add new task configs

available_splits.yaml

@@ -1,62 +1,128 @@
+bc_therapy:
+- er_status
+- grade
+- her2_status
+- residual_cancer_burden
 bcnb:
-    - er
-    - pr
-    - her2
-mut-het-rcc:
-    - BAP1_mutation
-    - PBRM1_mutation
-    - SETD2_mutation
-imp:
-    - grade
-panda:
-    - isup_grade
+- er
+- her2
+- pr
+boehmk_:
+- PFS
+bracs:
+- slidelevel_coarse
+- slidelevel_fine
+cervical_subtype:
+- subtype
+cptac_all:
+- organ
 cptac_brca:
-    - PIK3CA_mutation
-    - TP53_mutation
+- Immune_class
+- PIK3CA_mutation
+- TP53_mutation
 cptac_ccrcc:
-    - BAP1_mutation
-    - PBRM1_mutation
-    - OS
+- BAP1_mutation
+- Immune_class
+- OS
+- PBRM1_mutation
+- VHL_mutation
+cptac_ccrcc_dhmc:
+- OncoTreeCode
 cptac_coad:
-    - KRAS_mutation
-    - TP53_mutation
+- ACVR2A_mutation
+- APC_mutation
+- ARID1A_mutation
+- Immune_class
+- KRAS_mutation
+- MSI_H
+- PIK3CA_mutation
+- SETD1B_mutation
+- TP53_mutation
 cptac_gbm:
-    - EGFR_mutation
-    - TP53_mutation
+- EGFR_mutation
+- Immune_class
+- TP53_mutation
 cptac_hnsc:
-    - CASP8_mutation
-    - OS
+- CASP8_mutation
+- Histologic_Grade
+- Immune_class
+- OS
 cptac_lscc:
-    - KEAP1_mutation
-    - ARID1A_mutation
+- ARID1A_mutation
+- Histologic_Grade
+- Immune_class
+- KEAP1_mutation
 cptac_luad:
-    - EGFR_mutation
-    - STK11_mutation
-    - TP53_mutation
-    - OS
+- EGFR_mutation
+- Immune_class
+- KRAS_mutation
+- OS
+- STK11_mutation
+- TP53_mutation
+cptac_lung:
+- subtype
+cptac_ov:
+- Immune_class
 cptac_pda:
-    - SMAD4_mutation
-    - OS
-bracs:
-    - slidelevel_fine
-    - slidelevel_coarse
+- Immune_class
+- OS
+- SMAD4_mutation
+cptac_ucec:
+- CTNNB1_mutation
+- Immune_class
+- PTEN_mutation
+crc_outcomes:
+- OS_VALENTINO
+- PFS_VALENTINO
+- braf_grading
+- braf_lymphovas_invasion
+- braf_mmr
+- braf_synapto
+- braf_tils
+- valentino_molecular_subtype
+- valentino_msi
+dhmc_luad:
+- label
 ebrains:
-    - diagnosis
-    - diagnosis_group
-ovarian:
-    - response
+- diagnosis
+- diagnosis_group
+- idh_status
+hancook:
+- OS_treatment_rdc
+- grading_SCC_Conventional_Keratinizing
+- grading_SCC_Conventional_NonKeratinizing
+- lymphovascular_invasion_L
+- perineural_invasion_Pn
+- primarily_metastasis
+- primary_tumor_site
+- vascular_invasion_V
+herroi:
+- response
+imp:
+- grade
+mbc_:
+- OS
+- Recist
+mut-het-rcc:
+- BAP1_mutation
+- PBRM1_mutation
+- SETD2_mutation
 nadt:
-    - response
+- response
 natbrca:
-    - lymphovascular_invasion
+- lymphovascular_invasion
+ovarian:
+- response
+panda:
+- isup_grade
 sr386_:
-    - braf_mutant_binary
-    - ras_mutant_binary
-    - mmr_loss_binary
-    - died_within_5_years
-    - OS
-mbc_:
-    - Recist
-    - OS
-boehmk_:
-    - PFS
+- OS
+- braf_mutant_binary
+- died_within_5_years
+- mmr_loss_binary
+- ras_mutant_binary
+ucla_lung:
+- progression_regression
+visiomel:
+- relapse_noprev_melanoma
+- relapse_overall

bc_therapy/er_status/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- bc_therapy
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 166
+sample_col: case_id
+task_col: er_status
+task_type: classification

