refactor: transition to pathway-exclusive regression and clean up leg…#11
Merged
Conversation
…acy code Refactors baseline models, dataset loaders, CLI entry points, and documentation to align with the strictly pathway-exclusive regression architecture, removing legacy high-dimensional gene expression reconstruction. - Baselines & Models: Renamed `num_genes` to `num_pathways` in HE2RNA and ViT_ST to regress pathway activities directly. - CLI & Setup: Corrected pyproject.toml entry points to map to `recipes/hest/`. Updated setup scripts to point to `stf-compute-pathways`. - Deletions: Removed obsolete script `build_vocab.py` and document `GENE_ANALYSIS.md`. - Documentation: Aligned DATALOADER.md, MODELS.md, SC_BEST_PRACTICES.md, TRAINING_GUIDE.md, TESTING.md, PRECOMPUTED_WORKFLOW.md, and DATA_FORMAT.md with the pathway paradigm using relative repository links. - Moran's I: Documented and updated docstrings in `PATHWAY_MAPPING.md` and `spatial_stats.py` to highlight Moran's I as a diagnostic and spatial collapse validation metric. - Project History: Initialized CHANGELOG.md documenting repository history, milestones, and unreleased changes.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
…acy code
Refactors baseline models, dataset loaders, CLI entry points, and documentation to align with the strictly pathway-exclusive regression architecture, removing legacy high-dimensional gene expression reconstruction.
num_genestonum_pathwaysin HE2RNA and ViT_ST to regress pathway activities directly.recipes/hest/. Updated setup scripts to point tostf-compute-pathways.build_vocab.pyand documentGENE_ANALYSIS.md.PATHWAY_MAPPING.mdandspatial_stats.pyto highlight Moran's I as a diagnostic and spatial collapse validation metric.