflow to 2.7 by @arunppsg in https://github.com/deepchem/deepchem/pull/2789
Add precommit by @SauravMaheshkar in https://github.com/deepchem/deepchem/pull/2790
removed Model being an sklearn BaseEstimator by @arunppsg in https://github.com/deepchem/deepchem/pull/2724
Minor fixes by @arunppsg in https://github.com/deepchem/deepchem/pull/2799
Consolidating installation yml files and github workflows by @arunppsg in https://github.com/deepchem/deepchem/pull/2793
Multi-gpu distributed training for deepchem by @ncfrey in https://github.com/deepchem/deepchem/pull/2786
Multisequence alignment tutorial by @tonydavis629 in https://github.com/deepchem/deepchem/pull/2805
Fix bug for dataset.getshape() after dataset.setshard() by @DingQK in https://github.com/deepchem/deepchem/pull/2802
Updated type annotations to work with numpy 1.20 by @peastman in https://github.com/deepchem/deepchem/pull/2545
Minor fixes by @arunppsg in https://github.com/deepchem/deepchem/pull/2807

New Contributors

@Suzukazole made their first contribution in https://github.com/deepchem/deepchem/pull/2435
@NinadBhat made their first contribution in https://github.com/deepchem/deepchem/pull/2446
@PascalIversen made their first contribution in https://github.com/deepchem/deepchem/pull/2442
@JainSamyak8840 made their first contribution in https://github.com/deepchem/deepchem/pull/2460
@atreyamaj made their first contribution in https://github.com/deepchem/deepchem/pull/2473
@peterskipper made their first contribution in https://github.com/deepchem/deepchem/pull/2482
@OmerOzgur271 made their first contribution in https://github.com/deepchem/deepchem/pull/2506
@schithranandanurix made their first contribution in https://github.com/deepchem/deepchem/pull/2524
@autodataming made their first contribution in https://github.com/deepchem/deepchem/pull/2522
@kshen3778 made their first contribution in https://github.com/deepchem/deepchem/pull/2520
@niklashoelter made their first contribution in https://github.com/deepchem/deepchem/pull/2566
@arunppsg made their first contribution in https://github.com/deepchem/deepchem/pull/2571
@davidRFB made their first contribution in https://github.com/deepchem/deepchem/pull/2483
@walid0925 made their first contribution in https://github.com/deepchem/deepchem/pull/2507
@EvanKomp made their first contribution in https://github.com/deepchem/deepchem/pull/2654
@deloragaskins made their first contribution in https://github.com/deepchem/deepchem/pull/2729
@tonydavis629 made their first contribution in https://github.com/deepchem/deepchem/pull/2751
@puaykaipoh made their first contribution in https://github.com/deepchem/deepchem/pull/2746
@SauravMaheshkar made their first contribution in https://github.com/deepchem/deepchem/pull/2790
@DingQK made their first contribution in https://github.com/deepchem/deepchem/pull/2802

Full Changelog: https://github.com/deepchem/deepchem/compare/2.5.0...2.6.0

- Python
Published by rbharath about 4 years ago

deepchem - DeepChem 2.5.0

See full release notes at https://forum.deepchem.io/t/deepchem-2-5-0-release/439

- Python
Published by rbharath almost 5 years ago

deepchem - DeepChem 2.4.0

Read the full release notes at https://forum.deepchem.io/t/deepchem-2-4-0-release-notes/340

- Python
Published by rbharath about 5 years ago

deepchem - Keras Models as Default

This release of DeepChem swaps from our home-grown TensorGraph framework to using Keras as the foundation of our models. This swap leaves us well prepared for the jump to Tensorflow 2.0 which will happen in our next major release. This version also bumps the TensorFlow version to 1.14. This release also includes a number of improvements to MoleculeNet and our transfer learning infrastructure

