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Merge updates in main into release #115

Merged
merged 57 commits into from
Oct 23, 2024
Merged

Merge updates in main into release #115

merged 57 commits into from
Oct 23, 2024

Commits on Sep 26, 2024

  1. Add regression head

    @mattwoodx
    mattwoodx committed Sep 26, 2024
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  2. Add fine-tuning functionality to HyenaDNA

    @mattwoodx
    mattwoodx committed Sep 26, 2024
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  3. Add dataset for HyenaDNA for batching

    @mattwoodx
    mattwoodx committed Sep 26, 2024
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  4. Add batch processing for HyenaDNA get_embeddings

    @mattwoodx
    mattwoodx committed Sep 26, 2024
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  5. Update docstrings

    @mattwoodx
    mattwoodx committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. Update tests for Hyena-DNA

    @mattwoodx
    mattwoodx committed Sep 27, 2024
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Commits on Sep 30, 2024

  1. Add notebook for DNA fine-tuning

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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  2. Add detailed notebook and update inference notebook for HyenaDNA

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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  3. Add testing for fine-tuning HyenaDNA

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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  4. Remove softmax

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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  5. Remove softmax from forward

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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  6. More detailed testing for fine-tuning HyenaDNA

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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  7. Add subset percentages for notebook testing to avoid timing out

    @mattwoodx
    mattwoodx committed Sep 30, 2024
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Commits on Oct 1, 2024

  1. Remove identical head

    @mattwoodx
    mattwoodx committed Oct 1, 2024
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  2. Merge branch 'main' into feature/dna-fine-tune

    @mattwoodx
    mattwoodx committed Oct 1, 2024
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  3. Remove unused imports

    @mattwoodx
    mattwoodx committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Add regression head back

    @mattwoodx
    mattwoodx committed Oct 2, 2024
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  2. Add option for regression head in base

    @mattwoodx
    mattwoodx committed Oct 2, 2024
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  3. Replace accuracy with validation loss

    @mattwoodx
    mattwoodx committed Oct 2, 2024
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  4. Update docstrings

    @mattwoodx
    mattwoodx committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Update docstrings

    @mattwoodx
    mattwoodx committed Oct 3, 2024
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  2. downloading files again for UCE , for the Geneformer all the files ar… 

    …e now loaded in the init function.
    maxiallard committed Oct 3, 2024
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  3. n_proc to 1

    maxiallard committed Oct 3, 2024
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  4. fixed UCE download

    maxiallard committed Oct 3, 2024
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  5. removed nproc from notebook

    maxiallard committed Oct 3, 2024
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  6. Merge pull request #110 from helicalAI/init_load_files 

    Adding downloads where initial files might not be available anymore.
    @maxiallard
    maxiallard authored Oct 3, 2024
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  7. Change dependency strictness

    mattwoodx committed Oct 3, 2024
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  8. Merge pull request #111 from helicalAI/dependency-change 

    Change dependency strictness
    @maxiallard
    maxiallard authored Oct 3, 2024
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Commits on Oct 4, 2024

  1. Merge branch 'main' into feature/dna-fine-tune

    mattwoodx committed Oct 4, 2024
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  2. Remove duplicate merge code

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  3. Update parameter types and docstrings

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  4. Update import

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  5. Update testing

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  6. Change default batch size

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  7. Remove dict from geneformer process data in notebook

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  8. Custom attr dict no longer in process data

    @mattwoodx
    mattwoodx committed Oct 4, 2024
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  9. Merge pull request #101 from helicalAI/feature/dna-fine-tune 

    HyenaDNA Fine-Tuning Capabilities and Regression Head
    @mattwoodx
    mattwoodx authored Oct 4, 2024
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Commits on Oct 7, 2024

  1. Refactor Geneformer fine-tuning to instatiate the a standalone model … 

    …with configs
    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  2. Refactor Geneformer fine-tuning to instatiate the a standalone model … 

    …with configs
    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  3. Refactor HyenaDNA fine-tuning to be standalone

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  4. Update docs

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  5. Refactor scGPT fine-tuning to be standalone

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  6. Refactor UCE fine-tuning to be standalone

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  7. Update examples for UCE

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  8. Update Notebook

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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  9. Update workflow

    @mattwoodx
    mattwoodx committed Oct 7, 2024
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Commits on Oct 8, 2024

  1. Remove unused import

    @bputzeys
    bputzeys committed Oct 8, 2024
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  2. Raise error if download fails and include log message

    @bputzeys
    bputzeys committed Oct 8, 2024
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  3. Merge pull request #112 from helicalAI/refactor-fine-tuning 

    Refactor fine-tuning
    @bputzeys
    bputzeys authored Oct 8, 2024
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Commits on Oct 9, 2024

  1. Merge pull request #113 from helicalAI/raise-error-if-download-fails 

    Raise error if download fails and include log message
    @maxiallard
    maxiallard authored Oct 9, 2024
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Commits on Oct 14, 2024

  1. Open the file only after a successful response has been received. Oth… 

    …erwise file will be opened even if the request fails, resulting in an empty file.
    @bputzeys
    bputzeys committed Oct 14, 2024
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  2. Merge pull request #114 from helicalAI/raise-error-if-download-fails 

    Raise error if download fails
    @bputzeys
    bputzeys authored Oct 14, 2024
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Commits on Oct 18, 2024

  1. Update README.md

    @maxiallard
    maxiallard authored Oct 18, 2024
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  2. Update intro.md

    @maxiallard
    maxiallard authored Oct 18, 2024
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  3. Update intro.md

    @maxiallard
    maxiallard authored Oct 18, 2024
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  4. Update README.md

    @maxiallard
    maxiallard authored Oct 18, 2024
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Commits on Oct 21, 2024

  1. Merge pull request #116 from helicalAI/maxiallard-patch-1 

    Maxiallard patch 1
    @maxiallard
    maxiallard authored Oct 21, 2024
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