Add new regression and ensemble experiment configurations for V2-M and OrthoBridge
- Introduced multiple regression experiment configurations targeting vf_md, including: - cd_solo_reg_set.json: CD tower only regression setup. - img_solo_reg_set.json: Image tower only regression setup. - reg_head_epoch_sweep.json: Baseline regression sweeps at different epochs (50, 75, 100). - reg_head_set.json: Various regression setups including baseline and OrthoBridge configurations. - single_eye_reg.json: Single-eye regression setup for worst-eye aggregation analysis. - Added ensemble configurations for OrthoBridge with different inner bridges: - ortho_alts_ensemble.json: Ensemble tests with ConcatBridge, PairwiseAdditiveBridge, and GatedAdditiveBridge. - ortho_alts_tritower.json: Tritower tests with the same inner bridges. - Created V2-M specific configurations: - baseline_reg_nt50.json: Regression baseline with V2-M backbone. - geom_vec_gt.json and geom_vec_unet.json: Geometry vector injection experiments with V2-M. - single_l1_bridges.json: Single-eye ensemble experiments with various bridge types. - tritower_geom_gt.json: Tritower setup with GT contour-rasterized masks. - Promoted existing experiments to higher repetitions for robustness.
This commit is contained in:
rpotter6298
@@ -0,0 +1,102 @@
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{
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"_notes": [
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"CD tower only, regression head predicting vf_md.",
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"Mirrors ensemble_fused architecture (eye-level fusion → patient-level hb → head)",
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"with the img tower removed, so neg_mse is directly comparable to baseline_reg_nt50."
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],
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"run_name": "v4/cd_solo_reg",
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"num_classes": 2,
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"label_filter": [0, 1, 2],
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"split_identity_level": 1,
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"eval_stage": "hb",
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"save_predictions": true,
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"seed": 1234,
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"folds": 5,
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"fold_seed": 100,
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"output_root": "v4/results",
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"out_dir_tags": ["binary"],
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"data": {
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"module": "v4.classes.profiles.v4papila",
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"args": {
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"image_dir": "Papila/FundusImages",
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"clinical_dir": "Papila/ClinicalData",
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"label_col": "Diagnosis",
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"iop_corr_method": "ratio",
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"iop_drop_raw": true,
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"exclude_cols": ["Axial_Length"],
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"in_memory_cache": true
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}
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},
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"towers": [
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{
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"name": "cd",
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"module": "v4.classes.towers.clinical_tower",
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"class": "ClinicalEncoder",
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"data_source": "matrix",
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"args": { "hidden_dim": 128 }
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}
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],
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"stages": [
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{
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"name": "cd_warm",
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"type": "warm",
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"tower": "cd",
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"head_name": "cd_aux",
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"level": "eye",
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"epochs": 40
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},
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{
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"name": "cd_aux",
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"type": "head",
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"input": "cd",
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"train_with": "cd_fuse",
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"module": "v4.classes.heads.regression",
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"class": "RegressionHead",
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"args": { "dropout": 0.3, "target_key": "vf_md", "loss": "mse" }
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},
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{
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"name": "cd_fuse",
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"type": "fusion",
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"module": "v4.classes.bridges.mono_bridge",
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"class": "MonoBridge",
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"inputs": ["cd"],
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"level": "eye",
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"epochs": 50,
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"train_towers": true,
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"args": { "use_ln": false }
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},
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{
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"name": "cd_fuse_head",
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"type": "head",
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"input": "cd_fuse",
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"train_with": "cd_fuse",
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"module": "v4.classes.heads.regression",
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"class": "RegressionHead",
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"args": { "dropout": 0.3, "target_key": "vf_md", "loss": "mse" }
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},
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{
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"name": "hb",
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"type": "fusion",
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"module": "v4.classes.bridges.hyperbridge",
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"class": "HyperBridge",
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"inputs": { "a": "cd_fuse", "b": "cd_fuse" },
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"level": "patient",
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"epochs": 10,
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"args": { "hidden_dim": 256, "mode": "embedding_mlp" }
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},
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{
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"name": "hb_head",
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"type": "head",
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"input": "hb",
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"train_with": "hb",
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"module": "v4.classes.heads.regression",
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"class": "RegressionHead",
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"args": { "dropout": 0.3, "target_key": "vf_md", "loss": "mse" }
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}
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],
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"training": {
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"lr": 1e-4,
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"batch_size": 8,
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"tune_binary_threshold": true
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}
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}
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@@ -0,0 +1,89 @@
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{
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"_notes": [
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"Clinical-only at patient level (bilateral). Mirrors clinical_solo.json but",
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"adds the hb stage so cd_fuse(OD) and cd_fuse(OS) are aggregated at",
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"patient level. Pairs with single-eye clinical_solo for the Figure 4",
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"bilateral comparison."
