Repository navigation

GRASS-MIL 1.0: preprint method, nested CV, niche discovery, statistics - #22

Merged

LRabuzin merged 23 commits into

mainfrom

feat/preprint-method

Oct 14, 2026

Merged

GRASS-MIL 1.0: preprint method, nested CV, niche discovery, statistics#22
LRabuzin merged 23 commits into
mainfrom
feat/preprint-method

Commits on Aug 17, 2026
- Strip a trailing blank line that failed end-of-file-fixer
  
  LRabuzin
  and
  claude
  committed
  6ad7bf5
Commits on Oct 13, 2026
- Untrack the 20 MB mibitof demo file; vignettes download it at runtime
  
  LRabuzin
  and
  claude
  committed
  86636b6
- Phase 1: preprint fidelity for graph, encoder and attention; composable model presets
  
  LRabuzin
  and
  claude
  committed
  e7ed3aa
- Phase 2: one region per bag, regimes with scaled learning rates, region-level selection
  
  LRabuzin
  and
  claude
  committed
  b16e4bc
- Phase 3: explicit splits, probe pre-fit and nested cross-validation
  
  LRabuzin
  and
  claude
  committed
  7902572
- Phase 4: BGRL A3 pretraining preset and fidelity
  
  LRabuzin
  and
  claude
  committed
  a6a365b
- Phase 5: cell cache extraction, patient-level aggregation, evaluation statistics
  
  LRabuzin
  and
  claude
  committed
  8eb9d60
- Phase 6: niche discovery on the cell cache
  
  LRabuzin
  and
  claude
  committed
  fc152aa
- Phase 7: cross-fold metaclusters, whole-dataset transfer, shared basis
  
  LRabuzin
  and
  claude
  committed
  4b63f2c
- Phase 8: classical spatial statistics
  
  LRabuzin
  and
  claude
  committed
  42f4b42
- Phase 9: cleanup, documentation, README, citation, vignettes
  
  LRabuzin
  and
  claude
  committed
  c291def
- Phase 10 (part): end-to-end synthetic test, bf16-safe exports, balanced synthetic folds
  
  LRabuzin
  and
  claude
  committed
  2d04415
- Phase 10 (part): per-unit eval metrics for patch/sample bags, resume validation, output dirs
  
  LRabuzin
  and
  claude
  committed
  a10e785
- nested CV: unit ids of patch and sample bags from the namespaced bag id
  
  LRabuzin
  and
  claude
  committed
  37f7df4
- Vignette 03 executed (nested CV, niches, metaclusters, scores, spatial statistics)
  
  LRabuzin
  and
  claude
  committed
  acff9bf
- method correspondence: probehead and spatial-statistics fidelity results
  
  LRabuzin
  and
  claude
  committed
  8648b84
- method correspondence: ftALL-reg fold-2 fidelity result
  
  LRabuzin
  and
  claude
  committed
  f31d500
- model loading ignores probe pre-fit and init checkpoints (the trained checkpoint carries the head)
  
  LRabuzin
  and
  claude
  committed
  e009a4d
- method correspondence: niche fidelity result
  
  LRabuzin
  and
  claude
  committed
  9d64073
- Lint: names and unused variables flagged by the pinned pre-commit ruff; notebooks formatted
  
  LRabuzin
  and
  claude
  committed
  16e5650
- Docs: getting-started walkthrough, configuration guide, cohort config template; pretraining as regime=pretrain_a3
  
  LRabuzin
  and
  claude
  committed
  676156d
- Repository map regenerated; generator kept in tools/
  
  LRabuzin
  and
  claude
  committed
  c4d4ff5
Commits on Oct 14, 2026
- e2e test: structural checks instead of a seed-dependent ranking assertion; test seed overridable
  
  LRabuzin
  and
  claude
  committed
  2cdc594

Commits

Commits on Aug 17, 2026

Commits on Oct 13, 2026

Commits on Oct 14, 2026