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Cleanup/lean package - #17

Merged

LRabuzin merged 25 commits into

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cleanup/lean-package

Aug 13, 2026

Merged

Cleanup/lean package#17
LRabuzin merged 25 commits into
mainfrom
cleanup/lean-package

Commits on Mar 5, 2026
- Dataset prep documentation
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Commits on Aug 12, 2026
- Wire up per-cluster enrichment plugin and multi-attribute scatters
  
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- Repackage src/ as an installable grass_mil package
  
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- Stop dropping node-level tensors when sampling, rename categorical codes
  
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- Add cell-type embedding and GINE-on-edge-length to the encoder
  
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Commits on Aug 13, 2026
- Make MIL attention per-class and assert the attribution identity
  
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- Add hull-interior seed sampling and ego-graph radius cutoff
  
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- Port degree-importance BGRL augmentations, fix asymmetric edge dropping
  
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- Add a survival task preset and vectorise the concordance index
  
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- Add exact additive attribution with bootstrap intervals
  
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- Add Moran's I, Ripley cross-L, and cross-space cluster agreement
  
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- Wire the new analyses into plugins and expose the attention head space
  
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- Remove the auxiliary objectives and learned graph pooling
  
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- Document method fidelity and correct the gap audit
  
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- Generalise margin attribution to multi-class with a one-vs-rest contrast
  
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- Use niche vocabulary, name Background, order niches by composition
  
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- Finish the niche rename in transfer helpers and output artifacts
  
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- Require per-class attention and merge the contracts modules
  
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- Make the augmentation generator functional and drop the duplicate path
  
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- Read the head bias from the checkpoint instead of asking for it by hand
  
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- Renumber niches by dendrogram order once, after clustering
  
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- Interpret through weighted logit margins only
  
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- Cleanups: one config resolver, honest loss names, no slow marker
  
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- Update docs to the current code and delete requirements.txt
  
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- Fix macOS CI: install torch-sparse from conda, not pip
  
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  85f2136

Commits

Commits on Mar 5, 2026

Commits on Aug 12, 2026

Commits on Aug 13, 2026