Remove uses of deprecated APIs #1550 Added attr-slow for the AtomicConvFeaturizer test #1552 Upgrade to TensorFlow 1.13.1 #1553 fix bug of load_pdbbind() and add new features #1561 Replaced Saver with Checkpoint #1566 Replaced uses of deprecated layers #1567 Convert TensorGraph layers to Keras layers #1578 Create KerasModel #1583 Update dependencies for DeepChem 2.2 #1584 Converted multitask models to KerasModel #1587 Remove contagious logger setup #1591 Converted graph models to KerasModel #1594 Construct dataset first time, even with reload set to True #1595 Loading thermosol and hppb datasets #1596 simple install one-liner #1602 Converted more models to Keras #1615 Smiles Based featurizers for ChemNet #1618 Converted progressive multitask models to KerasModel #1620 Swapping Split-Transform order #1621 Added ChemNet models with tests #1623 Swap Split-Transform order - II #1624 Converted GAN to KerasModel #1625 Converted reinforcement learning classes to Keras #1635 Created new MAML API #1636 SmilesToImage featurizer for Tox21, Sampl, HIV datasets #1637 ChemNet Fixes and Additions #1638 First version of pretrained loading #1643 Upgrade to TF 1.14 (Optional) #1645 Custom directories and SmilesToImage for MolNet #1649 ChemNet Fixes #1651 Created ValidationCallback #1652 Moved to Python 3.5 and 3.7 for Travis #1658 Stratified splitters, and minor changes for MolNet #1660 Updated installation instructions #1661 Workaround for bug in TF 1.14 #1662 Reorganized models directory #1664 Move test cases out of tensorgraph module #1666 Fixed broken and out of date examples #1671 Updated version number to 2.3.0 #1672 Update README.md #1682 DiskDataset.move() would not overwrite an existing dataset #1683

- Python
Published by rbharath over 6 years ago

deepchem - Improved Protein Structure, Microscopy, Interpretation Support

DeepChem 2.2 takes large steps towards making DeepChem a general purpose deep learning library for life science applications. Major improvements have been made to support for deep learning on protein structures, and significant support for image-based dataset and model handling has been added. In addition, tooling for interpreting deep models has been improved. A number of improvements to existing models have been added as well, including adding estimator support for a number of model classes. Many bugfixes and small improvements made it in as well. DeepChem 2.2 now depends on TensorFlow 1.12.

