In this tutorial, we predict Highest Occupied Molecular Orbital (HOMO) level of the molecules in QM9 dataset  by Neural Finger Print (NFP) . We concentrate on exaplaining usage of Chainer Chemistry briefly and do not look over the detail of NFP implementation.
- Chainer Chemistry >= 0.0.1 (See Installation)
- Chainer >= 2.0.2
- CUDA == 8.0, CuPy >= 1.0.3 (Required only when using GPU)
- For CUDA 9.0, CuPy >= 2.0.0 is required
- sklearn >= 0.17.1 (Only for preprocessing)
QM9 is a publicly available dataset of small organic molecule structures and their simulated properties for data driven researches of material property prediction and chemical space exploration. It contains 133,885 stable small organic molecules made up of CHONF. The available properties are geometric, energetic, electronic, and thermodynamic ones.
In this tutorial, we predict HOMO level in the properties. Physically, we need quantum chemical calculations to compute HOMO level. From mathematical viewpoint it requires a solution of an internal eigenvalue problem for a Hamiltonian matrix. It is a big challenge to predict HOMO level accurately by a neural network, because the network should approximate both calculating the Hamiltonian matrix and solving the internal eigenvalue problem.
HOMO prediction by NFP¶
At first you should clone the library repository from GitHub.
There is a Python script
examples/qm9/train_qm9.py in the repository.
It executes a whole training procedure, that is, downloads QM9 dataset, preprocess it, define an NFP model and run trainning on them.
Execute the following commands on a machine satisfying the tested environment in environment.
~$ git clone firstname.lastname@example.org:pfnet-research/chainer-chemistry.git ~$ cd chainer-chemistry/examples/qm9/
Hereafter all shell commands should be executed in this directory.
If you are a beginner for Chainer, Chainer handson will greatly help you. Especially the explanation of inclusion relationship of Chainer classes in Sec. 4 in Chap. 2 is helpful when you read the sample script.
Chainer Chemistry accepts the same dataset type with Chainer, such as
In this section we learn how to download QM9 dataset and use it as a Chainer dataset.
The following Python script downloads and saves the dataset in
#!/usr/bin/env python from chainer_chemistry import datasets as D from chainer_chemistry.dataset.preprocessors import preprocess_method_dict from chainer_chemistry.datasets import NumpyTupleDataset preprocessor = preprocess_method_dict['nfp']() dataset = D.get_qm9(preprocessor, labels='homo') cache_dir = 'input/nfp_homo/' os.makedirs(cache_dir) NumpyTupleDataset.save(cache_dir + 'data.npz', dataset)
The last two lines save the dataset to
input/nfp_homo/data.npz and we need not to download the dataset next time.
The following Python script read the dataset from the saved
.npz file and split the data points into training and validation sets.
#!/usr/bin/env python from chainer.datasets import split_dataset_random from chainer_chemistry import datasets as D from chainer_chemistry.dataset.preprocessors import preprocess_method_dict from chainer_chemistry.datasets import NumpyTupleDataset cache_dir = 'input/nfp_homo/' dataset = NumpyTupleDataset.load(cache_dir + 'data.npz') train_data_ratio = 0.7 train_data_size = int(len(dataset) * train_data_ratio) train, val = split_dataset_random(dataset, train_data_size, 777) print('train dataset size:', len(train)) print('validation dataset size:', len(val))
split_dataset_random() returns a tuple of two
chainer.datasets.SubDataset objects (training and validation set).
Now you have prepared training and validation data points and you can construct
chainer.iterator.Iterator objects, needed for updaters in Chainer.
In Chainer, a neural network model is defined as a
Graph convolutional networks such as NFP are generally connection of graph convolution layers and multi perceptron layers.
Therefore it is convenient to define a class which inherits
chainer.Chain and compose two
chainer.Chain objects corresponding to the two kind of layers.
Execute the following Python script and check you can define such a class.
MLP are already defined
#!/usr/bin/env python import chainer from chainer_chemistry.models import MLP, NFP class GraphConvPredictor(chainer.Chain): def __init__(self, graph_conv, mlp): super(GraphConvPredictor, self).__init__() with self.init_scope(): self.graph_conv = graph_conv self.mlp = mlp def __call__(self, atoms, adjs): x = self.graph_conv(atoms, adjs) x = self.mlp(x) return x n_unit = 16 conv_layers = 4 model = GraphConvPredictor(NFP(n_unit, n_unit, conv_layers), MLP(n_unit, 1))
You have defined the dataset and the NFP model on Chainer. There are no other procedures specific to Chainer Chemistry. Hereafter you should just follow the usual procedures in Chainer to execute training.
The sample script
examples/qm9/train_qm9.py contains all the procedures and you can execute training just by invoking the script.
The following command starts training for 20 epochs and reports loss and accuracy during training.
They are reported for each of
main (dataset for training) and
validation (dataset for validation).
--gpu 0 option is to utilize a GPU with device id = 0.
If you do not have a GPU, set
--gpu -1 or just drop
--gpu 0 to use CPU for all the calculation.
In most cases, calculation with GPU is much faster than that only with CPU.
~/chainer-chemistry/examples/qm9$ python train_qm9.py --method nfp --label homo --gpu 0 # If GPU is unavailable, set --gpu -1 Train NFP model... epoch main/loss main/accuracy validation/main/loss validation/main/accuracy elapsed_time 1 0.746135 0.0336724 0.680088 0.0322597 58.4605 2 0.642823 0.0311715 0.622942 0.0307055 113.748 (...) 19 0.540646 0.0277585 0.532406 0.0276445 1052.41 20 0.537062 0.0276631 0.551695 0.0277499 1107.29
After finished, you will find
log file in
In the loss and accuracy report, we are mainly interested in
Although it decreases during training, the
accuracy field is actually mean absolute error.
The unit is Hartree.
Therefore the last line means validation mean absolute error is 0.0277499 Hartree.
scaled_abs_error() function in
train_qm9.py for the detailed definition of mean absolute error.
You can also train other type models like GGNN, SchNet or WeaveNet, and other target values like LUMO, dipole moment and internal energy, just by changing
--label options, respectively.
See output of
python train_qm9.py --help.
Using your own dataset¶
You can use your own dataset in Chainer Chemistry. example/own_dataset shows an example.
 L. Ruddigkeit, R. van Deursen, L. C. Blum, J.-L. Reymond, Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17, J. Chem. Inf. Model. 52, 2864–2875, 2012.
 R. Ramakrishnan, P. O. Dral, M. Rupp, O. A. von Lilienfeld, Quantum chemistry structures and properties of 134 kilo molecules, Scientific Data 1, 140022, 2014.
 Duvenaud, D. K., Maclaurin, D., Iparraguirre, J., Bombarell, R., Hirzel, T., Aspuru-Guzik, A., & Adams, R. P. (2015). Convolutional networks on graphs for learning molecular fingerprints. In Advances in neural information processing systems (pp. 2224-2232).
 Gilmer, J., Schoenholz, S. S., Riley, P. F., Vinyals, O., & Dahl, G. E. (2017). Neural message passing for quantum chemistry. arXiv preprint arXiv:1704.01212.