Add files using upload-large-folder tool

.gitattributes

@@ -68,3 +68,7 @@ Helios/_DEV3/demo_data/Vidprom_filtered_extended.txt filter=lfs diff=lfs merge=l
 Helios/checkpoints/Helios-Base/tokenizer/tokenizer.json filter=lfs diff=lfs merge=lfs -text
 Helios/checkpoints/Helios-Distilled/tokenizer/tokenizer.json filter=lfs diff=lfs merge=lfs -text
 Helios/checkpoints/Helios-Mid/tokenizer/tokenizer.json filter=lfs diff=lfs merge=lfs -text
+CT/lung/paper.pdf filter=lfs diff=lfs merge=lfs -text
+CT/lung2/参考论文.pdf filter=lfs diff=lfs merge=lfs -text
+CT/liver/logs/download_msd_liver.log filter=lfs diff=lfs merge=lfs -text
+CT/liver/logs/download_waw_tace.log filter=lfs diff=lfs merge=lfs -text

CT/liver/configs/benchmark/densenet121_ct_only.yaml

@@ -0,0 +1,50 @@
+stage: waw_deep_outcome
+root: .
+seed: 2026
+device: auto
+amp: true
+epochs: 60
+output_dir: experiments/benchmark/densenet121_ct_only/checkpoints
+result_dir: experiments/benchmark/densenet121_ct_only
+
+data:
+  manifest: manifests/waw_tace_training_manifest.csv
+  val_fraction: 0.2
+  stratify_column: label_progression
+  patch_shape: [64, 96, 96]
+  foreground_prob: 0.9
+  survival_bins_days: [180, 365, 540, 730, 1095]
+
+loader:
+  batch_size: 1
+  num_workers: 2
+  persistent_workers: false
+
+model:
+  architecture: densenet121
+  in_channels: 4
+  feature_dim: 256
+  clinical_dim: 0
+  num_response_classes: 3
+  survival_bins: 5
+  dropout: 0.2
+
+optimizer:
+  lr: 0.0002
+  weight_decay: 0.0001
+  eta_min: 0.000001
+
+loss:
+  lambda_response: 1.0
+  lambda_progression: 1.0
+  lambda_survival: 0.5
+  lambda_brier: 0.05
+  response_class_weights: [1.0, 3.5, 0.6]
+  progression_pos_weight: 3.0
+
+selection:
+  metrics:
+    progression_auc: 0.45
+    response_acc: 0.25
+    pfs_cindex: 0.15
+    os_cindex: 0.15

CT/liver/configs/benchmark/full_multitask_clean.yaml

@@ -0,0 +1,86 @@
+stage: waw_multitask
+root: .
+seed: 2026
+device: auto
+amp: true
+epochs: 80
+output_dir: experiments/benchmark/full_multitask/checkpoints
+result_dir: experiments/benchmark/full_multitask
+
+data:
+  manifest: manifests/waw_tace_training_manifest.csv
+  val_fraction: 0.2
+  stratify_column: label_progression
+  patch_shape: [64, 96, 96]
+  foreground_prob: 0.9
+  survival_bins_days: [180, 365, 540, 730, 1095]
+  clinical_csv: data/processed/waw_tace/clinical.csv
+  clinical_columns:
+    - age
+    - gender_woman
+    - etiology_mixed
+    - etiology_HCV
+    - etiology_HBV
+    - etiology_alcoholic
+    - etiology_NASH
+    - etiology_cryptogenic
+    - lesions_number
+    - lesion1_localisation
+    - lesion1_diameter
+    - lesion1_LIRADS
+    - lesion2_localisation
+    - lesion2_diameter
+    - lesion2_LIRADS
+    - lesion3_localisation
+    - lesion3_diameter
+    - lesion3_LIRADS
+    - biopsy
+    - lab_albumin
+    - lab_creatinine
+    - lab_bilirubin
+    - lab_afp
+    - lab_inr
+    - lab_alt
+    - cps
+    - bclc
+    - hap_score
+    - mhap_2
+    - albi_tae
+
+loader:
+  batch_size: 1
+  num_workers: 2
+  persistent_workers: false
+
+model:
+  init_filters: 32
+  dropout: 0.2
+  num_seg_classes: 3
+  num_response_classes: 3
+  survival_bins: 5
+  pretrained_checkpoint: experiments/checkpoints/msd_liver_seg/best.pt
+
+optimizer:
+  lr: 0.0002
+  weight_decay: 0.0001
+  eta_min: 0.000001
+
+loss:
+  lambda_seg: 1.0
+  lambda_cls: 1.0
+  lambda_surv: 0.5
+  lambda_util: 0.2
+  lambda_cal: 0.05
+  seg_class_weights: [0.1, 1.0, 8.0]
+  response_class_weights: [1.0, 3.5, 0.6]
+  progression_pos_weight: 3.0
+  seg_include_background: true
+  seg_lambda_dice: 1.0
+  seg_lambda_ce: 1.0
+
+selection:
+  metrics:
+    dice_class_1: 0.2
+    dice_class_2: 0.45
+    progression_auc: 0.25
+    response_acc: 0.1

