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logs/clinical_queue_gpu1_v2.log

@@ -0,0 +1,7 @@
+[2026-05-20 23:44:06] start brainfm_frozen gpu=1
+[2026-05-20 23:44:06] done brainfm_frozen
+[2026-05-20 23:44:06] start sam_med3d_frozen gpu=1
+[2026-05-20 23:44:06] done sam_med3d_frozen
+[2026-05-20 23:44:06] start swinunetr_frozen gpu=1
+[2026-05-20 23:44:06] done swinunetr_frozen
+[2026-05-20 23:44:06] GPU1 queue DONE

logs/clinical_remap_pet.log

@@ -0,0 +1,11 @@
+[2026-05-20 21:42:14] start remap_pet gpu=0 ckpt=runs/foundation/medicalnet_layer4_regalign_best.pt
+checkpoint=runs/foundation/medicalnet_layer4_regalign_best.pt
+wrote=runs/clinical/remap_pet_clinical_probe.csv
+{'task': 'clinical_label_3way', 'type': 'classification', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 0.03, 'accuracy': 0.43137254901960786, 'balanced_accuracy': 0.535591424146083, 'macro_f1': 0.4503556588785566, 'auroc': 0.7519803721733793}
+{'task': 'ad_vs_cn', 'type': 'classification', 'n_train': 332, 'n_val': 69, 'n_test': 59, 'selected_param': 0.3, 'accuracy': 0.847457627118644, 'balanced_accuracy': 0.8482758620689655, 'macro_f1': 0.8472821397756687, 'auroc': 0.945977011494253}
+{'task': 'pmci_vs_smci', 'type': 'classification', 'n_train': 269, 'n_val': 51, 'n_test': 69, 'selected_param': 1.0, 'accuracy': 0.7246376811594203, 'balanced_accuracy': 0.7116745283018868, 'macro_f1': 0.6703545385969324, 'auroc': 0.7865566037735849}
+{'task': 'mmse', 'type': 'regression', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 10.0, 'mae': 1.7146922217475042, 'rmse': 2.091147911642773, 'r2': 0.38492797807998114, 'pearson': 0.6204554437730443}
+{'task': 'cdrsb', 'type': 'regression', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 30.0, 'mae': 0.9265968826861163, 'rmse': 1.2161289395322572, 'r2': 0.48159828538858773, 'pearson': 0.6950593441641384}
+{'task': 'adas13', 'type': 'regression', 'n_train': 707, 'n_val': 151, 'n_test': 148, 'selected_param': 3.0, 'mae': 5.582729248356175, 'rmse': 6.7359510000579075, 'r2': 0.48305105383103975, 'pearson': 0.7047911862844782}
+{'task': 'faq', 'type': 'regression', 'n_train': 704, 'n_val': 152, 'n_test': 153, 'selected_param': 10.0, 'mae': 3.895523732004602, 'rmse': 5.393642057918233, 'r2': 0.36431779522151775, 'pearson': 0.6054221549516138}
+[2026-05-20 21:42:59] done remap_pet

logs/clinical_remap_pet_v2.log

@@ -0,0 +1,9 @@
+checkpoint=runs/foundation/medicalnet_layer4_regalign_best.pt
+wrote=runs/clinical/remap_pet_clinical_probe.csv
+{'task': 'clinical_label_3way', 'type': 'classification', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 0.03, 'accuracy': 0.43137254901960786, 'balanced_accuracy': 0.535591424146083, 'macro_f1': 0.4503556588785566, 'auroc': 0.7519803721733793}
+{'task': 'ad_vs_cn', 'type': 'classification', 'n_train': 332, 'n_val': 69, 'n_test': 59, 'selected_param': 0.3, 'accuracy': 0.847457627118644, 'balanced_accuracy': 0.8482758620689655, 'macro_f1': 0.8472821397756687, 'auroc': 0.945977011494253}
+{'task': 'pmci_vs_smci', 'type': 'classification', 'n_train': 269, 'n_val': 51, 'n_test': 69, 'selected_param': 1.0, 'accuracy': 0.7246376811594203, 'balanced_accuracy': 0.7116745283018868, 'macro_f1': 0.6703545385969324, 'auroc': 0.7865566037735849}
+{'task': 'adas11', 'type': 'regression', 'n_train': 709, 'n_val': 151, 'n_test': 153, 'selected_param': 3.0, 'mae': 3.8732052566179265, 'rmse': 4.7123139030849615, 'r2': 0.5017415117292021, 'pearson': 0.7205379868133169}
+{'task': 'mmse', 'type': 'regression', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 10.0, 'mae': 1.7146922217475042, 'rmse': 2.091147911642773, 'r2': 0.38492797807998114, 'pearson': 0.6204554437730443}
+{'task': 'ravlt_immediate', 'type': 'regression', 'n_train': 708, 'n_val': 152, 'n_test': 153, 'selected_param': 3.0, 'mae': 9.046953999139125, 'rmse': 10.885174074889555, 'r2': 0.2703618472974266, 'pearson': 0.5470005545082554}
+{'task': 'ldeltotal', 'type': 'regression', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 10.0, 'mae': 3.4089977943819334, 'rmse': 4.274877699707625, 'r2': 0.20693636437943053, 'pearson': 0.47727077434647963}

