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Commits on Jun 29, 2026

• docs: audit comments/docs, fix stf-predict, relicense to Apache-2.0 (#14)

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• Feature/bilinear head (#13)

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Commits on Jun 28, 2026

• Experiment/compare performance (#12)

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Commits on Jun 10, 2026

• test: skip compile tests when Triton is missing on Windows

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• refactor: transition to pathway-exclusive regression and clean up legacy code (#11)

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Commits on Jun 9, 2026

• feat: add CCC, Huber, and CLIP losses with per-pathway validation metrics and SVG analysis (#10)

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Commits on Apr 5, 2026

• Feat/primary pathway loss (#9)

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Commits on Mar 26, 2026

• README.md: (#8)

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• Implementing svg (#7)

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Commits on Mar 12, 2026

• - Added some docs on possible ideas and recommendations to explore to improve the model based on the online book SC Best Practises. I will go off and learn more about these to make sense of this in…

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• Update README.md API quickstart with missing code for feature extraction.

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Commits on Mar 11, 2026

• New Feature - API Framework (#6)

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Commits on Mar 4, 2026

• Update and Major fixes to the Model and Pathway Loss (#5)

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Commits on Feb 27, 2026

• docs: clarify licensing and add third-party attributions

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• - Add specific copyright (2004-2025) and version (v6.0+) info for

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• docs: clarify licensing for foundation models and HEST-1k dataset

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• docs: clarify licensing terms for third-party foundation models

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Commits on Feb 26, 2026

• feat: integrate auxiliary pathway loss and sparsity regularization (#4)

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• refactor: improve setup UX, HF authentication, and download docs (#3)

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• Improving unit tests (#2)

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Commits on Feb 25, 2026

• Merge pull request #1 from BenjaminIsaac0111/InteractionModelDebugging

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• Forgot this one, oops hehe

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• Fixed TypeError: Resolved a TypeError in SpatialTranscriptFormer by correctly placing enable_nested_tensor=False in the TransformerEncoder constructor.

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• docs: implement branch protections and code ownership

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Commits on Feb 24, 2026

• feat: implement quad-flow interaction system and major architectural cleanup

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Commits on Feb 23, 2026

• chore: handle gated HF dataset and add CI authentication support

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• feat: comprehensive infrastructure overhaul for SpatialTranscriptFormer

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Commits on Feb 22, 2026

• - Applied black formatting.

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• ci: add GitHub Actions workflow for automated testing

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Commits on Feb 20, 2026

• feat(spatial): fix spatial alignment bug and refine loss landscape

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Commits on Feb 19, 2026

• refactor: unify interaction model around Jaume pipeline (Early Fusion)

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• feat(interaction): add LocalPatchMixer (Scatter-Gather depthwise Conv)

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Commits on Feb 17, 2026

• - Update to MODEL.md documentation.

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• feat(model): refactor early fusion and add spatial inductive biases

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• Widget: added a little application in matplotlib to look at predicted pathways overlay over a given sample.

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