CSCI4949-6969 Assign5

Assign5: Graph Neural Networks

Due Date: Mar 25th, before midnight (EST 11:59:59PM)

In this assignment, you will use two different graph neural networks (GNNs) for graph property prediction: Graph Convolution Network (GCN) and Message Passing Neural Network (MPNN).

You can use the starter code from the graph classification tutorial on the DGL site, but modify it to a regression task.

For training the GNNs, you will use the that contains 130,831 molecules (there are several QM9 datasets, but use the "Edge" one). This dataset has multiple regression targets, but we will predict only the "mu" target values. That is, this is a graph regression problem, where each of the molecules has one mu value, and our goal is to predict that real value.

On the DCS cluster, it will not download the dataset automatically so you should download it from and put it under "./data" directory, and then load the data via data = QM9EdgeDataset(label_keys=['mu'], raw_dir="./data") to extract only the "mu" values as labels.

Each graph has both node features (g.ndata['attr']) and edge features (g.edata['edge_attr']). The GCN model makes use only of the node features, whereas the MPNN uses both node and edge features. The two models will differ in the type of GNN layers they will use. GCN uses the regular dgl.nn.GraphConv layers, whereas MPNN uses the dgllife.model.gnn.mpnn.MPNNGNN layer. However, once the GNN is done, in the forward function of each model, you should do graph node pooling via dgl.readout_nodes to extract the final node features. These should then be fed to a two layer FFN comprised of two linear layers with ReLU and dropout in between. The first FFN linear layer will map the graph feature to a hidden MLP layer, and the second will map the hidden MLP layer to a single neuron output for regression.

To evaluate and compare the two models, namely GCN and MPNN, you should use the nn.L1Loss, which is also called the Mean Absolute Error. You should divide the input graphs into 80% training, 10% validation, and 10% testing, at random. You can use for this.

Use the validation set to select the number of GNN layers, size of the hidden layers, learning rate, which pooling operator to use (max, min, mean, etc.), and so on, for both models. Finally, report the test performance, and compare which model is better. For example, you can use 5-fold cross-validation, or use 5 different splits to evaluate both models and compare which has better average performance.


You will have to install the DGL graph library, and the DGL-LifeSci companion library (for MPNN model). This is straightforward on the Amazon StudioLab machine, but instructions on how to install these on the DCS cluster will be shared on CampusWire.


Submit your jupyter notebook with both models, and the comparison output, via submitty.

You should acknowledge the source of any code you use from the web.