Fix/senkin match original - #68
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The 2026-08-14 run had senkin_tmp_train hit the 8h walltime on the CITE datasets and OOM/crash on the rest. Two causes: 1. LightGBM set no num_threads, so it defaulted to one thread per core the container *sees* (the whole node) while the job is cgroup-throttled to meta["cpus"] -- the threads oversubscribe and thrash. The original solution ran on Kaggle with dedicated cores so never hit this. Pin num_threads to meta["cpus"] (results-preserving; same class of fix as guanlab in #59). 2. senkin has no applicability guard, so it ran on all 8 datasets including Multiome and the ADT->GEX swap, where it wastes hours and OOMs. Add an exit_non_applicable guard (via src/utils/exit_codes.py) so it only runs on the GEX->ADT CITE direction, and point the component test at bmmc_cite/normal. Verified: viash test passes (2/2) on the normal (GEX->ADT) direction; the guard correctly skips the swap direction. Note: pinning threads removes the oversubscription, but senkin runs 4 LightGBM models (134 targets x 5 folds) + 2 NNs in one job, which the original spread across separate multi-hour Kaggle sessions - it may still need a walltime above 8h or a lighter config on the full data.
…agnostic Uses the fixed senkin-tmp-cite-pred (fix/match-original-pipeline) and restores the original feature blocks: log1p(CPM) inputs, CLR-TSVD 200, correlated genes selected on the log-normalized RNA per batch (plus genes whose name matches a protein), TSVD-100 and PCA-64 of the sqrt/z-score/ batch-median normalization, and the four LightGBM prediction blocks, all z-scored per cell before the two neural networks. The batch column is used as is (or a single batch when absent) instead of parsing day/donor out of it, which only made sense for the NeurIPS 2022 naming. Predictions are rescaled to the target scale with one global affine transform fitted on the out-of-fold training predictions, so RMSE/MAE are meaningful while every per-cell and per-protein correlation is unchanged. The predict step checks that the test cells match the trained bundle and uses light resource labels. Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
…tmp-cite-pred#5 is merged Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
rcannood
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* senkin: pin LightGBM threads and skip non-applicable datasets * senkin_tmp: match the original pipeline and make the wrapper dataset agnostic * senkin_tmp: pin the library to the verified commit * senkin_tmp: pin the library to the commit merged with main (#4) * senkin_tmp: pin the library to a830343 (robust correlation_score) * senkin_tmp: install the library from main now that lueckenlab/senkin-tmp-cite-pred#5 is merged --------- Co-authored-by: Benjamin Frey <124636707+benjaminfreyuu@users.noreply.github.com>
rcannood
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that referenced
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Sep 16, 2026
* senkin: pin LightGBM threads and skip non-applicable datasets * senkin_tmp: match the original pipeline and make the wrapper dataset agnostic * senkin_tmp: pin the library to the verified commit * senkin_tmp: pin the library to the commit merged with main (#4) * senkin_tmp: pin the library to a830343 (robust correlation_score) * senkin_tmp: install the library from main now that lueckenlab/senkin-tmp-cite-pred#5 is merged --------- Co-authored-by: Benjamin Frey <124636707+benjaminfreyuu@users.noreply.github.com>
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Fix the implementation to match the competition 2022 results
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Proposed changes are described in the CHANGELOG.md
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