pre-refactor 041426
This commit is contained in:
rpotter6298
@@ -0,0 +1,144 @@
|
||||
{
|
||||
"_notes": [
|
||||
"Phase 6 — Geometry augmentation: vector injection and dedicated geometry tower.",
|
||||
"Goal: test whether derived structural geometry (CDR, rim ratio, etc.) improves performance",
|
||||
" injected either as a 5-dim vector appended to the clinical stream (Part A)",
|
||||
" or as a dedicated geometry tower feeding into bridge fusion (Part B).",
|
||||
"Tower modes under test: single, ensemble, fused-head (ensemble + --fused-head).",
|
||||
"Geometry sources: GT contour annotations (no annotator-bias concern at this stage —",
|
||||
" labels were assigned by same clinicians, GT seg merely measures CDR directly)",
|
||||
" and U-Net segmentations (REFUGE-trained, fine-tuned on PAPILA folds — unbiased).",
|
||||
"Part A (geometry_vector): vector injection — dispatch_phase6a.py covers this.",
|
||||
" Requires: --geometry-dim and --geometry-source wired into v3_hypertower.py.",
|
||||
"Part B (geometry_tower): dedicated geometry tower — needs architecture implementation.",
|
||||
" Will get its own dispatch_phase6b.py once built.",
|
||||
"Ensemble and fused-head baselines come from phase5. Single has no equivalent with all tuned",
|
||||
" hyperparameters, so a phase6 single baseline is included here.",
|
||||
"Best settings from all prior phases: refugelike backbone, iop_ratio_drop_raw, bcd_p05.",
|
||||
"Geometry features: [area_cdr, rim_ratio, vertical_cdr, horizontal_cdr, centre_shift] (dim=5).",
|
||||
"common_args are prepended to every run's args list."
|
||||
],
|
||||
|
||||
"common_args": [
|
||||
"--eval-mode", "binary",
|
||||
"--bridge-mode", "fused",
|
||||
"--epochs", "30",
|
||||
"--in-memory-cache",
|
||||
"--augment",
|
||||
"--tune-binary-threshold",
|
||||
"--backbone", "refugelike",
|
||||
"--iop-corr-method", "ratio",
|
||||
"--iop-drop-raw",
|
||||
"--exclude-cols", "Axial_Length",
|
||||
"--img-crop-manifest", "manifest.csv",
|
||||
"--output-root", "v3/results"
|
||||
],
|
||||
|
||||
"_common_args_implicit_defaults": {
|
||||
"--tower-loss-mode": "bcd",
|
||||
"--bcd-prob": "0.5",
|
||||
"--warmup-cd-epochs": "40",
|
||||
"--single-warmup-tower-epochs": "3",
|
||||
"--single-warmup-fused-epochs": "3",
|
||||
"--bilat-warmup-tower-epochs": "3",
|
||||
"--bilat-warmup-fused-epochs": "3"
|
||||
},
|
||||
|
||||
"baseline": {
|
||||
"run_name": "phase6/single_no_geom",
|
||||
"description": "Single-eye + clinical data, no geometry — needed as Phase 6 baseline since no prior phase ran single with all tuned hyperparameters (iop_ratio_drop_raw, bcd_p05, refugelike).",
|
||||
"extra_args": ["--tower-mode", "single"]
|
||||
},
|
||||
|
||||
"groups": [
|
||||
{
|
||||
"name": "geometry_vector_gt",
|
||||
"description": "Part A — Inject 5-dim geometry vector from GT annotations alongside clinical data. Three aggregation modes: single-eye, ensemble (independent OD+OS), ensemble with fused head.",
|
||||
"runs": [
|
||||
{
|
||||
"run_name": "phase6/vec_gt_single",
|
||||
"description": "Single-eye + clinical + GT geometry vector appended to clinical stream.",
|
||||
"extra_args": ["--tower-mode", "single", "--geometry-dim", "5", "--geometry-source", "gt"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/vec_gt_ensemble",
|
||||
"description": "Ensemble + clinical + GT geometry vector (per-eye geometry, independent OD+OS mean).",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--geometry-dim", "5", "--geometry-source", "gt"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/vec_gt_fused_head",
|
||||