PDBBind and Protein Structure Improvements

1366, #1383, #1411, #1413, #1476 Atomic Convolution Improvements

1503, #1430, #1432 PDBBind bugfixes

1497 Using binding pockets to load PDBBind

1498 DeepMHC for protein peptide binding

1369, #1360, #1372, #1397 Featurziation Improvements

1498 DeepMHC for protein peptide binding

Image Handling Improvements

1516 Image Transformation improvements

1324 Cell counting dataset added. `ImageLoader` added

1414 Diabetic Retinopathy example model

1439 `ImageDataset` class

Dataset and Splitter Additions, Improvements and fixes

1507, #1540, #1406 Bugfixes

1514 Handling verbose=False when transforming data

1499 Butina splitter improvement

1347 Adds USPTO dataset.

1348 BBBC002 dataset addition

1339 Split datasets on ID

1416 Molnet loaders for UV/Kinase/Factors datasets

1327 BBBC001 dataset addition

1447 SDFLoader improvements

1425 Binary classification metric improvements

Model and Layer Additions and Improvemetns

1500 Seq2seq model improvements

1513 Clean up symmetry functions

1488 New graph convolution

1365 Average pooling for conv-nets

1370 ResNet50 improvements

1450 Layer output shapes

1452 Pad batch improvements

1453 Example distributed multitask classifier

1335 GraphConv improvements

1343 Making it easy to pull out neural fingerprints

1433 TensorGraph get layer weights

1325 UNet model changes

1334 First Resnet50 build

1473, #1142 TextCNN make_estimator support

1475 DTNN make_estimator support

1495 ANIRegression, BPSymmetryFunction make_estimator

Better Interpretability

1393 Saliency Mapping

1445 Saliency maps for diabetic retinopathy

Tests, Docs, Housekeeping

1527, #1457 Readme cleanup

1548 Version bump

1515 Upgrade to TF 1.12

1462 Typo fix predict_proba

1385, #1418 Build Fixes

1423 Yapf updates

1408 indentation cleanup

1344 Python 3.6 updates

1330: Docs updates

1337 Large screens tutorial

1338 Colab notebook version

1437 Python3 fixes

1454 Make RDKit a soft requirement

1455 Make simdna a soft requirement

1456, #1484 Make six a soft requirement

1458 Add tutorial section

1420 genomics code grouping into single file

1535, #1485, #1487, #1371, #1421, #1479, #1480 Test Improvements and Fixes

- Python
Published by rbharath almost 7 years ago

deepchem - Eager mode Support and Uncertainty Estimation

This release of DeepChem includes major upgrades to the TensorGraph framework by enabling support for TensorFlow Eager and Uncertainty estimation. TensorGraph layers can now be used in Eager mode to build dynamic models. In addition, a number of TensorGraph models, notably regression models, have been upgraded to allow for uncertainty estimates in model predictions. In addition, this release features a host of other improvements and bugfixes to TensorGraph, including support for saving submodels and significant refactoring to simplify underlying code. We've also simplified the names of TensorGraph models: TextCNNTensorGraph is now TextCNN with similar changes for other models. Old names are still supported, but deprecated and will be removed in DeepChem 3.0. We've also added a number of new IPython notebook tutorials explaining new DeepChem features.

This release also lays some groundwork for upgraded support for and image based datasets that will be coming in future releases.

Eager Mode and Uncertainty Estimation
- Eager Mode support #1191 #1176
- Uncertainty estimation support #1226 #1218
TensorGraph Improvements and Fixes
- TensorBoard improvements #1295 #1261
- TensorGraph refactoring #1286 #1259 #1196
- TensorGraph Submodel saving support #1264
- TensorGraph model improvements #1274 #1229 #1195 #1181 #1178 #1174 #1167
- Improved TensorGraph Estimator support #1153
- PowerSign optimizer #1233
- Hinge loss improvements/fixes #1242 #1189
- Rename MultiTask to Multitask #1249
New TensorGraph Models
- TensorGraph UNet Implementation #1272
- TensorGraph Progressive Multitask Classifier #1151
Example/Tutorial Improvements
- Example/MoleculeNet Fixes #1310 #1308 #1307 #1305 #1298 #1296 #1251 #1227 #1215 #1183 #1141 #1131
New IPython Notebook Tutorials
- tf.data and tf.estimator Notebook #1136
- Lime Notebook (model agnostic method explanation) #1202
- Synthetic feasibility scoring notebook #1182
Initial support for Image and Genomics based models
- New Image Transformations API #1300
- Improved support for genomic applications #1313 #1278
Builds, tests, and bugfixes
- Build improvements #1291 #1290 #1276 #1221 #1201 #1165 #1134 #1132 #1320
- Miscellaneous Bugfixes/Cleanup #1228 #1164 #1145 #1135
- Python 3 Fixes #1235
- Fix NumpyDataset reshaping #1260
Featurization Improvements
- Hashable Featurizers #1267
- Atom based features support for graph-convs #1156

- Python
Published by rbharath over 7 years ago

deepchem - Second Major DeepChem Release

This major version release finishes consolidating the DeepChem codebase around our TensorGraph API for constructing complex models in DeepChem. We've made a variety of improvements to TensorGraph's saving/loading features and added a number of new tutorials improving our documentation of TensorGraph. We've also removed a number of older deprecated submodules and models in favor of the new, standardized TensorGraph implementations.

In addition, we've implemented a number of new deep models and algorithms, including DRAGONNs, Molecular Autoencoders, MIX+GANs, continuous space A3C, MCTS for RL, Mol2Vec and more. We've also continued improving our core graph convolutional implementations.

We've also made a variety of documentation, build, and website improvements and fixes.

Our thanks to our contributors for all the hard work!