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],
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"run_name": "v4/clinical_solo_bilateral",
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"num_classes": 2,
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"label_filter": [0, 1],
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"split_identity_level": 1,
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"eval_stage": "hb",
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"save_predictions": true,
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"seed": 1234,
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"folds": 5,
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"fold_seed": 100,
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"output_root": "v4/results",
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"out_dir_tags": ["binary"],
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"data": {
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"module": "v4.classes.profiles.v4papila",
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"args": {
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"image_dir": "Papila/FundusImages",
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"clinical_dir": "Papila/ClinicalData",
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"label_col": "Diagnosis",
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"iop_corr_method": "ratio",
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"iop_drop_raw": true,
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"exclude_cols": ["Axial_Length"],
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"in_memory_cache": false
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}
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},
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"towers": [
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{
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"name": "cd",
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"module": "v4.classes.towers.clinical_tower",
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"class": "ClinicalEncoder",
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"data_source": "matrix",
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"args": { "hidden_dim": 128 }
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}
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],
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"stages": [
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{
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"name": "cd_warm",
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"type": "warm",
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"tower": "cd",
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"head_name": "cd_aux",
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"level": "eye",
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"epochs": 40
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},
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{
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"name": "cd_aux",
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"type": "head",
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"input": "cd",
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"train_with": "cd_fuse"
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},
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{
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"name": "cd_fuse",
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"type": "fusion",
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"module": "v4.classes.bridges.mono_bridge",
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"class": "MonoBridge",
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"inputs": ["cd"],
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"level": "eye",
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"epochs": 36,
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"train_towers": true,
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"args": { "use_ln": false }
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},
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{
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"name": "hb",
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"type": "fusion",
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"module": "v4.classes.bridges.hyperbridge",
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"class": "HyperBridge",
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"inputs": { "a": "cd_fuse", "b": "cd_fuse" },
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"level": "patient",
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"epochs": 10,
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"args": { "hidden_dim": 256, "mode": "embedding_mlp" }
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},
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{
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"name": "hb_head",
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"type": "head",
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"input": "hb",
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"train_with": "hb",
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"args": { "dropout": 0.3 }
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}
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],
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"training": {
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"lr": 1e-4,
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"batch_size": 16,
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"tune_binary_threshold": true
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}
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}
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@@ -0,0 +1,102 @@
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{
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"_notes": [
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"Single-eye variant of ensemble_fused: stops at nt (eye-level fusion),",
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"drops the bilateral hb stage. Each eye is classified independently.",
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"For comparing patient-level bilateral (hb) vs single-eye (nt) — the v3",
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"single/bilateral standardization in the new modular architecture."
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],
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"run_name": "v4/ensemble_fused_single",
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"num_classes": 2,
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"label_filter": [0, 1],
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"split_identity_level": 1,
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"eval_stage": "nt",
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"save_predictions": true,
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"seed": 1234,
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"folds": 5,
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"fold_seed": 100,
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"output_root": "v4/results",
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"out_dir_tags": ["binary"],
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"data": {
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"module": "v4.classes.profiles.v4papila",
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"args": {
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"image_dir": "Papila/FundusImages",
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"clinical_dir": "Papila/ClinicalData",
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"label_col": "Diagnosis",
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"iop_corr_method": "ratio",
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"iop_drop_raw": true,
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"exclude_cols": ["Axial_Length"],
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"in_memory_cache": true
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}
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},
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"towers": [
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{
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"name": "img",
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"module": "v4.classes.towers.image_tower",
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"class": "ImageEncoder",
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"data_source": "image",
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"args": {
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"backbone": "refugelike",
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"freeze_ratio": 0.0,
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"augment": true
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}
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},
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{
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"name": "cd",
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"module": "v4.classes.towers.clinical_tower",
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"class": "ClinicalEncoder",
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"data_source": "matrix",
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"args": { "hidden_dim": 128 }
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}
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],
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"stages": [
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{
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"name": "cd_warm",
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"type": "warm",
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"tower": "cd",
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"head_name": "cd_aux",
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"level": "eye",
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"epochs": 40
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},
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{
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"name": "img_aux",
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"type": "head",
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"input": "img",