CT/liver/configs/benchmark/full_multitask_improved.yaml

@@ -0,0 +1,101 @@
+stage: waw_multitask
+root: .
+seed: 2026
+device: auto
+amp: true
+epochs: 80
+output_dir: experiments/benchmark/full_multitask_improved/checkpoints
+result_dir: experiments/benchmark/full_multitask_improved
+
+data:
+  manifest: manifests/waw_tace_training_manifest.csv
+  val_fraction: 0.2
+  stratify_column: label_progression
+  patch_shape: [64, 96, 96]
+  foreground_prob: 0.95
+  tumor_focus_sampling: true
+  small_tumor_voxel_threshold: 10000
+  small_tumor_weight: 2.5
+  hard_cases_csv: experiments/benchmark/full_multitask/case_metrics.csv
+  num_hard_cases: 24
+  hard_case_weight: 3.0
+  phase_dropout_prob: 0.15
+  single_phase_prob: 0.20
+  survival_bins_days: [180, 365, 540, 730, 1095]
+  clinical_csv: data/processed/waw_tace/clinical.csv
+  clinical_columns:
+    - age
+    - gender_woman
+    - etiology_mixed
+    - etiology_HCV
+    - etiology_HBV
+    - etiology_alcoholic
+    - etiology_NASH
+    - etiology_cryptogenic
+    - lesions_number
+    - lesion1_localisation
+    - lesion1_diameter
+    - lesion1_LIRADS
+    - lesion2_localisation
+    - lesion2_diameter
+    - lesion2_LIRADS
+    - lesion3_localisation
+    - lesion3_diameter
+    - lesion3_LIRADS
+    - biopsy
+    - lab_albumin
+    - lab_creatinine
+    - lab_bilirubin
+    - lab_afp
+    - lab_inr
+    - lab_alt
+    - cps
+    - bclc
+    - hap_score
+    - mhap_2
+    - albi_tae
+
+loader:
+  batch_size: 1
+  num_workers: 2
+  persistent_workers: false
+  weighted_sampling: true
+
+model:
+  init_filters: 32
+  dropout: 0.2
+  num_seg_classes: 3
+  num_response_classes: 3
+  survival_bins: 5
+  pretrained_checkpoint: experiments/checkpoints/msd_liver_seg/best.pt
+
+optimizer:
+  lr: 0.0002
+  weight_decay: 0.0001
+  eta_min: 0.000001
+
+loss:
+  lambda_seg: 1.0
+  lambda_cls: 1.15
+  lambda_surv: 0.6
+  lambda_util: 0.04
+  lambda_cal: 0.05
+  utility_balance_weight: 0.5
+  seg_class_weights: [0.05, 1.0, 12.0]
+  response_class_weights: [1.0, 3.5, 0.6]
+  progression_pos_weight: 3.0
+  seg_include_background: true
+  seg_lambda_dice: 1.0
+  seg_lambda_ce: 0.7
+  seg_tversky_alpha: 0.25
+  seg_tversky_beta: 0.75
+  seg_lambda_tversky: 0.6
+  seg_focal_gamma: 2.0
+  seg_lambda_focal: 0.25
+
+selection:
+  metrics:
+    dice_class_1: 0.15
+    dice_class_2: 0.55
+    progression_auc: 0.2
+    response_acc: 0.1

CT/liver/configs/benchmark/full_multitask_improved_v2.yaml

@@ -0,0 +1,101 @@
+stage: waw_multitask
+root: .
+seed: 2026
+device: auto
+amp: true
+epochs: 80
+output_dir: experiments/benchmark/full_multitask_improved_v2/checkpoints
+result_dir: experiments/benchmark/full_multitask_improved_v2
+
+data:
+  manifest: manifests/waw_tace_training_manifest.csv
+  val_fraction: 0.2
+  stratify_column: label_progression
+  patch_shape: [64, 96, 96]
+  foreground_prob: 0.9
+  tumor_focus_sampling: true
+  small_tumor_voxel_threshold: 10000
+  small_tumor_weight: 1.5
+  hard_cases_csv: experiments/benchmark/full_multitask/case_metrics.csv
+  num_hard_cases: 16
+  hard_case_weight: 1.5
+  phase_dropout_prob: 0.05
+  single_phase_prob: 0.05
+  survival_bins_days: [180, 365, 540, 730, 1095]
+  clinical_csv: data/processed/waw_tace/clinical.csv
+  clinical_columns:
+    - age
+    - gender_woman
+    - etiology_mixed
+    - etiology_HCV
+    - etiology_HBV
+    - etiology_alcoholic
+    - etiology_NASH
+    - etiology_cryptogenic
+    - lesions_number
+    - lesion1_localisation
+    - lesion1_diameter
+    - lesion1_LIRADS
+    - lesion2_localisation
+    - lesion2_diameter
+    - lesion2_LIRADS
+    - lesion3_localisation
+    - lesion3_diameter
+    - lesion3_LIRADS
+    - biopsy
+    - lab_albumin
+    - lab_creatinine
+    - lab_bilirubin
+    - lab_afp
+    - lab_inr
+    - lab_alt
+    - cps
+    - bclc
+    - hap_score
+    - mhap_2
+    - albi_tae
+
+loader:
+  batch_size: 1
+  num_workers: 2
+  persistent_workers: false
+  weighted_sampling: true
+
+model:
+  init_filters: 32
+  dropout: 0.2
+  num_seg_classes: 3
+  num_response_classes: 3
+  survival_bins: 5
+  pretrained_checkpoint: experiments/benchmark/full_multitask/checkpoints/best.pt
+
+optimizer:
+  lr: 0.00008
+  weight_decay: 0.0001
+  eta_min: 0.000001
+
+loss:
+  lambda_seg: 1.0
+  lambda_cls: 1.0
+  lambda_surv: 0.5
+  lambda_util: 0.02
+  lambda_cal: 0.05
+  utility_balance_weight: 0.25
+  seg_class_weights: [0.1, 1.0, 8.0]
+  response_class_weights: [1.0, 3.5, 0.6]
+  progression_pos_weight: 3.0
+  seg_include_background: true
+  seg_lambda_dice: 1.0
+  seg_lambda_ce: 0.8
+  seg_tversky_alpha: 0.3
+  seg_tversky_beta: 0.7
+  seg_lambda_tversky: 0.25
+  seg_focal_gamma: 2.0
+  seg_lambda_focal: 0.10
+
+selection:
+  metrics:
+    dice_class_1: 0.15
+    dice_class_2: 0.55
+    progression_auc: 0.2
+    response_acc: 0.1