TensorGraph Conversion and Upgrades
- #925 Sequential API for Model Construction
- #949 Cleanup of Examples plus bugfixes
- #952 Using Queues for prediction
- #954 GraphConvTensorGraph Classification with Multiple Tasks
- #965 Can restore from any checkpoint
- #966 Simplified names of TensorGraph graph conv models
- #970 Added TensorGraph LSTM Layer
- #972 Add Model Configuration params to GraphConvTensorGraph
- #975 Swap examples to use new TensorGraph models
- #976 Remove deprecated TensorFlow classes
- #989 Remove tf_new_models old submodule
- #992 Remove the deprecated old fully connected models
- #1007 Add ability to change loss functions after reload
- #1023 Add TensorGraph Cast layer
- #1024 Can move saved TensorGraph models on disk
- #1054 Implement IRV TensorGraph Model
- #1082 Move tensorflow_models and autoencoder_models into contrib
- #1083 Add one-shot code back into contrib
- #1085 Saving and loading Weave models
- #1086 Implementation of robust models in TensorGraph
- #1090 Move dc.nn to contrib
Reinforcement Learning Upgrades
- #931 Monte Carlo Tree Search for RL
- #1022 A3C supporting continuous action spaces.
Graph Convolution Improvements:
- #1033 Adding master atoms to graph convolutions
- #1080 Adding chirality to Atom and Bond features
- #1081 Pinning Graph Gather to CPU for TF Bug
- #1105 Graph Normalization
MoleculeNet Improvements
- #933 Run MoleculeNet on Jenkins
- #958 Building multi-assay datasets from PubChem based on genes
- #996 PCBA dataset generation based on a single gene
- #1032 Simplify Tox21 loading
- #1042 Update MoleculeNet to latest models
- #1049 Fixes for MoleculeNet update
New models added to DeepChem
- #939 Mol2Vec implementation added to contrib
- Add DRAGONN models
- #979 Adding DRAGONN example to contrib
- #1003 Removing some commented out DRAGONN code
- #1008 Adding DNA Simulation code
- #1020 Implementing FASTALoader
- #981 MIX+GAN implemented
- #1026 Molecular Autoencoder Implementation in TensorGraph
dc.data improvements
- #930 Complete Shuffle Disk Dataset
- #1031 Bugfix for merging DiskDatasets
- #1034 Enabling merging of NumpyDataset
- #1091 Adding dataset.make_iterator to create tf.data.Iterator instances from Dataset objects
Improvements to featurization and data splits
- #1005 Enable choice of featurizer to be searched as a hyperparameter
- #1009 Add Maxmin splitter
DeepChem tutorial additions and improvements
- #940 Update datasets for protein-ligand complex tutorial
- #961 Fix BACE tutorial
- #998 Fix GraphConv tutorial
- #1051 New TensorBoard usage tutorial
- #1104 New splitter tutorial
#1072 DeepChem Organizational Structure and Governance
Documentation improvements
- #957 Bump to 1.3.1
- #997 Docstring for dc.utils.load_from_disk
- #1018 Add README link
- #1050 Improve README
- #1053 README fixes
- #1067 Docs fix to keep numpy docstrings rendering
- #1068 Update SAMPL example docstrings to read correctly
- #1077 Fix README links
- #1107 Better installation from source examples
- #1117 Fixes to prevent test modules from being generated in docs
- #1123 Convert some leftover GPL license tags to MIT
- #1124 Version bump for 2.0.0
Build Improvements
- #928 Bump conda, docker to 1.3.1 version
- #1013 Add manifest to include data files
- #1028 Install simdna from conda-forge
- #1056 Turn off PyPi uploading to deal with bugs
- #1059 TensorFlow 1.5 Upgrade
Website improvements
- #932 Bump Website version
- #1057 Number of website fixes
Bugfixes, Tests, and Miscellaneous Improvements
- #934 Upgrade yapf version to 0.19
- #945 Fix import bug
- #948 Write values not tensors to TensorBoard
- #964 Fix infinite loop caused by shards of size 0
- #973 Fix featurizer name error
- #982 Fix import errors from ICU package
- #987 Speed up tests
- #1001 Upgrade yapf version to 0.20
- #1061 Fix gaussian process optimization bug
- #1063 Install pbr package properly
- #1088 Fix import bugs
- #1113 Using logger instead of print

- Python
Published by rbharath almost 8 years ago

deepchem - HD5 Backend for DiskDataset Metadata

This minor release swaps the backend metadata storage for DiskDataset to hd5 from pickle files. This change was necessary since pickle is a brittle file format. (A recurring issue was that py2 pickles and py3 pickles were not compatible). This minor release introduces a transition implementation: loading any DiskDataset on disk with the dc.data.DiskDataset implementation in this release will automatically swap from pickle to hd5 format on disk with no extra input needed from users.