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"train_with": "nt",
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"bcd": true
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},
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{
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"name": "cd_aux",
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"type": "head",
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"input": "cd",
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"train_with": "nt",
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"bcd": true
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},
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{
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"name": "nt",
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"type": "fusion",
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"module": "v4.classes.bridges.fusion_bridge",
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"class": "FusionBridge",
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"inputs": ["img", "cd"],
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"level": "eye",
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"epochs": 36,
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"train_towers": true,
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"warmup": {
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"tower_epochs": 3,
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"fused_epochs": 3
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},
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"args": { "fusion_dim": 256 }
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},
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{
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"name": "nt_head",
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"type": "head",
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"input": "nt",
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"train_with": "nt"
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}
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],
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"training": {
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"lr": 1e-4,
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"batch_size": 8,
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"bcd_prob": 0.5,
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"tune_binary_threshold": true
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}
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}
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@@ -0,0 +1,92 @@
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{
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"_notes": [
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"Single-rep checkpointed run of the production bilateral img+cd ensemble",
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"at the refuge_efficientnet_v2_m backbone. Per-fold tower and stage_models",
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"state_dicts are saved under {output_root}/{run_name}/binary/checkpoints/",
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"fold{N}/ for downstream explainability (Grad-CAM, attribution, etc.).",
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"",
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"Same architecture as ensemble_fused.json — only changes are:",
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" • img.args.backbone = refuge_efficientnet_v2_m",
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" • save_checkpoints = true",
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" • run_name = experiments/explainability/ensemble_v2m_ckpt"
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],
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"run_name": "experiments/explainability/ensemble_v2m_ckpt",
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"num_classes": 2,
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"label_filter": [0, 1],
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"split_identity_level": 1,
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"eval_stage": "hb",
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"save_predictions": true,
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"save_checkpoints": true,
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"seed": 1234,
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"folds": 5,
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"fold_seed": 100,
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"output_root": "v4/results",
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"out_dir_tags": ["binary"],
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"data": {
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"module": "v4.classes.profiles.v4papila",
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"args": {
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"image_dir": "Papila/FundusImages",
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"clinical_dir": "Papila/ClinicalData",
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"label_col": "Diagnosis",
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"iop_corr_method": "ratio",
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"iop_drop_raw": true,
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"exclude_cols": ["Axial_Length"],
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"in_memory_cache": true
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}
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},
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"towers": [
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{
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"name": "img",
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"module": "v4.classes.towers.image_tower",
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"class": "ImageEncoder",
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"data_source": "image",
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"args": {
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"backbone": "refuge_efficientnet_v2_m",
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"freeze_ratio": 0.0,
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"augment": true
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}
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},
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{
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"name": "cd",
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"module": "v4.classes.towers.clinical_tower",
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"class": "ClinicalEncoder",
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"data_source": "matrix",
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"args": { "hidden_dim": 128 }
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}
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],
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"stages": [
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{ "name": "cd_warm", "type": "warm", "tower": "cd", "head_name": "cd_aux", "level": "eye", "epochs": 40 },
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{ "name": "img_aux", "type": "head", "input": "img", "train_with": "nt", "bcd": true },
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{ "name": "cd_aux", "type": "head", "input": "cd", "train_with": "nt", "bcd": true },
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{
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"name": "nt",
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"type": "fusion",
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"module": "v4.classes.bridges.fusion_bridge",
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"class": "FusionBridge",
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"inputs": ["img", "cd"],
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"level": "eye",
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"epochs": 36,
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"train_towers": true,
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"warmup": { "tower_epochs": 3, "fused_epochs": 3 },
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"args": { "fusion_dim": 256 }
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},
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{ "name": "nt_head", "type": "head", "input": "nt", "train_with": "nt" },
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{
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"name": "hb",
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"type": "fusion",
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"module": "v4.classes.bridges.hyperbridge",
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"class": "HyperBridge",
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"inputs": { "a": "nt", "b": "nt" },
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"level": "patient",
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"epochs": 10,
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"args": { "hidden_dim": 256, "mode": "embedding_mlp" }
|
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},
|
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{ "name": "hb_head", "type": "head", "input": "hb", "train_with": "hb", "args": { "dropout": 0.3 } }
|
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],
|
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"training": {
|
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"lr": 1e-4,
|
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"batch_size": 8,
|
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"bcd_prob": 0.5,
|
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"tune_binary_threshold": true
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}
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}
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@@ -0,0 +1,84 @@
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{
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"_notes": [
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"Image tower only, binary classification. Mirrors ensemble_fused architecture",
|
||||
"(eye-level fusion → patient-level hb → head) with the cd tower removed,",
|
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"so test AUC is directly comparable to baseline_ensemble."
