more yamls

bcnb/er/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - bcnb
+
+task_col: er
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: negative
+  1: positive
+
+sample_col: case_id
+num_samples: 1058

bcnb/her2/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - bcnb
+
+task_col: pr
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: negative
+  1: positive
+
+sample_col: case_id
+num_samples: 1058

bcnb/pr/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - bcnb
+
+task_col: her2
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: negative
+  1: positive
+
+sample_col: case_id
+num_samples: 1058

boehmk_/PFS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - boehmk_
+
+task_col: PFS
+extra_cols:  # Extra columns to copy from raw metadata to split TSVs
+  - PFS_event
+  - PFS_days
+task_type: survival
+metrics:
+  - cindex
+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"
+
+sample_col: case_id
+num_samples: 183

bracs/slidelevel_coarse/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - bracs
+
+task_col: slidelevel_coarse
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: AT
+  1: BT
+  2: MT
+
+sample_col: slide_id
+num_samples: 547

bracs/slidelevel_fine/config.yaml

@@ -0,0 +1,19 @@
+datasets:
+  - bracs
+
+task_col: slidelevel_fine
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: "ADH"
+  1: "DCIS"
+  2: "FEA"
+  3: "IC"
+  4: "N"
+  5: "PB"
+  6: "UDH"
+
+sample_col: slide_id
+num_samples: 547

cptac_brca/PIK3CA_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_brca
+
+task_col: PIK3CA_mutation
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 103

cptac_brca/TP53_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_brca
+
+task_col: TP53_mutation
+extra_cols: []  # Extra columns to copy from raw metadata to split TSVs
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 103

cptac_ccrcc/BAP1_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_ccrcc
+
+task_col: BAP1_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 103

cptac_ccrcc/OS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - cptac_ccrcc
+
+task_col: OS
+extra_cols:
+  - OS_event
+  - OS_days
+task_type: survival
+metrics:
+  - cindex
+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"
+
+sample_col: case_id
+num_samples: 94

cptac_ccrcc/PBRM1_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_ccrcc
+
+task_col: PBRM1_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 103

cptac_coad/KRAS_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_coad
+
+task_col: KRAS_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 94

cptac_coad/TP53_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_coad
+
+task_col: TP53_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 94

cptac_gbm/EGFR_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_gbm
+
+task_col: EGFR_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 99

cptac_gbm/TP53_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_gbm
+
+task_col: TP53_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 99

cptac_hnsc/CASP8_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_hnsc
+
+task_col: CASP8_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 107

cptac_hnsc/OS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - cptac_hnsc
+
+task_col: OS
+extra_cols:
+  - OS_event
+  - OS_days
+task_type: survival
+metrics:
+  - cindex
+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
+
+sample_col: case_id
+num_samples: 102

cptac_lscc/ARID1A_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_lscc
+
+task_col: ARID1A_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 108

cptac_lscc/KEAP1_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_lscc
+
+task_col: KEAP1_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 108

cptac_luad/EGFR_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_luad
+
+task_col: EGFR_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 108

cptac_luad/OS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - cptac_luad
+
+task_col: OS
+extra_cols:
+  - OS_event
+  - OS_days
+task_type: survival
+metrics:
+  - cindex
+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
+
+sample_col: case_id
+num_samples: 105

cptac_luad/STK11_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_luad
+
+task_col: STK11_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 108

cptac_luad/TP53_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_luad
+
+task_col: TP53_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 108

cptac_pda/OS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - cptac_pda
+
+task_col: OS
+extra_cols:
+  - OS_event
+  - OS_days
+task_type: survival
+metrics:
+  - cindex
+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
+
+sample_col: case_id
+num_samples: 97

cptac_pda/SMAD4_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - cptac_pda
+
+task_col: SMAD4_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 105

ebrains/diagnosis/config.yaml

@@ -0,0 +1,42 @@
+datasets:
+  - ebrains
+
+task_col: diagnosis
+extra_cols: []
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: "Glioblastoma, IDH-wildtype"
+  1: "Gliosarcoma"
+  2: "Transitional meningioma"
+  3: "Anaplastic meningioma"
+  4: "Pituitary adenoma"
+  5: "Oligodendroglioma, IDH-mutant and 1p/19q codeleted"
+  6: "Haemangioma"
+  7: "Ganglioglioma"
+  8: "Pilocytic astrocytoma"
+  9: "Schwannoma"
+  10: "Anaplastic oligodendroglioma, IDH-mutant and 1p/19q codeleted"
+  11: "Fibrous meningioma"
+  12: "Anaplastic astrocytoma, IDH-wildtype"
+  13: "Angiomatous meningioma"
+  14: "Haemangioblastoma"
+  15: "Adamantinomatous craniopharyngioma"
+  16: "Anaplastic astrocytoma, IDH-mutant"
+  17: "Glioblastoma, IDH-mutant"
+  18: "Diffuse astrocytoma, IDH-mutant"
+  19: "Ependymoma"
+  20: "Anaplastic ependymoma"
+  21: "Atypical meningioma"
+  22: "Metastatic tumours"
+  23: "Meningothelial meningioma"
+  24: "Langerhans cell histiocytosis"
+  25: "Diffuse large B-cell lymphoma of the CNS"
+  26: "Secretory meningioma"
+  27: "Haemangiopericytoma"
+  28: "Lipoma"
+  29: "Medulloblastoma, non-WNT/non-SHH"
+
+sample_col: slide_id
+num_samples: 2319