The next DeepChem release is going to be a 2.0 release which will consolidate on the hd5 format, so we encourage users to upgrade to 1.3.1 and transition any data stored on disk in preparation.

Thanks as always to our core developers and special thanks to our first-time contributors!

Detailed Changes: - Pickle to hd5 transition for DiskDataset (#899) - TensorGraph Improvements (#895, #901, #917) - Dataset fixes (#914, #916) - MoleculeNet Jenkins build (#910) - Major refactoring/improvements to RDKIT grid featurizer (#879) - Installation/Testing/Docs improvements (#892, #904, #907, #909, #920, #923)

- Python
Published by rbharath over 8 years ago

deepchem - TensorGraph Consolidation

This major version release consolidates around TensorGraph as DeepChem's high-level deep learning API of choice. Lots of improvements and bugfixes have been made to the core TensorGraph library, and many new layers and models have been added. In particular, DeepChem now features GANs, Seq2Seq models, Model Agnostic Meta Learning and more! Many improvements to tutorials, examples, website, and installation have been added as well.

Our thanks to all the developers who contributed to this release, with a particular shout-out to those who made their first PRs to DeepChem!

Detailed Changes: - TensorGraph Improvements (#693, #705, #723, #730, #731, #746, #751, #753, #758, #760, #763, #766, #774, #778, #782, #783, #788, #791, #794, #799, #811, #817, #822, #824, #826, #833, #847, #850, #853, #854, #860, #871) - RL Improvements: Hindsight Experience Replay, Proximal Policy Optimization, API cleanup (#686, #688, #697, #713, #719, #729, #740) - IPython Notebook Improvements (#703, #706, #709, #711, #717, #721, #727, #745, #750, #829) - Cleaning up examples (#755, #816, #819, #830, #840) - MoleculeNet Improvements (#696, #718, #772, #854, #880, #738) - Rehaul Website (#800, #801, #806, #807) - Improvements and extensions to dc.splits (#690, #765, #784) - Improvements to rdkit-grid-featurizer (#868, #873, #883) - Miscellaneous cleanups/fixes (#701, #712, #724, #732, #735, #739, #796, #848, #885, - DeepChem installation/import improvements (#737, #793, #802, #803, #804, #813, #814, #815, #852, #857, #859, #885, #888)

Detailed listing of new models added:

GANs (#855, #866)
Model Agnostic Meta Learning (#759)
Seq2seq models (#828)
ANI-1 Models (#823, #839)
Spatial Filtering Graph Convs (#851)
Message Passing Neural Networks (#710)
TextCNNs (#874)
Sluice Networks (#805)

- Python
Published by rbharath over 8 years ago

deepchem - Reinforcement Learning

The major new change in this release is a new reinforcement learning framework. There have also been many upgrades and bugfixes to TensorGraph, large upgrades to MoleculeNet, and significant effort spent cleaning up and solidifying our test suite, documentation, and community standards.

Detailed Changes: - MoleculeNet Upgrades (#556, #578, #589, #592, #594, #606, #628, #629, #633, #661, #665, #667 ) - Reinforcement Learning Support (#557, #618, #640, #652, #656) - Cleaning up tests and making robust (#560, #561, #563, #566, #582, #584, #595, #611, #662) - GPU Docker support (#574) - Documentation Improvements (#575, #597, #609, #615, #641, #670, #674) - TensorGraph Refinements and Debugging (#552, #567, #569, #577, #603, #608, #636, #637, #638, #642, #655, #666) - Added code of conduct (#580) - PyTorch Model Upgrades (#646, #652)

- Python
Published by rbharath over 8 years ago

deepchem - TensorGraph Implementation

This minor release version adds TensorGraph, a new backend for DeepChem models inspired by Keras's functional API. TensorGraph should now be ready for early users to start experimenting with. Over the next few releases, we will deprecate non-TensorGraph models in favor of the newer implementations. This release also contains a number of major improvements to MoleculeNet, with new models, datasets, and metrics.