|
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],
|
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"run_name": "v4/img_solo",
|
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"num_classes": 2,
|
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"label_filter": [0, 1],
|
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"split_identity_level": 1,
|
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"eval_stage": "hb",
|
||||
"save_predictions": true,
|
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"seed": 1234,
|
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"folds": 5,
|
||||
"fold_seed": 100,
|
||||
"output_root": "v4/results",
|
||||
"out_dir_tags": ["binary"],
|
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"data": {
|
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"module": "v4.classes.profiles.v4papila",
|
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"args": {
|
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"image_dir": "Papila/FundusImages",
|
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"clinical_dir": "Papila/ClinicalData",
|
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"label_col": "Diagnosis",
|
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"iop_corr_method": "ratio",
|
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"iop_drop_raw": true,
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"exclude_cols": ["Axial_Length"],
|
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"in_memory_cache": true
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||||
}
|
||||
},
|
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"towers": [
|
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{
|
||||
"name": "img",
|
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"module": "v4.classes.towers.image_tower",
|
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"class": "ImageEncoder",
|
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"data_source": "image",
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"args": {
|
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"backbone": "refugelike",
|
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"freeze_ratio": 0.0,
|
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"augment": true
|
||||
}
|
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}
|
||||
],
|
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"stages": [
|
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{
|
||||
"name": "img_fuse",
|
||||
"type": "fusion",
|
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"module": "v4.classes.bridges.mono_bridge",
|
||||
"class": "MonoBridge",
|
||||
"inputs": ["img"],
|
||||
"level": "eye",
|
||||
"epochs": 36,
|
||||
"train_towers": true,
|
||||
"args": { "use_ln": false }
|
||||
},
|
||||
{
|
||||
"name": "img_fuse_head",
|
||||
"type": "head",
|
||||
"input": "img_fuse",
|
||||
"train_with": "img_fuse"
|
||||
},
|
||||
{
|
||||
"name": "hb",
|
||||
"type": "fusion",
|
||||
"module": "v4.classes.bridges.hyperbridge",
|
||||
"class": "HyperBridge",
|
||||
"inputs": { "a": "img_fuse", "b": "img_fuse" },
|
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"level": "patient",
|
||||
"epochs": 10,
|
||||
"args": { "hidden_dim": 256, "mode": "embedding_mlp" }
|
||||
},
|
||||
{
|
||||
"name": "hb_head",
|
||||
"type": "head",
|
||||
"input": "hb",
|
||||
"train_with": "hb",
|
||||
"args": { "dropout": 0.3 }
|
||||
}
|
||||
],
|
||||
"training": {
|
||||
"lr": 1e-4,
|
||||
"batch_size": 8,
|
||||
"tune_binary_threshold": true
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,89 @@
|
||||
{
|
||||
"_notes": [
|
||||
"Image tower only, regression head predicting vf_md.",
|
||||
"Mirrors ensemble_fused architecture (eye-level fusion → patient-level hb → head)",
|
||||
"with the cd tower removed, so neg_mse is directly comparable to baseline_reg_nt50."