ebrains/diagnosis_group/config.yaml

@@ -0,0 +1,24 @@
+datasets:
+  - ebrains
+
+task_col: diagnosis_group
+extra_cols: []
+task_type: classification
+metrics:
+  - bacc
+label_dict:
+  0: "Adult-type diffuse gliomas"
+  1: "Meningiomas"
+  2: "Tumours of the sellar region"
+  3: "Mesenchymal, non-meningothelial tumours involving the CNS"
+  4: "Glioneuronal and neuronal tumours"
+  5: "Circumscribed astrocytic gliomas"
+  6: "Cranial and paraspinal nerve tumours"
+  7: "Paediatric-type diffuse low-grade gliomas "
+  8: "Ependymal Tumours"
+  9: "Metastatic tumours"
+  10: "Haematolymphoid tumours involving the CNS"
+  11: "Embryonal Tumors"
+
+sample_col: slide_id
+num_samples: 2319

imp/grade/config.yaml

@@ -0,0 +1,15 @@
+datasets:
+  - imp
+
+task_col: grade
+extra_cols: []
+task_type: classification
+metrics:
+  - weighted_kappa
+label_dict:
+  0: "Non-neoplastic"
+  1: "Low-grade lesions"
+  2: "High-grade lesions"
+
+sample_col: slide_id
+num_samples: 5333

mbc_/OS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - mbc_
+
+task_col: OS
+extra_cols:
+  - OS_event
+  - OS_days
+task_type: survival
+metrics:
+  - cindex
+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"
+
+sample_col: case_id
+num_samples: 75

mbc_/Recist/config.yaml

@@ -0,0 +1,16 @@
+datasets:
+  - mbc_
+
+task_col: Recist
+extra_cols: []
+task_type: classification
+metrics:
+  - weighted_kappa
+label_dict:
+  0: SD
+  1: PD
+  2: PR
+  3: CR
+
+sample_col: case_id
+num_samples: 76

mut-het-rcc/BAP1_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - mut-het-rcc
+
+task_col: BAP1_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 1291

mut-het-rcc/PBRM1_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - mut-het-rcc
+
+task_col: PBRM1_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 1291

mut-het-rcc/SETD2_mutation/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - mut-het-rcc
+
+task_col: SETD2_mutation
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 1291

nadt/response/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - nadt
+
+task_col: response
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: negative
+  1: positive
+
+sample_col: case_id
+num_samples: 36

natbrca/lymphovascular_invasion/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - natbrca
+
+task_col: lymphovascular_invasion
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: negative
+  1: positive
+
+sample_col: slide_id
+num_samples: 53

ovarian/response/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - ovarian
+
+task_col: response
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: negative
+  1: positive
+
+sample_col: case_id
+num_samples: 36

panda/isup_grade/config.yaml

@@ -0,0 +1,18 @@
+datasets:
+  - panda
+
+task_col: isup_grade
+extra_cols: []
+task_type: classification
+metrics:
+  - weighted_kappa
+label_dict:
+  0: grade_0
+  1: grade_1
+  2: grade_2
+  3: grade_3
+  4: grade_4
+  5: grade_5
+
+sample_col: slide_id
+num_samples: 9555

sr386_/OS/config.yaml

@@ -0,0 +1,22 @@
+datasets:
+  - sr386_
+
+task_col: OS
+extra_cols:
+  - OS_event
+  - OS_days
+task_type: survival
+metrics:
+  - cindex
+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"
+
+sample_col: case_id
+num_samples: 144

sr386_/braf_mutant_binary/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - sr386_
+
+task_col: braf_mutant_binary
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 388

sr386_/died_within_5_years/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - sr386_
+
+task_col: died_within_5_years
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: no
+  1: yes
+
+sample_col: case_id
+num_samples: 387

sr386_/mmr_loss_binary/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - sr386_
+
+task_col: mmr_loss_binary
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 389

sr386_/ras_mutant_binary/config.yaml

@@ -0,0 +1,14 @@
+datasets:
+  - sr386_
+
+task_col: ras_mutant_binary
+extra_cols: []
+task_type: classification
+metrics:
+  - macro-ovr-auc
+label_dict:
+  0: wildtype
+  1: mutant
+
+sample_col: case_id
+num_samples: 389