Code

Geneformer server#326

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amva13 merged 27 commits intomainmims-harvard/TDC:mainfrom geneformer_servermims-harvard/TDC:geneformer_serverCopy head branch name to clipboardOct 27, 2024

+91-33

Commits

Commits on Oct 22, 2024

• geneformer tokenizer fails on scperturb

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• check if test runs on azure ok... see failure log

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Commits on Oct 23, 2024

• does this work

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• mend

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• fix tests to check list of cells and not individual cell embeddings since some are expected to be empty.

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• mend

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• mend

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• mend

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• mend

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• reshape fix

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• debug reshape

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Commits on Oct 24, 2024

• use tokenizer dataset function

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Commits on Oct 25, 2024

• debug -- use tokenizer dataset function

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• mend

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Commits on Oct 26, 2024

• huggingface geneformer

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• remove create .dataset after geneformer hugingface replacement

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• remove geneformer package dependency

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• squeeze last dim in test

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• mend

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• make all tokenized cells be the confirmed pkl values

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• add padding to the geneformer test case

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• mend

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• process per batch model(batch)

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Commits on Oct 27, 2024

• add attention mask

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• bad tests

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• yapf and cleanup

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