|
||||
],
|
||||
"run_name": "v4/img_solo_reg",
|
||||
"num_classes": 2,
|
||||
"label_filter": [0, 1, 2],
|
||||
"split_identity_level": 1,
|
||||
"eval_stage": "hb",
|
||||
"save_predictions": true,
|
||||
"seed": 1234,
|
||||
"folds": 5,
|
||||
"fold_seed": 100,
|
||||
"output_root": "v4/results",
|
||||
"out_dir_tags": ["binary"],
|
||||
"data": {
|
||||
"module": "v4.classes.profiles.v4papila",
|
||||
"args": {
|
||||
"image_dir": "Papila/FundusImages",
|
||||
"clinical_dir": "Papila/ClinicalData",
|
||||
"label_col": "Diagnosis",
|
||||
"iop_corr_method": "ratio",
|
||||
"iop_drop_raw": true,
|
||||
"exclude_cols": ["Axial_Length"],
|
||||
"in_memory_cache": true
|
||||
}
|
||||
},
|
||||
"towers": [
|
||||
{
|
||||
"name": "img",
|
||||
"module": "v4.classes.towers.image_tower",
|
||||
"class": "ImageEncoder",
|
||||
"data_source": "image",
|
||||
"args": {
|
||||
"backbone": "refugelike",
|
||||
"freeze_ratio": 0.0,
|
||||
"augment": true
|
||||
}
|
||||
}
|
||||
],
|
||||
"stages": [
|
||||
{
|
||||
"name": "img_fuse",
|
||||
"type": "fusion",
|
||||
"module": "v4.classes.bridges.mono_bridge",
|
||||
"class": "MonoBridge",
|
||||
"inputs": ["img"],
|
||||
"level": "eye",
|
||||
"epochs": 50,
|
||||
"train_towers": true,
|
||||
"args": { "use_ln": false }
|
||||
},
|
||||
{
|
||||
"name": "img_fuse_head",
|
||||
"type": "head",
|
||||
"input": "img_fuse",
|
||||
"train_with": "img_fuse",
|
||||
"module": "v4.classes.heads.regression",
|
||||
"class": "RegressionHead",
|
||||
"args": { "dropout": 0.3, "target_key": "vf_md", "loss": "mse" }
|
||||
},
|
||||
{
|
||||
"name": "hb",
|
||||
"type": "fusion",
|
||||
"module": "v4.classes.bridges.hyperbridge",
|
||||
"class": "HyperBridge",
|
||||
"inputs": { "a": "img_fuse", "b": "img_fuse" },
|
||||
"level": "patient",
|
||||
"epochs": 10,
|
||||
"args": { "hidden_dim": 256, "mode": "embedding_mlp" }
|
||||
},
|
||||
{
|
||||
"name": "hb_head",
|
||||
"type": "head",
|
||||
"input": "hb",
|
||||
"train_with": "hb",
|
||||
"module": "v4.classes.heads.regression",
|
||||
"class": "RegressionHead",
|
||||
"args": { "dropout": 0.3, "target_key": "vf_md", "loss": "mse" }
|
||||
}
|
||||
],
|
||||
"training": {
|
||||
"lr": 1e-4,
|
||||
"batch_size": 8,
|
||||
"tune_binary_threshold": true
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,115 @@
|
||||
{
|
||||
"_notes": [
|
||||
"Smoke test: convnextv2_tiny backbone, single fold, few epochs.",
|
||||
"Goal is to verify the new ConvNeXt-V2 path works end-to-end (load weights,",
|
||||
"forward, backward, save summary). Not for measuring quality."
|
||||
],
|
||||
"run_name": "smoke/convnextv2_tiny",
|
||||
"num_classes": 2,
|
||||
"label_filter": [
|
||||
0,
|
||||
1,
|
||||
2
|
||||
],
|
||||
"split_identity_level": 1,
|
||||
"eval_stage": "hb",
|
||||
"save_predictions": false,
|
||||
"seed": 1234,
|
||||
"folds": 3,
|
||||
"fold_seed": 100,
|
||||
"output_root": "v4/results",
|
||||
"out_dir_tags": [
|
||||
"binary"
|
||||
],
|
||||
"data": {
|
||||
"module": "v4.classes.profiles.v4papila",
|
||||
"args": {
|
||||
"image_dir": "Papila/FundusImages",
|
||||
"clinical_dir": "Papila/ClinicalData",
|
||||
"label_col": "Diagnosis",
|
||||
"iop_corr_method": "ratio",
|
||||
"iop_drop_raw": true,
|
||||
"exclude_cols": [
|
||||
"Axial_Length"
|
||||
],
|
||||
"in_memory_cache": true
|
||||
}
|
||||
},
|
||||
"towers": [
|
||||
{
|
||||
"name": "img",
|
||||
"module": "v4.classes.towers.image_tower",
|
||||
"class": "ImageEncoder",
