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  ![TRACE method overview](figures/TRACE_method.png)
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- **Research code accompanying the TRACE ICLR 2027 submission.**
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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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  - `benchmark_table.ot_plan()` attempts exact EMD but has an approximate fallback if EMD fails. Confirm whether the fallback was triggered in archived paper runs before claiming exact reproduction.
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  - This release does not yet reproduce all manuscript components (Slingshot curvature, external method baselines, interpolation-family ablations, or saved checkpoints).
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- ## Review and licensing
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  The present Hub metadata retains the repository's CC BY-NC-ND 4.0 designation, which restricts derivative works and may not be the desired license for software; confirm the final code license with the lab before public release.
 
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  ![TRACE method overview](figures/TRACE_method.png)
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+ TRACE 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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  - `benchmark_table.ot_plan()` attempts exact EMD but has an approximate fallback if EMD fails. Confirm whether the fallback was triggered in archived paper runs before claiming exact reproduction.
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  - This release does not yet reproduce all manuscript components (Slingshot curvature, external method baselines, interpolation-family ablations, or saved checkpoints).
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+ ## Licensing
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  The present Hub metadata retains the repository's CC BY-NC-ND 4.0 designation, which restricts derivative works and may not be the desired license for software; confirm the final code license with the lab before public release.