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Record all removed vars in novel_train #33

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Merged
rcannood merged 2 commits into from
Jul 29, 2026
Merged

Record all removed vars in novel_train #33

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record all removed vars in novel_train
rcannood Jul 29, 2026
e7bcb8f
Merge branch 'main' into fix/novel-removed-vars
rcannood Jul 29, 2026
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -26,6 +26,8 @@

* `process_dataset`: Add the `--seed` argument the API and README already advertised, and pass it through from the `process_datasets` workflow. Without it `par$seed` was `NULL`, and `set.seed(NULL)` re-seeds from the clock -- so the test-cell and ATAC-peak subsampling were not reproducible (PR #27).

* `novel`: Record every all-zero training feature in `uns["removed_vars"]`, not just the first. With more than one such feature, `novel_predict` left extra columns in the test matrix and the model dimensions no longer lined up (PR #33).

# task_predict_modality 0.1.1

## NEW FUNCTIONALITY
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2 changes: 1 addition & 1 deletion src/methods/novel/novel_train/script.py
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Expand Up @@ -150,7 +150,7 @@
# Add model dim for use in predict part
adata.uns["model_dim"] = {"mod1": n_vars_mod1, "mod2": n_vars_mod2}
if rem_var is not None:
adata.uns["removed_vars"] = [rem_var[0]]
adata.uns["removed_vars"] = list(rem_var)
adata.write_h5ad(output_h5ad, compression="gzip")

if mod1 != 'ADT':
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