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  TRACE (formerly BioCHIME in the development scripts) modulates the reference path of temporal single-cell conditional flow matching using transcription-factor regulon derivatives. It first couples retained population snapshots with balanced optimal transport, constructs PCHIP/Hermite reference paths, maps regulon activity derivatives into PCA coordinates with a ridge fit \(Z pprox AW+b\), calibrates their norms, and blends the mapped tangents with geometric PCHIP tangents before shape-preserving projection.
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- This is an **initial code-only release**. Input matrices, frozen TF-target prior, pretrained weights, and third-party benchmark implementations are not included. The code has been distilled from the original research scripts; the reorganized runner has **not yet been checked for numerical equivalence against archived paper runs**.
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  ## Submitted TRACE configuration
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  TRACE (formerly BioCHIME in the development scripts) modulates the reference path of temporal single-cell conditional flow matching using transcription-factor regulon derivatives. It first couples retained population snapshots with balanced optimal transport, constructs PCHIP/Hermite reference paths, maps regulon activity derivatives into PCA coordinates with a ridge fit \(Z pprox AW+b\), calibrates their norms, and blends the mapped tangents with geometric PCHIP tangents before shape-preserving projection.
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+ This is an **initial code-only release**. Input matrices, frozen TF-target prior, pretrained weights, and third-party benchmark implementations are not included.
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  ## Submitted TRACE configuration
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