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Geneformer server #326

Merged
merged 27 commits into from
Oct 27, 2024
Merged

Geneformer server #326

merged 27 commits into from
Oct 27, 2024

Commits on Oct 22, 2024

  1. geneformer tokenizer fails on scperturb

    @amva13
    amva13 committed Oct 22, 2024
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  2. check if test runs on azure ok... see failure log

    @amva13
    amva13 committed Oct 22, 2024
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Commits on Oct 23, 2024

  1. does this work

    @amva13
    amva13 committed Oct 23, 2024
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  2. mend

    @amva13
    amva13 committed Oct 23, 2024
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  3. fix tests to check list of cells and not individual cell embeddings s… 

    …ince some are expected to be empty.
    @amva13
    amva13 committed Oct 23, 2024
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  4. mend

    @amva13
    amva13 committed Oct 23, 2024
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  5. mend

    @amva13
    amva13 committed Oct 23, 2024
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  6. mend

    @amva13
    amva13 committed Oct 23, 2024
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  7. mend

    @amva13
    amva13 committed Oct 23, 2024
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  8. mend

    @amva13
    amva13 committed Oct 23, 2024
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  9. reshape fix

    @amva13
    amva13 committed Oct 23, 2024
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  10. debug reshape

    @amva13
    amva13 committed Oct 23, 2024
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Commits on Oct 24, 2024

  1. use tokenizer dataset function

    @amva13
    amva13 committed Oct 24, 2024
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Commits on Oct 25, 2024

  1. debug -- use tokenizer dataset function

    @amva13
    amva13 committed Oct 25, 2024
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  2. mend

    @amva13
    amva13 committed Oct 25, 2024
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Commits on Oct 26, 2024

  1. huggingface geneformer

    @amva13
    amva13 committed Oct 26, 2024
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  2. remove create .dataset after geneformer hugingface replacement

    @amva13
    amva13 committed Oct 26, 2024
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  3. remove geneformer package dependency

    @amva13
    amva13 committed Oct 26, 2024
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  4. squeeze last dim in test

    @amva13
    amva13 committed Oct 26, 2024
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  5. mend

    @amva13
    amva13 committed Oct 26, 2024
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  6. make all tokenized cells be the confirmed pkl values

    @amva13
    amva13 committed Oct 26, 2024
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  7. add padding to the geneformer test case

    @amva13
    amva13 committed Oct 26, 2024
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  8. mend

    @amva13
    amva13 committed Oct 26, 2024
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  9. process per batch model(batch)

    @amva13
    amva13 committed Oct 26, 2024
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Commits on Oct 27, 2024

  1. add attention mask

    @amva13
    amva13 committed Oct 27, 2024
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  2. bad tests

    @amva13
    amva13 committed Oct 27, 2024
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  3. yapf and cleanup

    @amva13
    amva13 committed Oct 27, 2024
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