bc_therapy/grade/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- bc_therapy
+extra_cols: []
+label_dict:
+  0: 2
+  1: 3
+metrics:
+- weighted_kappa
+num_samples: 166
+sample_col: case_id
+task_col: grade
+task_type: classification

bc_therapy/her2_status/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- bc_therapy
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 166
+sample_col: case_id
+task_col: her2_status
+task_type: classification

bc_therapy/residual_cancer_burden/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+- bc_therapy
+extra_cols: []
+label_dict:
+  0: pCR
+  1: RCB-I
+  2: RCB-II
+  3: RCB-III
+metrics:
+- bacc
+num_samples: 159
+sample_col: case_id
+task_col: residual_cancer_burden
+task_type: classification

bracs/slidelevel_coarse/config.yaml

@@ -7,9 +7,9 @@ task_type: classification
 metrics:
   - bacc
 label_dict:
-  0: AT
-  1: BT
-  2: MT
+  0: Atypical tumor
+  1: Benign tumor
+  2: Malignant tumor
 
 sample_col: slide_id
 num_samples: 547

bracs/slidelevel_fine/config.yaml

@@ -7,13 +7,13 @@ task_type: classification
 metrics:
   - bacc
 label_dict:
-  0: "ADH"
-  1: "DCIS"
-  2: "FEA"
-  3: "IC"
-  4: "N"
-  5: "PB"
-  6: "UDH"
+  0: Atypical ductal hyperplasia
+  1: Ductal carcinoma in situ
+  2: Flat epithelial atypia
+  3: Invasive carcinoma
+  4: Normal
+  5: Pathological benign
+  6: Usual ductal hyperplasia
 
 sample_col: slide_id
-num_samples: 547
+num_samples: 547

cervical_subtype/subtype/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+- cervical_subtype
+extra_cols: []
+label_dict:
+  0: Non-neoplastic (NNeo)
+  1: Low-grade squamous intraepithelial lesion (LSIL)
+  2: High-grade squamous intraepithelial lesion (HSIL)
+  3: Non-representative (other)
+metrics:
+- macro-ovr-auc
+num_samples: 599
+sample_col: case_id # the task is slide level, but for easier access using case_id
+task_col: subtype
+task_type: classification

cptac_all/organ/config.yaml

@@ -0,0 +1,31 @@
+datasets:
+  - cptac_brca
+  - cptac_ccrcc
+  - cptac_coad
+  - cptac_gbm
+  - cptac_hnsc
+  - cptac_lscc
+  - cptac_luad
+  - cptac_pda
+  - cptac_ov
+  - cptac_ucec
+
+task_col: organ
+extra_cols: [] # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: Breast cancer (BRCA)
+  1: Clear cell renal cell carcinoma (CCRCC)
+  2: Colon adenocarcinoma (COAD)
+  3: Glioblastoma (GBM)
+  4: Head and neck squamous cell carcinoma (HNSC)
+  5: Lung squamous cell carcinoma (LSCC)
+  6: Lung adenocarcinoma (LUAD)
+  7: Pancreatic ductal adenocarcinoma (PDA)
+  8: Ovarian cancer (OV)
+  9: Uterine corpus endometrial carcinoma (UCEC)
+
+sample_col: slide_id
+num_samples: 2154

cptac_brca/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_brca
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 103

cptac_ccrcc/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_ccrcc
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 103

cptac_ccrcc/VHL_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_ccrcc
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 103
+sample_col: case_id
+task_col: VHL_mutation
+task_type: classification

cptac_ccrcc_dhmc/OncoTreeCode/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_ccrcc_dhmc
+
+task_col: OncoTreeCode
+extra_cols: []
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: Clear cell renal cell carcinoma (CCRCC)
+  1: Papillary renal cell carcinoma (PRCC)
+  2: Chromophobe renal cell carcinoma (CHRCC)
+
+sample_col: slide_id
+num_samples: 871

cptac_coad/ACVR2A_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_coad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 94
+sample_col: case_id
+task_col: ACVR2A_mutation
+task_type: classification

cptac_coad/APC_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_coad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 94
+sample_col: case_id
+task_col: APC_mutation
+task_type: classification

cptac_coad/ARID1A_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_coad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 94
+sample_col: case_id
+task_col: ARID1A_mutation
+task_type: classification

cptac_coad/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_coad
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 94

