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ncfrey
approved these changes
Jul 9, 2025
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| Handles variable-length tensors that can't be stacked by default collation. | ||
| """ | ||
| inputs = [] |
Contributor
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how about
inputs, targets = zip(*batch)
inputs = list(inputs)
targets = list(targets)
| PEERTask.PDBBIND, | ||
| } | ||
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| # Define high memory-intensive tasks that need batch_size=1 |
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special handling = small batch size?
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Author
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Yeah, I'll clarify
| with torch.no_grad(): | ||
| for batch in dataloader: | ||
| x, y = batch | ||
| def _get_standard_embeddings( |
Contributor
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this module is getting pretty big - maybe some of these convenience functions can be factored out into a _peer_utils.py
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Author
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Good idea, just simplified things quite a bit
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Description
Fixing four PEER tasks: fold, subcellular localization, proteinnet & secodary structure & updating base linear probe callback accordingly. All changes are backwards compatible
Update: omitting ProteinNET as a default task because of the O(N^2) memory for residue-residue level contact map prediction. Will update in a separate MR with outer-product mean on lower-rank tensors
Type of Change
Testing
Checklist