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Commits on Apr 2, 2026

• Add Figshare links and full model paths to reproducibility guide (#32)

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  justjhong

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• Realistic semisynthetic sweep update (#31)

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  khushidesai1

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• Add reproducibility guide (#26)

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  justjhong

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Commits on Apr 1, 2026

• add script for crossvalidation on real dataset (#30)

  khushidesai1

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• Add cross-validation option for realistic semisynthetic dataset (#28)

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  khushidesai1

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• Sweeps for benchmarking methods (#18)

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  khushidesai1

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• Test for segmentation on interaction genes for GITIII (#24)

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  khushidesai1

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• Compare interaction scores for lower resolution Xenium labels (#25)

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Commits on Mar 31, 2026

• Add LR gene analysis for Xenium interactions (#27)

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  justjhong

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• Clean up GSEA butterfly chart formatting (#29)

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Commits on Mar 26, 2026

• Save sensitivity test figures to figures directory (#22)

  justjhong

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• Add Monte Carlo null z-distribution notebook (#21)

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  justjhong

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• Add runtime benchmark for Xenium dataset (#20)

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  justjhong

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• GSEA validation for communication hubs (#17)

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Commits on Mar 10, 2026

• Communication hub refactor and sensitivity analysis (#14)

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  justjhong

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Commits on Feb 24, 2026

• sensitivity plot for length scale semisyn (#16)

  justjhong

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Commits on Feb 2, 2026

• Pin transformers<5 to fix AttributeError on fresh install (#15)

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  justjhong

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Commits on Jan 29, 2026

• Bootstrap ci intervals for length scales (#13)

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Commits on Jan 12, 2026

• bootstrap ci intervals for length scale and change defaults

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Commits on Oct 13, 2025

• Update LICENSE (#11)

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Commits on Sep 27, 2025

• Update README.md (#9)

  justjhong

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• Update README.md (#8)

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• Add Readthedocs documentation (#5)

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  justjhong

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• fix tutorial link and uncomment pip install (#7)

  khushidesai1

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• Create AMICI tutorial notebook (#6)

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• Add vector and memory optimization to ablation and counterfactual modules (#3)

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Commits on Sep 26, 2025

• Merge pull request #2 from azizilab/jhong/changelog

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  khushidesai1

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Commits on Sep 25, 2025

• add changelog file

  justjhong

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Commits on Sep 24, 2025

• Update README.md with citation information

  justjhong

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• Update README.md

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• Merge pull request #1 from azizilab/jhong/fixbuild

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  justjhong

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• modify pyproject.toml to build properly

  justjhong

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• Merge branch 'main' of github.com:azizilab/amici

  justjhong

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• correct package metadata target for build

  justjhong

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• modify build target

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