"description": "Ensemble + fused head + clinical + GT geometry vector.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--fused-head", "--geometry-dim", "5", "--geometry-source", "gt"]
|
||||
}
|
||||
]
|
||||
},
|
||||
|
||||
{
|
||||
"name": "geometry_vector_unet",
|
||||
"description": "Part A — Same three modes but geometry from U-Net segmentations (REFUGE-trained, fine-tuned). Tests whether GT annotator bias affects the geometry signal.",
|
||||
"runs": [
|
||||
{
|
||||
"run_name": "phase6/vec_unet_single",
|
||||
"description": "Single-eye + clinical + U-Net geometry vector.",
|
||||
"extra_args": ["--tower-mode", "single", "--geometry-dim", "5", "--geometry-source", "unet"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/vec_unet_ensemble",
|
||||
"description": "Ensemble + clinical + U-Net geometry vector.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--geometry-dim", "5", "--geometry-source", "unet"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/vec_unet_fused_head",
|
||||
"description": "Ensemble + fused head + clinical + U-Net geometry vector.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--fused-head", "--geometry-dim", "5", "--geometry-source", "unet"]
|
||||
}
|
||||
]
|
||||
},
|
||||
|
||||
{
|
||||
"name": "geometry_tower_gt",
|
||||
"description": "Part B — Dedicated geometry tower (MLP on 5-dim vector, separate from clinical tower) with GT geometry. Requires tri-tower bridge architecture.",
|
||||
"needs_implementation": "Geometry tower not yet built — requires GeometryTower MLP, bridge reconfiguration for n>=3 towers, and --geometry-tower CLI flag.",
|
||||
"runs": [
|
||||
{
|
||||
"run_name": "phase6/tower_gt_single",
|
||||
"description": "Single-eye + clinical tower + dedicated GT geometry tower.",
|
||||
"extra_args": ["--tower-mode", "single", "--geometry-tower", "--geometry-source", "gt"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/tower_gt_ensemble",
|
||||
"description": "Ensemble + clinical tower + dedicated GT geometry tower.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--geometry-tower", "--geometry-source", "gt"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/tower_gt_fused_head",
|
||||
"description": "Ensemble + fused head + clinical tower + dedicated GT geometry tower.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--fused-head", "--geometry-tower", "--geometry-source", "gt"]
|
||||
}
|
||||
]
|
||||
},
|
||||
|
||||
{
|
||||
"name": "geometry_tower_unet",
|
||||
"description": "Part B — Same three modes with dedicated geometry tower, U-Net geometry source.",
|
||||
"needs_implementation": "Geometry tower not yet built — requires GeometryTower MLP, bridge reconfiguration for n>=3 towers, and --geometry-tower CLI flag.",
|
||||
"runs": [
|
||||
{
|
||||
"run_name": "phase6/tower_unet_single",
|
||||
"description": "Single-eye + clinical tower + dedicated U-Net geometry tower.",
|
||||
"extra_args": ["--tower-mode", "single", "--geometry-tower", "--geometry-source", "unet"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/tower_unet_ensemble",
|
||||
"description": "Ensemble + clinical tower + dedicated U-Net geometry tower.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--geometry-tower", "--geometry-source", "unet"]
|
||||
},
|
||||
{
|
||||
"run_name": "phase6/tower_unet_fused_head",
|
||||
"description": "Ensemble + fused head + clinical tower + dedicated U-Net geometry tower.",
|
||||
"extra_args": ["--tower-mode", "ensemble", "--fused-head", "--geometry-tower", "--geometry-source", "unet"]
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
Reference in New Issue
Block a user