Quick Start

Tensor-based Graphs

Graphs

Graphs are the fundamental data structure used in TorchDrug. They can be viewed as a generalization of graph processing libraries (e.g., NetworkX) in a tensor framework, while enjoy the GPU acceleration and auto differentiation.

import torchdrug as td
from torchdrug import data

edge_list = [[0, 1], [1, 2], [2, 3], [3, 4], [4, 5], [5, 0]]
graph = data.Graph(edge_list, num_node=6)
graph.visualize()
_images/graph1.png

Molecules

A specfic instance of graphs in drug discovery is a molecule, which may have additional chemical constraints and features. For example, we can construct a molecule from SMILES string. SMILES is a language that describes complex molecule structures using a linear string.

mol = data.Molecule.from_smiles("C1=CC=CC=C1")
mol.visualize()
print(mol.node_feature.shape)
print(mol.edge_feature.shape)
_images/benzene1.png
torch.Size([6, 69])
torch.Size([12, 19])

Graph Operations

A group of arbitrary graphs can also be processed as a batch to maximize the utilization of hardware. They can also be transferred between CPUs and GPUs using cpu() and cuda() methods.

smiles_list = ["CCSCCSP(=S)(OC)OC", "CCOC(=O)N",
               "N(Nc1ccccc1)c2ccccc2", "NC(=O)c1cccnc1"]
mols = data.PackedMolecule.from_smiles(smiles_list)
mols.visualize()
mols = mols.cuda()
print(mols)
_images/mol_batch.png
PackedMolecule(batch_size=4, num_nodes=[12, 6, 14, 9], num_edges=[22, 10, 30, 18],
               device='cuda:0')

Just like original PyTorch tensors, graphs support a wide range of indexing operations. Typical usages include applying node masking, edge masking or graph masking. The following example shows how to select edges that contain at least one carbon. For more graph operations, please see the notes.

node_in, node_out, bond_type = mols.edge_list.t()
edge_mask = (mols.atom_type[node_in] == td.CARBON) | \
            (mols.atom_type[node_out] == td.CARBON)
mols = mols.edge_mask(edge_mask)
mols.visualize()
_images/mol_edge_mask.png

A Molecule Classifier

Now we demonstrate how to use TorchDrug to create a molecule classifier. Specifically, TorchDrug provides us with a large collection of popular datasets and models for drug discovery and graph representation learning. These help us avoid writing and debugging boilerplate code.

For this tutorial, we use the ClinTox dataset. This dataset requires to predict whether a molecule is toxic in clinical trials, and whether it is approved by FDA.

_images/clintox_by_category.png

Load and Prepare Dataset Splits

First of all, we load the dataset with TorchDrug. TorchDrug will automatically download the dataset into the path you specify.

We then split the dataset into train, validation and test, with a ratio of 8:1:1.

import torch
from torchdrug import datasets

dataset = datasets.ClinTox("~/molecule-datasets/")
lengths = [int(0.8 * len(dataset)), int(0.1 * len(dataset))]
lengths += [len(dataset) - sum(lengths)]
train_set, valid_set, test_set = torch.utils.data.random_split(dataset, lengths)

Define a Graph Neural Network for Classification

We define a graph neural network to encode the molecule graphs. Specifically, we use the a Graph Isomorphism Network (GIN) with 4 hidden layers.

from torchdrug import core, models, tasks

model = models.GIN(input_dim=dataset.node_feature_dim,
                   hidden_dims=[256, 256, 256, 256],
                   short_cut=True, batch_norm=True, concat_hidden=True)

Note the model is simply a neural network without any training target. To adapt it for classification, we wrap it with a property prediction module. We define the classification task by the binary cross entropy (BCE) criterion.

task = tasks.PropertyPrediction(model, task=dataset.tasks,
                                criterion="bce", metric=("auprc", "auroc"))

Train the Model

We create an optimizer for the parameters in the task, and combine everything into core.Engine. The engine provides convenient routines for training and test.

optimizer = torch.optim.Adam(task.parameters(), lr=1e-3)
solver = core.Engine(task, train_set, valid_set, test_set, optimizer,
                     batch_size=1024)
solver.train(num_epoch=100)

If we have any GPU, we can specify it in the engine to accelerate training.

solver = core.Engine(task, train_set, valid_set, test_set, optimizer,
                     batch_size=1024, gpus=[0])

More acceleration can be achieved by multiple GPUs. In this case, we need to launch the script using python -m torch.distributed.launch --nproc_per_node=4.

solver = core.Engine(task, train_set, valid_set, test_set, optimizer,
                     batch_size=256, gpus=[0, 1, 2, 3])

Test the Model

To test the model on validation set, it only takes one line.

solver.evaluate("valid")

Alternatively, we can make prediction on arbitrary input batches. The following code shows the prediction for the first 8 samples in the validation set.

batch = data.graph_collate(valid_set[:8])
pred = task.predict(batch)

Save and Load

Let’s save our trained model. We dump our model into two parts, where clintox_gin.json contains the hyperparameters, and clintox_gin.pth contains the trained weights.

import json

with open("clintox_gin.json", "w") as fout:
    json.dump(solver.config_dict(), fout)
solver.save("clintox_gin.pth")

To load a pretrained model, we don’t bother to define the model again. Use core.Configurable.load_config_dict and TorchDrug will automatically parse the model from the hyperparameters.

with open("clintox_gin.json", "r") as fin:
    solver = core.Configurable.load_config_dict(json.load(fin))
solver.load("clintox_gin.pth")