Commit History
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docs: correct the reproduction instructions
Verified signature--check stops at 20k rows, so document the count it actually prints. Add the missing extract+rebase commands for BRACS, BreakHis and SPIDER. Name the two further SPIDER classes that lose ~45% of their patches. Point the baseline comparison at baselines/graphist_v1/embeddings.dde2db6 -
docs: correct the SPIDER probe path
Verified signatureThe command named spider_breast, which does not exist at the repository root. The CSVs that flag wants are in graphs/spider_breast, alongside a data/ subdirectory holding the graph shards.894ff1f -
docs: finish the GrapHist++ rename
Verified signatureThe first pass matched only the exact string GrapHist v2 and missed a bare v2 here.3ce7328 -
docs: rename the model to GrapHist++ in prose
Verified signatureBranding only. The checkpoint filename graphist_v2.pt and the repository ids stay: Hugging Face rejects '+' in a repository name, and renaming the checkpoint would break every documented command and every copy already downloaded.5852a98
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Fix stale paths and resync the shipped modeling code
Verified signatureThe survival commands in DATA.md still pointed at src/survival_analysis/, which moved to studies/survival/ when the code repository was reorganised. Every flag in both commands was already correct; only the paths were wrong. modeling/models/ had drifted from the code repository: it still carried seven constructor parameters left over from a GAT backbone that nothing reads. The three affected files are resynced, and the model card's Args block no longer defines them. Those two changes have to land together, since the card's snippet imports build_model from this folder. The checkpoint is unaffected: the removed parameters create no modules, so the state dict is unchanged and graphist_v2.pt loads exactly as before. The batch-effect heading was styled like the sibling studies/ headings that name real directories, but that study ships no directory; it reuses baselines/ and labels/. The heading and the studies/ preamble now say so.36d3a9f
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Correct the repository tree description
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Bring the studies contents in line with what actually ships
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Update README.md
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Link the code repository; point script paths at its layout
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Link the code repository
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Link the authors to their sites
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Link the authors to their sites
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Cite every source cohort, note LTS4 supervision
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Cite every source cohort, note LTS4 supervision and the separate code repository
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Move analysis and pipeline code to the code repository; keep the model, its loader, the data and the docs
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Remove a non-runnable duplicate survival script (PATH/TO placeholders)
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Drop LFS rules for the old data/ layout
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Make every command runnable from the repo root; fix the folder-limit and gate wording
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Restore the full parameter counts, correct the control value, clarify what inference needs
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Remove hardcoded paths from src_at_ef0b17d.tar
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Remove hardcoded paths from src_at_9d74e93.tar
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Replace hardcoded paths with placeholders: pooled_edge_homophily.json
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Replace hardcoded paths with placeholders: compute_pooled_edge_homophily.py
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Replace hardcoded paths with placeholders: run_cellvit_pipeline.sh
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Replace hardcoded paths with placeholders: fat_tail_followup.py
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Replace hardcoded paths with placeholders: run_fullregen.sh
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Replace hardcoded paths with placeholders: nucls_super_source_args.json
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Replace hardcoded paths with placeholders: run_optuna_repro.sh
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Replace hardcoded paths with placeholders: commands.txt
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Replace hardcoded paths with placeholders: rebase_graph_paths.py
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Ship the parameterized survival scripts (no hardcoded paths, CLI args)
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Add authorship, remove em dashes
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Correct library versions, add authorship, remove em dashes
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Remove internal reproduction notes; their content is now in DATA.md
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Rewrite DATA.md for a general audience: no branches, per-dataset reference, absorbs the study numbers
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Move data docs to DATA.md and rewrite every path for the new structure
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New model card: GrapHist v2 only, shorter, matches the new layout
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Restructure: move batch 30/30
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Restructure: move batch 29/30
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Restructure: move batch 18/30
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