cptac_coad/MSI_H/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_coad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 93
+sample_col: case_id
+task_col: MSI_H
+task_type: classification

cptac_coad/PIK3CA_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_coad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 94
+sample_col: case_id
+task_col: PIK3CA_mutation
+task_type: classification

cptac_coad/SETD1B_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_coad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 94
+sample_col: case_id
+task_col: SETD1B_mutation
+task_type: classification

cptac_gbm/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_gbm
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 99

cptac_hnsc/Histologic_Grade/config.yaml

@@ -0,0 +1,13 @@
+datasets:
+- cptac_hnsc
+extra_cols: []
+label_dict:
+  0: 1
+  1: 2
+  2: 3
+metrics:
+- weighted_kappa
+num_samples: 107
+sample_col: case_id
+task_col: Histologic_Grade
+task_type: classification

cptac_hnsc/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_hnsc
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 107

cptac_lscc/Histologic_Grade/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_lscc
+extra_cols: []
+label_dict:
+  0: Well differentiated
+  1: Moderately differentiated
+metrics:
+- weighted_kappa
+num_samples: 104
+sample_col: case_id
+task_col: Histologic_Grade
+task_type: classification

cptac_lscc/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_lscc
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 108

cptac_luad/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_luad
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 108

cptac_luad/KRAS_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_luad
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 102
+sample_col: case_id
+task_col: KRAS_mutation
+task_type: classification

cptac_lung/subtype/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_lung
+extra_cols: []
+label_dict:
+  0: Lung adenocarcinoma (LUAD)
+  1: Lung squamous cell carcinoma (LSCC)
+metrics:
+- macro-ovr-auc
+num_samples: 206
+sample_col: case_id
+task_col: subtype
+task_type: classification

cptac_ov/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_ov
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 51

cptac_pda/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_pda
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 105

cptac_ucec/CTNNB1_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_ucec
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 93
+sample_col: case_id
+task_col: CTNNB1_mutation
+task_type: classification

cptac_ucec/Immune_class/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - cptac_ucec
+
+task_col: Immune_class
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: low
+  1: medium
+  2: high
+
+sample_col: case_id
+num_samples: 94

cptac_ucec/PTEN_mutation/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- cptac_ucec
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 93
+sample_col: case_id
+task_col: PTEN_mutation
+task_type: classification

crc_outcomes/OS_VALENTINO/config.yaml

@@ -0,0 +1,23 @@
+datasets:
+- crc_outcomes
+
+extra_cols:
+- OS_VALENTINO_event
+- OS_VALENTINO_days
+
+label_dict:
+  0: Quartile 1, Event 0
+  1: Quartile 2, Event 0
+  2: Quartile 3, Event 0
+  3: Quartile 4, Event 0
+  4: Quartile 1, Event 1
+  5: Quartile 2, Event 1
+  6: Quartile 3, Event 1
+  7: Quartile 4, Event 1
+  
+metrics:
+- cindex
+num_samples: 170
+sample_col: case_id
+task_col: OS_VALENTINO
+task_type: survival

crc_outcomes/PFS_VALENTINO/config.yaml

@@ -0,0 +1,23 @@
+datasets:
+- crc_outcomes
+
+extra_cols:
+- PFS_VALENTINO_event
+- PFS_VALENTINO_days
+
+label_dict:
+  0: Quartile 1, Event 0
+  1: Quartile 2, Event 0
+  2: Quartile 3, Event 0
+  3: Quartile 4, Event 0
+  4: Quartile 1, Event 1
+  5: Quartile 2, Event 1
+  6: Quartile 3, Event 1
+  7: Quartile 4, Event 1
+  
+metrics:
+- cindex
+num_samples: 170
+sample_col: case_id
+task_col: PFS_VALENTINO
+task_type: survival

crc_outcomes/braf_grading/config.yaml

@@ -0,0 +1,13 @@
+datasets:
+- crc_outcomes
+extra_cols: []
+label_dict:
+  0: Low
+  1: Medium
+  2: High
+metrics:
+- weighted_kappa
+num_samples: 134
+sample_col: case_id
+task_col: braf_grading
+task_type: classification

crc_outcomes/braf_lymphovas_invasion/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- crc_outcomes
+extra_cols: []
+label_dict:
+  0: low grade
+  1: high grade
+metrics:
+- macro-ovr-auc
+num_samples: 111
+sample_col: case_id
+task_col: braf_lymphovas_invasion
+task_type: classification

