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GNNModular #3339

Merged
merged 26 commits into from
Apr 10, 2023
Merged

GNNModular #3339

merged 26 commits into from
Apr 10, 2023

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tonydavis629
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This PR adds GNNModular to torch_models. GNNModular allows users to define graph convolutional encoders, prediction heads, and specific tasks such as node prediction, edge prediction, regression, classification, etc. This PR implements edge prediction only, using the GINEConv layer from torch geometric. as the GCN

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  • My code follows the style guidelines of this project
    • Run yapf -i <modified file> and check no errors (yapf version must be 0.32.0)
    • Run mypy -p deepchem and check no errors
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  • I have performed a self-review of my own code
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rbharath
rbharath reviewed Apr 4, 2023
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Good start! Mostly requests for more documentation below

deepchem/models/torch_models/gnn.py Show resolved Hide resolved
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deepchem/models/torch_models/gnn.py Outdated
The number of negative edges added is equal to half the number of edges in the original graph. This is useful for tasks like edge prediction, where the model needs to learn to differentiate between existing and non-existing edges.
"""

def __call__(self, data):
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Can you add a docstring?

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done

deepchem/models/torch_models/gnn.py Show resolved Hide resolved
deepchem/models/torch_models/modular.py Outdated
@@ -84,7 +84,7 @@ def __init__(self, model: nn.Module, components: dict, **kwargs):
super().__init__(self.model, self.loss_func, **kwargs)
self.model.to(self.device)
self.components = {
k: v.to(self.device) for k, v in self.components.items()
k: v.to(self.device) for k, v in self.components.items() if isinstance(v, nn.Module)
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When would we expect to have a non nn.module in self.components?

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In this GNNModular class. The pooling components can be either a function or parameterized nn.module.

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rbharath
rbharath reviewed Apr 5, 2023
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One minor refactoring request below (self.JK -> self.jump_knowledge). Once that's done and a requested comment below is added this should be ready to merge in

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rbharath
rbharath approved these changes Apr 6, 2023
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LGTM, feel free to merge once CI is clear

@tonydavis629 tonydavis629 merged commit 6ab6bf5 into deepchem:master Apr 10, 2023
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@rbharath rbharath rbharath approved these changes

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