|
||||
"data_source": "image",
|
||||
"args": {
|
||||
"backbone": "convnextv2_tiny",
|
||||
"freeze_ratio": 0.6,
|
||||
"augment": true
|
||||
}
|
||||
}
|
||||
],
|
||||
"stages": [
|
||||
{
|
||||
"name": "img_fuse",
|
||||
"type": "fusion",
|
||||
"module": "v4.classes.bridges.mono_bridge",
|
||||
"class": "MonoBridge",
|
||||
"inputs": [
|
||||
"img"
|
||||
],
|
||||
"level": "eye",
|
||||
"epochs": 2,
|
||||
"train_towers": true,
|
||||
"args": {
|
||||
"use_ln": false
|
||||
}
|
||||
},
|
||||
{
|
||||
"name": "img_fuse_head",
|
||||
"type": "head",
|
||||
"input": "img_fuse",
|
||||
"train_with": "img_fuse",
|
||||
"module": "v4.classes.heads.regression",
|
||||
"class": "RegressionHead",
|
||||
"args": {
|
||||
"dropout": 0.3,
|
||||
"target_key": "vf_md",
|
||||
"loss": "mse"
|
||||
}
|
||||
},
|
||||
{
|
||||
"name": "hb",
|
||||
"type": "fusion",
|
||||
"module": "v4.classes.bridges.hyperbridge",
|
||||
"class": "HyperBridge",
|
||||
"inputs": {
|
||||
"a": "img_fuse",
|
||||
"b": "img_fuse"
|
||||
},
|
||||
"level": "patient",
|
||||
"epochs": 2,
|
||||
"args": {
|
||||
"hidden_dim": 256,
|
||||
"mode": "embedding_mlp"
|
||||
}
|
||||
},
|
||||
{
|
||||
"name": "hb_head",
|
||||
"type": "head",
|
||||
"input": "hb",
|
||||
"train_with": "hb",
|
||||
"module": "v4.classes.heads.regression",
|
||||
"class": "RegressionHead",
|
||||
"args": {
|
||||
"dropout": 0.3,
|
||||
"target_key": "vf_md",
|
||||
"loss": "mse"
|
||||
}
|
||||
}
|
||||
],
|
||||
"training": {
|
||||
"lr": 1e-4,
|
||||
"batch_size": 8,
|
||||
"tune_binary_threshold": true
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,67 @@
|
||||
{
|
||||
"_notes": [
|
||||
"Single-eye img-only variant. Eye-level MonoBridge fusion, no patient-level hb.",
|
||||
"Each eye is classified independently. For comparing single vs bilateral",
|
||||
"in the img-only architecture."
|
||||
],
|
||||
"run_name": "v4/img_solo_single",
|
||||
"num_classes": 2,
|
||||
"label_filter": [0, 1],
|
||||
"split_identity_level": 1,
|
||||
"eval_stage": "img_fuse",
|
||||
"save_predictions": true,
|
||||
"seed": 1234,
|
||||
"folds": 5,
|
||||
"fold_seed": 100,
|
||||
"output_root": "v4/results",
|
||||
"out_dir_tags": ["binary"],
|
||||
"data": {
|
||||
"module": "v4.classes.profiles.v4papila",
|
||||
"args": {
|
||||
"image_dir": "Papila/FundusImages",
|
||||
"clinical_dir": "Papila/ClinicalData",
|
||||
"label_col": "Diagnosis",
|
||||
"iop_corr_method": "ratio",
|
||||
"iop_drop_raw": true,
|
||||
"exclude_cols": ["Axial_Length"],
|
||||
"in_memory_cache": true
|
||||
}
|
||||
},
|
||||
"towers": [
|
||||
{
|
||||
"name": "img",
|
||||
"module": "v4.classes.towers.image_tower",
|
||||
"class": "ImageEncoder",
|
||||
"data_source": "image",
|
||||
"args": {
|
||||
"backbone": "refugelike",
|
||||
"freeze_ratio": 0.0,
|
||||
"augment": true
|
||||
}
|
||||
}
|
||||
],
|
||||
"stages": [
|
||||
{
|
||||
"name": "img_fuse",
|
||||
"type": "fusion",
|
||||
"module": "v4.classes.bridges.mono_bridge",
|
||||
"class": "MonoBridge",
|
||||
"inputs": ["img"],
|
||||
"level": "eye",
|
||||
"epochs": 36,
|
||||
"train_towers": true,
|
||||
"args": { "use_ln": false }
|
||||
},
|
||||
{
|
||||
"name": "img_fuse_head",
|
||||
"type": "head",
|
||||
"input": "img_fuse",
|
||||
"train_with": "img_fuse"
|
||||
}
|
||||
],
|
||||
"training": {
|
||||
"lr": 1e-4,
|
||||
"batch_size": 8,
|
||||
"tune_binary_threshold": true
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user