Detailed Changes:

Added a contrib/ folder to allow users to contribute models/code more easily.
PyTorch multitask models merged into contrib/ (#481)
XGBoost models added (#483)
A number of new datasets integrated with dc.molnet (#484)
Basic queue support added . Allows for higher GPU utilization to be achieved (#488)
Introduction of TensorGraph, a new backend for DeepChem inspired by Keras's function API (#493, #505, #517, #520, #523, #544, #546 )
Adding support for weight-sharing between layers in TensorGraph (#521)
Porting of multitask classifiers/regressors into TensorGraph and adding Dropout support (#522)
Implementation of molecular DAG models (#495)
Implementation of weave convolutions (#496)
Adding atomic convolutions (#509, #537 )
MPNNs added to contrib/ (#512)
Made dc.splits work with NumpyDataset (#513)
Adding auPRC metric (#531)

- Python
Published by rbharath almost 9 years ago

Recent Releases of deepchem

deepchem - 2.8.0 Initial Release

What's Changed

New Contributors

deepchem - 2.8.0.pre

deepchem - 2.7.1

deepchem - DeepChem 2.7.0

Highlights

Porting Models to PyTorch

New Features

Featurizers

New Layers

Deprecations

Examples and Tutorials

Documentation

Improvements

Refactors

Bug Fixes

Maintenance

What's Changed

New Contributors

deepchem - Minor version bump for numpy

What's Changed

New Contributors

deepchem - DeepChem 2.6.0

What's Changed

New Contributors

deepchem - DeepChem 2.5.0

deepchem - DeepChem 2.4.0

deepchem - Keras Models as Default

deepchem - Improved Protein Structure, Microscopy, Interpretation Support

PDBBind and Protein Structure Improvements

1366, #1383, #1411, #1413, #1476 Atomic Convolution Improvements

1503, #1430, #1432 PDBBind bugfixes

1497 Using binding pockets to load PDBBind

1498 DeepMHC for protein peptide binding

1369, #1360, #1372, #1397 Featurziation Improvements

1498 DeepMHC for protein peptide binding

Image Handling Improvements

1516 Image Transformation improvements

1324 Cell counting dataset added. ImageLoader added

1414 Diabetic Retinopathy example model

1439 ImageDataset class

Dataset and Splitter Additions, Improvements and fixes

1507, #1540, #1406 Bugfixes

1514 Handling verbose=False when transforming data

1499 Butina splitter improvement

1347 Adds USPTO dataset.

1348 BBBC002 dataset addition

1339 Split datasets on ID

1416 Molnet loaders for UV/Kinase/Factors datasets

1327 BBBC001 dataset addition

1447 SDFLoader improvements

1425 Binary classification metric improvements

Model and Layer Additions and Improvemetns

1500 Seq2seq model improvements

1513 Clean up symmetry functions

1488 New graph convolution

1365 Average pooling for conv-nets

1370 ResNet50 improvements

1450 Layer output shapes

1452 Pad batch improvements

1453 Example distributed multitask classifier

1335 GraphConv improvements

1343 Making it easy to pull out neural fingerprints

1433 TensorGraph get layer weights

1325 UNet model changes

1334 First Resnet50 build

1473, #1142 TextCNN make_estimator support

1475 DTNN make_estimator support

1495 ANIRegression, BPSymmetryFunction make_estimator

Better Interpretability

1393 Saliency Mapping

1445 Saliency maps for diabetic retinopathy

Tests, Docs, Housekeeping

1527, #1457 Readme cleanup

1548 Version bump

1515 Upgrade to TF 1.12

1462 Typo fix predict_proba

1385, #1418 Build Fixes

1324 Cell counting dataset added. `ImageLoader` added

1439 `ImageDataset` class