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Machine-Learning Neural Spatiotemporal Signal Processing with PyTorch Geometric Temporal by@benitorosenberg

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by Benedek RozemberczkiFebruary 19th, 2021

PyTorch Geometric Temporal is a deep learning library for neural spatiotemporal signal processing. This library is an open-source project. It consists of various dynamic and temporal geometric deep learning, embedding, and Spatiotemporal regression methods from a variety of published research papers.

In addition, it comes with an easy-to-use dataset loader, an iterator for dynamic and temporal graphs, and gpu-support. It also comes with a number of benchmark datasets with temporal and dynamic graphs (you can also create your own datasets).

In the following, we will overview a case study where PyTorch Geometric Temporal can be used to solve a real-world relevant machine learning problem.

We are using the Hungarian Chickenpox Cases dataset in this case study. We will train a regressor to predict the weekly cases reported by the counties using a recurrent graph convolutional network. First, we will load the dataset and create an appropriate spatio-temporal split.

```
from torch_geometric_temporal.data.dataset import ChickenpoxDatasetLoader
from torch_geometric_temporal.data.splitter import discrete_train_test_split
loader = ChickenpoxDatasetLoader()
dataset = loader.get_dataset()
train_dataset, test_dataset = discrete_train_test_split(dataset, train_ratio=0.2)
```

Next, we will define the **recurrent graph neural network **architecture used for solving the supervised task. The constructor defines a DCRNN layer and a feedforward layer. It is important to note that the final

non-linearity is not integrated into the recurrent graph convolutional operation. This design principle is used consistently and it was taken from PyTorch Geometric.

Because of this, we defined a ReLU non-linearity between the recurrent and linear layers manually. The final linear layer is not followed by a non-linearity as we solve a regression problem.

In the next steps, we will define the **recurrent graph neural network** architecture used for solving the supervised task.

```
import torch
import torch.nn.functional as F
from torch_geometric_temporal.nn.recurrent import DCRNN
class RecurrentGCN(torch.nn.Module):
def __init__(self, node_features):
super(RecurrentGCN, self).__init__()
self.recurrent = DCRNN(node_features, 32, 1)
self.linear = torch.nn.Linear(32, 1)
def forward(self, x, edge_index, edge_weight):
h = self.recurrent(x, edge_index, edge_weight)
h = F.relu(h)
h = self.linear(h)
return h
```

Let us define a model (we have 4 node features) and train the model on

the training split (first 20% of the temporal snapshots) for 200 epochs. We backpropagate when the loss from every snapshot is accumulated. We will use the **Adam optimizer** with a learning rate of **0.01**. The *tqdm *function is used for measuring the runtime need for each training epoch.

```
from tqdm import tqdm
model = RecurrentGCN(node_features = 4)
optimizer = torch.optim.Adam(model.parameters(), lr=0.01)
model.train()
for epoch in tqdm(range(200)):
cost = 0
for time, snapshot in enumerate(train_dataset):
y_hat = model(snapshot.x, snapshot.edge_index, snapshot.edge_attr)
cost = cost + torch.mean((y_hat-snapshot.y)**2)
cost = cost / (time+1)
cost.backward()
optimizer.step()
optimizer.zero_grad()
```

Using the holdout we will evaluate the performance of the trained

recurrent graph convolutional network and calculate the mean squared

error across **all of the spatial units and time periods**.

```
model.eval()
cost = 0
for time, snapshot in enumerate(test_dataset):
y_hat = model(snapshot.x, snapshot.edge_index, snapshot.edge_attr)
cost = cost + torch.mean((y_hat-snapshot.y)**2)
cost = cost / (time+1)
cost = cost.item()
print("MSE: {:.4f}".format(cost))
>>> Accuracy: 0.6866
```

*Previously published at **https://pytorch-geometric-temporal.readthedocs.io/en/latest/notes/introduction.html*

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