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Fix novel on cells without counts in the hvg peaks - #76

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rcannood merged 3 commits into
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fix/novel_empty_cells
Sep 29, 2026
Merged

rcannood merged 3 commits into
mainfrom
fix/novel_empty_cells

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In run_2026-09-28 novel_predict failed on the multiome swap datasets with a missing tensor.pt. On bmmc_multiome/swap, 3092 cells have no counts in the 1000 hvg peaks the LSI uses, so the TF-IDF divided by zero and the LSI was NaN for those cells. The validation RMSE was then never better than the initial 100000, so train_and_valid() never saved a model, while novel_train itself still exited 0.

Describe your changes

  • novel: treat an empty row as having a row sum of 1 in the TF-IDF, and a zero standard deviation as 1 when scaling the LSI.

On the de.NBI copy of bmmc_multiome/swap, the LSI goes from 791552 NaN values to none.

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

@rcannood
rcannood merged commit 214364f into main Sep 29, 2026
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@rcannood
rcannood deleted the fix/novel_empty_cells branch September 29, 2026 18:43
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