Commit History
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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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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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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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Remove internal reproduction notes; their content is now in DATA.md
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Restructure: move batch 30/30
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Restructure: move batch 10/30
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Restructure: move batch 1/1
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