Make QSAR model with PyG and pytorch2.0 #RDKit #Chemoinfo

Recently, I updated version of pytorch on my env from 1.x to 2.0.

I think it’s worth to update because, original site says….

PYTORCH 2.X: FASTER, MORE PYTHONIC AND AS DYNAMIC AS EVER

Today, we announce torch.compile, a feature that pushes PyTorch performance to new heights and starts the move for parts of PyTorch from C++ back into Python. We believe that this is a substantial new direction for PyTorch – hence we call it 2.0. torch.compile is a fully additive (and optional) feature and hence 2.0 is 100% backward compatible by definition.

Underpinning torch.compile are new technologies – TorchDynamo, AOTAutograd, PrimTorch and TorchInductor.

And also, pytorch_geometric supports pytorch2.0. Previously I worte blog post about building QSAR model with PyG. Old version of PyG didn’t support graph from molecule. So I wrote my own function to do that. But recent version of PyG has the function!

You can check the details on the official documentation.

I have interest the new version of pyg and pytorch. So I rewrote the my code with new packages.

The code is shown below.

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By using compiled model, I got many worning masseges but it worked and got almost same figure to previous post.

This is first trial of using new version of pyg and pytorch for me. I would like to dive more deeply into the packages as soon as possible.

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Published by iwatobipen

I'm medicinal chemist in mid size of pharmaceutical company. I love chemoinfo, cording, organic synthesis, my family.

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