Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
This is the release note of v0.7.1.
The paper, “Weisfeiler-Lehman Embedding for Molecular Graph Neural Networks” official implementation (#422, thanks @k-ishiguro !)
This is the release note of v0.7.0. See here for the complete list of solved issues and merged PRs.
Note that this is planned to be the final major release. As announced in chainer blog, further development will be limited to only serious bug-fixes and maintenance.
See table below for usage
Chemical | Network | |
---|---|---|
adjacency matrix | NumpyTupleDataset |
PaddingGraphDataset |
scatter operation | SparseGraphDataset |
SparseGraphDataset |
sparse matmul | not supported | PaddingGraphDataset (use_coo=True) |
network_graph
example is added for cora, citeseer, reddit
dataset training (#398, thanks @knshnb!)This is the release note of v0.6.0. See here for the complete list of solved issues and merged PRs.
[Big Change] Unify arguments in model, update and readout (#368)
return svg text instead of ipython SVG object in MolVisualizer
and SmilesVisualizer
(#388)
Support ChainerX (#376)
fix typo (#358, Thank you @shllln)
This is the release note of v0.5.0. See here for the complete list of solved issues and merged PRs.
Add RelGCN (#269, #316)
Add RelGAT (#217, #299, #302, #315)
GGNN: support num_edge_type as argument (#294)
Add StandardScaler link (#309)
Add GraphMLP (#295)
GGNN input size invariant support (#297)
NFP input size invariant support (#296)
kekulize
option in preprocessor (#262)construct_discrete_edge_matrix
to common
(#260)permute_adj
(#277)device_id
inside BaseForwardModel
for chainer v6 (#280)This is the release note of v0.4.0. See here for the complete list of solved issues and merged PRs.
RandomSplitter
(#196)StratifiedSplitter
(#201)ScaffoldSplitter
(#202)mean_squared_error
(#190)mean_absolute_error
(#193)BatchEvaluator
(#210)PRCAUCEvaluator
(#210)DataFrameParser
(#203, #207)SMILESParser
(#204)return_is_successful
option to parsers (#219 #220)extract_total_num
(#221)raise_value_error
to ROCAUCEvaluator
(#157)examples/own_dataset/train.py
(#171)NumpyTupleDataset
when data_index
is a list of length 1 (#200)SDFFileParser
, which only affects to logging output (#220)out_size
is larger than the number of atoms (#169, Thank you @mihainorariu)InferenceLoop
from the Tox21 example (#184, #222)Classifier
from the Tox21 and QM9 examples (#185)datasets/qm9.py
(#176, Thank you @natsukium)predict
, predict_proba
methodspredict
methodsave_pickle
and load_pickle
to it (#139)target_index
to parse
method of CSVFileParser
and SDFFileParser
(#131)extract_total_num
to CSVFileParser
and SDFFileParser
(#131)target_index
option to get_qm9
(#131)train_target_index
, val_target_index
, and test_target_index
to get_tox21
(#131)dropout_ratio
to RSGCN.__init__
(#146).chainer_chemistry.dataset.preprocessors.weavenet_preprocessor.DEFAULT_NUM_MAX_ATOMS
has been removed. Use chainer_chemistry.WEAVE_DEFAULT_NUM_MAX_ATOMS
instead (#127).concat hidden
argument of GGNN (#117, #118)RSGCN
(#146)Also thank you @mihaimorariu (#144) and @ir5 for the implementation, documentation, bug report and example improvements!
This is the release of v0.2.0.
RSGCN
(Renormalized Sepectral Graph Convolutional Network) (#89 thank you @anaruse!)BalancedSerialIterator
for imbalanced data training (#59)ROCAUCEvaluator
for binary classification task evaluation (#62)self_connection
option in construct_adj_array
(#100)return_smiles
return numpy.ndarray
, instead of list
(#79)csv_file_parser.parse
and sdf_file_parser.parse
methods return dict
that contains dataset and smiles, instead variable length tuple
(#94)SchNet
inference example in tox21 example (#103)RSGCN
example in QM9, tox21 example (#89, #104)BalancedSerialIterator
, ROCAUCEvaluator
sample usage in tox21 example (#60, #62)Also thank you @amaotone (#50), @kazuyaujihara (#85), @msakai (#88) and @anaruse (#89) for the implementation, documentation and example improvements!
This is the first release of Chainer Chemistry.
We will follow Semantic Versioning 2.0.0, which means any API can change at anytime until Version 1.