crc_outcomes/braf_mmr/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- crc_outcomes
+extra_cols: []
+label_dict:
+  0: low grade
+  1: high grade
+metrics:
+- macro-ovr-auc
+num_samples: 135
+sample_col: case_id
+task_col: braf_mmr
+task_type: classification

crc_outcomes/braf_synapto/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- crc_outcomes
+extra_cols: []
+label_dict:
+  0: low grade
+  1: high grade
+metrics:
+- macro-ovr-auc
+num_samples: 135
+sample_col: case_id
+task_col: braf_synapto
+task_type: classification

crc_outcomes/braf_tils/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- crc_outcomes
+extra_cols: []
+label_dict:
+  0: low grade
+  1: high grade
+metrics:
+- macro-ovr-auc
+num_samples: 135
+sample_col: case_id
+task_col: braf_tils
+task_type: classification

crc_outcomes/valentino_molecular_subtype/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- crc_outcome
+extra_cols: []
+label_dict:
+  0: no RAS/BRAF
+  1: RAS/BRAF
+metrics:
+- macro-ovr-auc
+num_samples: 96
+sample_col: case_id
+task_col: valentino_molecular_subtype
+task_type: classification

crc_outcomes/valentino_msi/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- crc_outcome
+extra_cols: []
+label_dict:
+  0: No MSI
+  1: MSI
+metrics:
+- macro-ovr-auc
+num_samples: 136
+sample_col: case_id
+task_col: valentino_msi
+task_type: classification

dhmc_luad/label/config.yaml

@@ -0,0 +1,17 @@
+datasets:
+  - dhmc_luad
+
+task_col: label
+extra_cols: []
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: Acinar
+  1: Lepidic
+  2: Micropapillary
+  3: Papillary
+  4: Solid
+
+sample_col: slide_id
+num_samples: 143

ebrains/diagnosis_group/config.yaml

@@ -15,10 +15,10 @@ label_dict:
   5: "Circumscribed astrocytic gliomas"
   6: "Cranial and paraspinal nerve tumours"
   7: "Paediatric-type diffuse low-grade gliomas "
-  8: "Ependymal Tumours"
+  8: "Ependymal tumours"
   9: "Metastatic tumours"
   10: "Haematolymphoid tumours involving the CNS"
-  11: "Embryonal Tumors"
+  11: "Embryonal tumours"
 
 sample_col: slide_id
 num_samples: 2319

ebrains/idh_status/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - ebrains
+
+task_col: idh_status
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: slide_id
+num_samples: 848

hancook/OS_treatment_rdc/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+- hancook
+
+extra_cols:
+- OS_treatment_rdc_event
+- OS_treatment_rdc_days
+
+label_dict:
+  0: Quartile 1, Event 0
+  1: Quartile 2, Event 0
+  2: Quartile 3, Event 0
+  3: Quartile 4, Event 0
+  4: Quartile 1, Event 1
+  5: Quartile 2, Event 1
+  6: Quartile 3, Event 1
+  7: Quartile 4, Event 1
+metrics:
+- cindex
+num_samples: 203
+sample_col: case_id
+task_col: OS_treatment_rdc
+task_type: survival

hancook/grading_SCC_Conventional_Keratinizing/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- hancook
+extra_cols: []
+label_dict:
+  0: 2
+  1: 3
+metrics:
+- weighted_kappa
+num_samples: 383
+sample_col: case_id
+task_col: grading_SCC_Conventional_Keratinizing
+task_type: classification

hancook/grading_SCC_Conventional_NonKeratinizing/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- hancook
+extra_cols: []
+label_dict:
+  0: 2
+  1: 3
+metrics:
+- weighted_kappa
+num_samples: 74
+sample_col: case_id
+task_col: grading_SCC_Conventional_NonKeratinizing
+task_type: classification

hancook/lymphovascular_invasion_L/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- hancook
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 697
+sample_col: case_id
+task_col: lymphovascular_invasion_L
+task_type: classification

hancook/perineural_invasion_Pn/config.yaml

@@ -0,0 +1,12 @@
+datasets:
+- hancook
+extra_cols: []
+label_dict:
+  0: negative
+  1: positive
+metrics:
+- macro-ovr-auc
+num_samples: 697
+sample_col: case_id
+task_col: perineural_invasion_Pn
+task_type: classification