All pull requests

Pull requests

• [NUMERICAL CHANGE] Keep the bins x cells matrix in float32

  #24·by toresbe was merged Oct 11, 2026Owner·

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• [NUMERICAL CHANGE] Use the RNN Ward engine from 5,000 cells

  #23·by toresbe was merged Oct 11, 2026Owner·

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• [NUMERICAL CHANGE] Compute the step-4 silhouette with blocked GEMMs

  #21·by toresbe was merged Oct 11, 2026Owner·

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• Ward RNN engine speedups: FP32 candidate search, remembered candidates, physical cores

  #20·by toresbe was merged Oct 11, 2026Owner·

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• benchmarks: Patch step and segmentation hooks wherever the pipeline binds them

  #19·by toresbe was merged Oct 11, 2026Owner·

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• Fit step 4's cluster-consensus GMMs with the batched kernel

  #18·by toresbe was merged Oct 11, 2026Owner·

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• Keep sparse input column-major from filtering to smoothing

  #17·by toresbe was merged Oct 11, 2026Owner·

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• Build the cell-line relative expression in place

  #16·by toresbe was merged Oct 11, 2026Owner·

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• Run the Freeman-Tukey transform of each cell block in threads

  #15·by toresbe was merged Oct 11, 2026Owner·

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• Stream the transform and DLM smoothing over cell blocks

  #14·by toresbe was merged Oct 11, 2026Owner·

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• Compute segment means over cell blocks in parallel threads

  #13·by toresbe was merged Oct 11, 2026Owner·

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• Take baseline-adjustment statistics over row blocks

  #12·by toresbe was merged Oct 11, 2026Owner·

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• Replace linkage_vector with a parallel reciprocal-nearest-neighbour Ward (4.6x on 51k cells)

  #11·by toresbe was merged Oct 11, 2026Owner·

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• Compute per-cluster median profiles in parallel threads

  #10·by toresbe was merged Oct 11, 2026Owner·

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• Fit the per-cell GMM fallback in parallel numba threads

  #9·by toresbe was merged Oct 11, 2026Owner·

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• Consolidate benchmarks into one portable harness

  #8·by toresbe was merged Oct 10, 2026Owner·

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• refactor(copykat)!: split pipeline and centralize run configuration

  #7·by toresbe was merged Oct 10, 2026Owner·

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• Group annotated heatmap settings into options

  #6·by toresbe was merged Oct 10, 2026Owner·

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• Use dataclasses for internal pipeline results

  #5·by toresbe was merged Oct 10, 2026Owner·

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• Clarify final calling results and normal-cell handling

  #4·by toresbe was merged Oct 10, 2026Owner·

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• Extract final cell calling logic

  #3·by toresbe was merged Oct 10, 2026Owner·

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• Use enums for fixed pipeline choices

  #2·by toresbe was merged Oct 10, 2026Owner·

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• Modularize CopyKAT input and output helpers

  #1·by toresbe was merged Oct 10, 2026Owner·

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