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Linting and updates #53
Commits on Sep 1, 2023
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Arian Jamasb committed
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Commits on Sep 17, 2023
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Merge remote-tracking branch 'origin' into ipmp
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Commits on Sep 22, 2023
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Merge remote-tracking branch 'origin' into ipmp
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Commits on Oct 23, 2023
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add support for loading hparam override
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add optional hparam override to finetune run config
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set in memory=True as default for cath and fold classification datasets
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fix scenario where only seq_pos_enc is a node feature
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refactor logging to use a single logging call
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add pre-trained inverse folding config
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add find graph encoder hparams
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add baseline inverse folding config
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Add cpu index url for torch for CI
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Commits on Oct 26, 2023
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rollback to max python 3.10 due to lack of torchdrug support
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bump graphein to 1.7.4 for PyG 2.4+ support (and backwards compatibility
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add list to track processed files in case of overwrite
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update graphein version to 1.7.5+ and add captum dependency
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Commits on Oct 28, 2023
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add some more docstrings, clean up
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Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i…
…nto ipmp
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ignore igfold dataset in overwrite test
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add IGFold prediction datasets
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Commits on Nov 7, 2023
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fix binary graph classification config
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Commits on Nov 12, 2023
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add full model config for finetuning
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Commits on Nov 16, 2023
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speed up positional encoding computation
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add num_classes to GO datasets
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add multilabel classification task configs
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refactor f1_max for multilabel classif.
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add auprc to classification metrics, linting
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set in_memory=True as default for GO datasets
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add missing mace ca_angles hparams
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Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i…
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Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i…
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add ppi prediction task updates
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mask additional attributes in PPI site prediction
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Merge branch 'ipmp' of https://www.github.com/a-r-j/ProteinWorkshop i…
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Commits on Nov 30, 2023
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standardise default features for train and finetune configs #61
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Commits on Dec 26, 2023
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refactor to new recommended jaxtyping/beartype syntax
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typechecker refactor for dataset base
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remove merge artifact from poetry.lock
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fix broken poetry.lock and update jaxtyping dependency
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fix broken poetry.lock and update jaxtyping dependency
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fix pyg wheel link for torch > 2.1.0
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set dummy labels on example_batch
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Update install instructions to PyTorch 2.1.2+, and sync docs with REA…
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fix malformed HTML in quickstart components
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