logs/clinical_sam_med3d_frozen_v2.log

@@ -0,0 +1,27 @@
+creating model SAM-Med3D
+try to load pretrained weights from pretrained/sam-med3d/sam_med3d_turbo.pth
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 4.5040671636797924e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 9.822505830925365e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 4.511748130653359e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 9.895541097648675e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 4.482976834196961e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 9.894051800074521e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 4.511748130653359e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+/data/Albus/miniconda3/lib/python3.13/site-packages/sklearn/linear_model/_ridge.py:228: LinAlgWarning: An ill-conditioned matrix detected: slice 0 has rcond = 9.895541097648675e-08.
+  return linalg.solve(A, Xy, assume_a="pos", overwrite_a=True).T
+checkpoint=runs/foundation/sam_med3d_frozen_mlp_best.pt
+wrote=runs/clinical/sam_med3d_frozen_clinical_probe.csv
+{'task': 'clinical_label_3way', 'type': 'classification', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 10.0, 'accuracy': 0.47058823529411764, 'balanced_accuracy': 0.4868672046955245, 'macro_f1': 0.4509157509157509, 'auroc': 0.6999575462312609}
+{'task': 'ad_vs_cn', 'type': 'classification', 'n_train': 332, 'n_val': 69, 'n_test': 59, 'selected_param': 10.0, 'accuracy': 0.8135593220338984, 'balanced_accuracy': 0.8132183908045978, 'macro_f1': 0.813344837503595, 'auroc': 0.8505747126436782}
+{'task': 'pmci_vs_smci', 'type': 'classification', 'n_train': 269, 'n_val': 51, 'n_test': 69, 'selected_param': 0.01, 'accuracy': 0.7681159420289855, 'balanced_accuracy': 0.6963443396226415, 'macro_f1': 0.6877828054298643, 'auroc': 0.7594339622641509}
+{'task': 'adas11', 'type': 'regression', 'n_train': 709, 'n_val': 151, 'n_test': 153, 'selected_param': 3.0, 'mae': 3.8532716933107065, 'rmse': 4.9771912267716045, 'r2': 0.44415342400364755, 'pearson': 0.6766670035126044}
+{'task': 'mmse', 'type': 'regression', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 30.0, 'mae': 1.84983027838414, 'rmse': 2.2609941849077426, 'r2': 0.28095617966745545, 'pearson': 0.5310391758366578}
+{'task': 'ravlt_immediate', 'type': 'regression', 'n_train': 708, 'n_val': 152, 'n_test': 153, 'selected_param': 3.0, 'mae': 9.013250824672724, 'rmse': 10.993474436826162, 'r2': 0.2557707760828827, 'pearson': 0.5200026490225349}
+{'task': 'ldeltotal', 'type': 'regression', 'n_train': 710, 'n_val': 152, 'n_test': 153, 'selected_param': 3.0, 'mae': 3.613116303300546, 'rmse': 4.4170746792693025, 'r2': 0.15329888538494862, 'pearson': 0.42108312955461996}

logs/eval_remap_pet_layer4_cw05_test.log

@@ -0,0 +1,19 @@
+checkpoint=runs/foundation/remap_pet_layer4_cw05_best.pt
+manifest=metadata/splits/test.csv
+samples=153.000000
+mae=0.076581
+rmse=0.097949
+pearson=0.913951
+spearman=0.933835
+top5_high_overlap=0.605229
+top5_low_overlap=0.752941
+pet_to_suvr_recall@1=0.836601
+pet_to_suvr_recall@5=0.993464
+pet_to_suvr_recall@10=1.000000
+pet_to_suvr_mrr=0.901489
+pet_to_suvr_median_rank=1.000000
+suvr_to_pet_recall@1=0.915033
+suvr_to_pet_recall@5=0.993464
+suvr_to_pet_recall@10=0.993464
+suvr_to_pet_mrr=0.949826
+suvr_to_pet_median_rank=1.000000