CT/liver/configs/benchmark/resnet18_ct_only.yaml

@@ -0,0 +1,50 @@
+stage: waw_deep_outcome
+root: .
+seed: 2026
+device: auto
+amp: true
+epochs: 60
+output_dir: experiments/benchmark/resnet18_ct_only/checkpoints
+result_dir: experiments/benchmark/resnet18_ct_only
+
+data:
+  manifest: manifests/waw_tace_training_manifest.csv
+  val_fraction: 0.2
+  stratify_column: label_progression
+  patch_shape: [64, 96, 96]
+  foreground_prob: 0.9
+  survival_bins_days: [180, 365, 540, 730, 1095]
+
+loader:
+  batch_size: 1
+  num_workers: 2
+  persistent_workers: false
+
+model:
+  architecture: resnet18
+  in_channels: 4
+  feature_dim: 256
+  clinical_dim: 0
+  num_response_classes: 3
+  survival_bins: 5
+  dropout: 0.2
+
+optimizer:
+  lr: 0.0002
+  weight_decay: 0.0001
+  eta_min: 0.000001
+
+loss:
+  lambda_response: 1.0
+  lambda_progression: 1.0
+  lambda_survival: 0.5
+  lambda_brier: 0.05
+  response_class_weights: [1.0, 3.5, 0.6]
+  progression_pos_weight: 3.0
+
+selection:
+  metrics:
+    progression_auc: 0.45
+    response_acc: 0.25
+    pfs_cindex: 0.15
+    os_cindex: 0.15

CT/liver/configs/benchmark/waw_seg_only.yaml

@@ -0,0 +1,50 @@
+stage: waw_multitask
+root: .
+seed: 2026
+device: auto
+amp: true
+epochs: 60
+output_dir: experiments/benchmark/segresnet_seg_only/checkpoints
+result_dir: experiments/benchmark/segresnet_seg_only
+
+data:
+  manifest: manifests/waw_tace_training_manifest.csv
+  val_fraction: 0.2
+  stratify_column: label_progression
+  patch_shape: [64, 96, 96]
+  foreground_prob: 0.9
+  survival_bins_days: [180, 365, 540, 730, 1095]
+
+loader:
+  batch_size: 1
+  num_workers: 2
+  persistent_workers: false
+
+model:
+  init_filters: 32
+  dropout: 0.2
+  num_seg_classes: 3
+  num_response_classes: 3
+  survival_bins: 5
+  pretrained_checkpoint: experiments/checkpoints/msd_liver_seg/best.pt
+
+optimizer:
+  lr: 0.0002
+  weight_decay: 0.0001
+  eta_min: 0.000001
+
+loss:
+  lambda_seg: 1.0
+  lambda_cls: 0.0
+  lambda_surv: 0.0
+  lambda_util: 0.0
+  lambda_cal: 0.0
+  seg_class_weights: [0.1, 1.0, 8.0]
+  seg_include_background: true
+  seg_lambda_dice: 1.0
+  seg_lambda_ce: 1.0
+
+selection:
+  metrics:
+    dice_class_1: 0.25
+    dice_class_2: 0.75

CT/liver/data/extracted/msd_liver/Task03_Liver/dataset.json

@@ -0,0 +1,21 @@
+{ 
+ "name": "Liver", 
+ "description": "Liver, and cancer segmentation",
+"reference": "xxxx",
+"licence":"CC-BY-SA 4.0",
+"release":"1.0 04/05/2018",
+"tensorImageSize": "3D",
+"modality": { 
+   "0": "CT"
+ }, 
+ 
+ "labels": { 
+   "0": "background", 
+   "1": "liver", 
+   "2": "cancer"
+ }, 
+ "numTraining": 131, 
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