Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
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
Atomic Convolution Model in Pytorch by @JoseAntonioSiguenza in https://github.com/deepchem/deepchem/pull/3698
pydantic package by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3883
tfp, docker build by @shreyasvinaya in https://github.com/deepchem/deepchem/pull/3896
Full Changelog: https://github.com/deepchem/deepchem/compare/2.7.1...2.8.0
Pre-release for 2.8.0. If tests look stable, will release 2.8.0 shortly
The following models/layers have been ported to pytorch: GRU, InterAtomicL2Distance, WeightedLinearCombo, CombineMeanStd, AtomicConvolution layer, NeighborList, CNN, LSTMStep
math.isclose, np.isclose, np.allclose has been put in place.Full Changelog: https://github.com/deepchem/deepchem/compare/2.6.1...2.7.0
This release is a minor version bump that increases the required version of numpy.
Full Changelog: https://github.com/deepchem/deepchem/compare/2.6.0...2.6.1
DeepChem 2.6.0 adds a range of new features (detailed below) along with significant improvements to the robustness of our testing infrastructure.
Full Changelog: https://github.com/deepchem/deepchem/compare/2.5.0...2.6.0
See full release notes at https://forum.deepchem.io/t/deepchem-2-5-0-release/439
Read the full release notes at https://forum.deepchem.io/t/deepchem-2-4-0-release-notes/340
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
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.
#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
#1516 Image Transformation improvements
#1324 Cell counting dataset added. ImageLoader added
#1414 Diabetic Retinopathy example model
#1439 ImageDataset class
#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
#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
#1393 Saliency Mapping #1445 Saliency maps for diabetic retinopathy
#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