Add SenKin CITE-seq method (LightGBM + GRU ensemble) - #18
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benjaminfreyuu wants to merge 2 commits into
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VladimirShitov
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July 1, 2026 13:22
VladimirShitov
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Thanks! Looks very good overall, but some functionality should be moved to https://github.com/lueckenlab/senkin-tmp-cite-pred and imported from there for better reusability
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| __merge__: ../../../api/comp_method.yaml | |||
| name: senkin | |||
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Can we call it senkin_tmp? There were 2 team members, would be nice to mention both
| 45% MSE) of per-fold averaged outputs. | ||
| references: | ||
| doi: | ||
| - 10.1101/2022.04.11.487796 |
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Suggested change
| - 10.1101/2022.04.11.487796 | |
| - 10.64898/2026.02.24.707614v1 |
3 tasks
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Could you update this one with the updated code from senkin-tmp repo and then merge (or tell me to merge)? |
Replace the inline _lognorm and _clr_tsvd_fitted duplicates in senkin_train with the now-published library functions log_normalize() and clr_tsvd() from senkin_tmp_cite_pred.preprocess. Behaviour is unchanged: log_normalize uses target_sum=1e4 (CP10K + log1p) matching the old _lognorm, and clr_tsvd uses random_state=42 for reproducible components. The previously-kept fitted TSVD object was unused and is dropped.
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Replaced the inline _lognorm and _clr_tsvd_fitted duplicates in senkin_train Ready to merge @VladimirShitov |
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Proposed changes are described in the CHANGELOG.md
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