diff --git a/available_splits.yaml b/available_splits.yaml index cfbb091d369980c808c3ef11b46855cfcc80dc4c..d9b37d0a1d0e70b4d3f0b5b31a36d1badb724576 100644 --- a/available_splits.yaml +++ b/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 diff --git a/bc_therapy/er_status/config.yaml b/bc_therapy/er_status/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..0d6a39dd17186dd98fc509918ac0e947c9d6a2f0 --- /dev/null +++ b/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 diff --git a/bc_therapy/grade/config.yaml b/bc_therapy/grade/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9b26af27ec65a2bd81ba9f69c1d396e8d423f875 --- /dev/null +++ b/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 diff --git a/bc_therapy/her2_status/config.yaml b/bc_therapy/her2_status/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2ecdd5bfa97fe641751c02849e488272d941b13d --- /dev/null +++ b/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 diff --git a/bc_therapy/residual_cancer_burden/config.yaml b/bc_therapy/residual_cancer_burden/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..133f271d7288633f3524626b508caef65bfd623c --- /dev/null +++ b/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 diff --git a/bracs/slidelevel_coarse/config.yaml b/bracs/slidelevel_coarse/config.yaml index f288220c4a8f1afd276918c0fb1ea455ff057c7c..4cd5e5be263310dbdaf332d02488ce7cc3c44a22 100644 --- a/bracs/slidelevel_coarse/config.yaml +++ b/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 diff --git a/bracs/slidelevel_fine/config.yaml b/bracs/slidelevel_fine/config.yaml index a5b762b683a95fe2cdcbad353baf5f0f172e1881..ae1ebfd1e7d62964fe33fd1ab14d91ae0067923d 100644 --- a/bracs/slidelevel_fine/config.yaml +++ b/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 \ No newline at end of file diff --git a/cervical_subtype/subtype/config.yaml b/cervical_subtype/subtype/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..dba19b94c387cdfe9f102d7e404b556cee12dfdf --- /dev/null +++ b/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 diff --git a/cptac_all/organ/config.yaml b/cptac_all/organ/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..767f47df25c076b1d5faf73d32d7f3b585b70ba0 --- /dev/null +++ b/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 diff --git a/cptac_brca/Immune_class/config.yaml b/cptac_brca/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ab23641d00aa3318f5feebfe4794057231bdf4d0 --- /dev/null +++ b/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 diff --git a/cptac_ccrcc/Immune_class/config.yaml b/cptac_ccrcc/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a720060f3d4bd86c65024f9be3bde8c1f26238a9 --- /dev/null +++ b/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 diff --git a/cptac_ccrcc/VHL_mutation/config.yaml b/cptac_ccrcc/VHL_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9aad05a1f7011847f699e302cc1f86f8337c358b --- /dev/null +++ b/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 diff --git a/cptac_ccrcc_dhmc/OncoTreeCode/config.yaml b/cptac_ccrcc_dhmc/OncoTreeCode/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..342bdf818c2efbe2f2660bbdee676d1955795356 --- /dev/null +++ b/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 diff --git a/cptac_coad/ACVR2A_mutation/config.yaml b/cptac_coad/ACVR2A_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..afb3183c328e18035ba87b7853241cd93ec1c790 --- /dev/null +++ b/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 diff --git a/cptac_coad/APC_mutation/config.yaml b/cptac_coad/APC_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..8d4439f0af9dfeb2deabd93cb4a0a1390fdbd9d0 --- /dev/null +++ b/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 diff --git a/cptac_coad/ARID1A_mutation/config.yaml b/cptac_coad/ARID1A_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..3dc4b81d8412b58dc45b2e93574ee9b4336f49a8 --- /dev/null +++ b/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 diff --git a/cptac_coad/Immune_class/config.yaml b/cptac_coad/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..732816457ab921b7a7f9ea69a2d9e95db31a391c --- /dev/null +++ b/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 diff --git a/cptac_coad/MSI_H/config.yaml b/cptac_coad/MSI_H/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..faadc4f4cd05048d4ee269a6a2a9a61401cb1b7c --- /dev/null +++ b/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 diff --git a/cptac_coad/PIK3CA_mutation/config.yaml b/cptac_coad/PIK3CA_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..faa55bd074a78579e3a3437ef703ba3e81847b92 --- /dev/null +++ b/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 diff --git a/cptac_coad/SETD1B_mutation/config.yaml b/cptac_coad/SETD1B_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9a3c6ff5bfa72308584802cc87ef68f5909b402c --- /dev/null +++ b/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 diff --git a/cptac_gbm/Immune_class/config.yaml b/cptac_gbm/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a461b3beeb7f31c1ed33883f7117eb22c330bd70 --- /dev/null +++ b/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 diff --git a/cptac_hnsc/Histologic_Grade/config.yaml b/cptac_hnsc/Histologic_Grade/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..376d253d5f48fbd0e10654e5f4e2bbc399cc5d8c --- /dev/null +++ b/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 diff --git a/cptac_hnsc/Immune_class/config.yaml b/cptac_hnsc/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..42c6ff91de8c509fcf3aee0a285741b4de51f921 --- /dev/null +++ b/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 diff --git a/cptac_lscc/Histologic_Grade/config.yaml b/cptac_lscc/Histologic_Grade/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..1ad1ba457ffdd6b4c08661bd1ee8ede1be2c8db7 --- /dev/null +++ b/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 diff --git a/cptac_lscc/Immune_class/config.yaml b/cptac_lscc/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..656d0d78d971ca7a5cb6d78112084a87165750d7 --- /dev/null +++ b/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 diff --git a/cptac_luad/Immune_class/config.yaml b/cptac_luad/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..edc15f413b13dd1b564bd57e1889f97060fa5327 --- /dev/null +++ b/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 diff --git a/cptac_luad/KRAS_mutation/config.yaml b/cptac_luad/KRAS_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..2a2ab899cc74547b1707b60f530449247ab9c2b4 --- /dev/null +++ b/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 diff --git a/cptac_lung/subtype/config.yaml b/cptac_lung/subtype/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..61c0b3d1b0a0f14d83f6f76469fcadf7154f3463 --- /dev/null +++ b/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 diff --git a/cptac_ov/Immune_class/config.yaml b/cptac_ov/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..64226c97edc8f3a1675367984b06c643f7cfe00a --- /dev/null +++ b/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 diff --git a/cptac_pda/Immune_class/config.yaml b/cptac_pda/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6accecc8926951bb8d5f83c35f7823da29dc8f53 --- /dev/null +++ b/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 diff --git a/cptac_ucec/CTNNB1_mutation/config.yaml b/cptac_ucec/CTNNB1_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..c475e3f1dfc018bf93a92f607b5138e3cf2dc150 --- /dev/null +++ b/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 diff --git a/cptac_ucec/Immune_class/config.yaml b/cptac_ucec/Immune_class/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7e88c61e70b9389da5b2f451df897d1babf293ed --- /dev/null +++ b/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 diff --git a/cptac_ucec/PTEN_mutation/config.yaml b/cptac_ucec/PTEN_mutation/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7abafb423d8d654b4cd6702f07e01824cd114219 --- /dev/null +++ b/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 diff --git a/crc_outcomes/OS_VALENTINO/config.yaml b/crc_outcomes/OS_VALENTINO/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4d8338b85c7b3bf3d93ea19801de72c8dd1dce0d --- /dev/null +++ b/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 diff --git a/crc_outcomes/PFS_VALENTINO/config.yaml b/crc_outcomes/PFS_VALENTINO/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cda57c5114b32a44042420e28c6d9ed0d8341b16 --- /dev/null +++ b/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 diff --git a/crc_outcomes/braf_grading/config.yaml b/crc_outcomes/braf_grading/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cc91a1188f664ae7013b2f9e5780827dab000ff0 --- /dev/null +++ b/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 diff --git a/crc_outcomes/braf_lymphovas_invasion/config.yaml b/crc_outcomes/braf_lymphovas_invasion/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7097dd86592ec0604a79b07686fefc8ff08ba4cf --- /dev/null +++ b/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 diff --git a/crc_outcomes/braf_mmr/config.yaml b/crc_outcomes/braf_mmr/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..f857f9497e82d8fb3c606e0b0c2aa20e5c312a2c --- /dev/null +++ b/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 diff --git a/crc_outcomes/braf_synapto/config.yaml b/crc_outcomes/braf_synapto/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..4216a1732dcf0c97b00250a1a14eee7834ef1b89 --- /dev/null +++ b/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 diff --git a/crc_outcomes/braf_tils/config.yaml b/crc_outcomes/braf_tils/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..37a91538ec00f2ccef59a907fa85ff4c05482731 --- /dev/null +++ b/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 diff --git a/crc_outcomes/valentino_molecular_subtype/config.yaml b/crc_outcomes/valentino_molecular_subtype/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..867dbf1d4e61336d14997d2d30b4fb17db596640 --- /dev/null +++ b/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 diff --git a/crc_outcomes/valentino_msi/config.yaml b/crc_outcomes/valentino_msi/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d7c2a31c3a42f49968e21ee4134e7738ef158b6e --- /dev/null +++ b/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 diff --git a/dhmc_luad/label/config.yaml b/dhmc_luad/label/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..d081944f269a67c5ba5027fa7f25f42fbc5720cb --- /dev/null +++ b/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 diff --git a/ebrains/diagnosis_group/config.yaml b/ebrains/diagnosis_group/config.yaml index ba3213c4147514dddb06e19b0f973b77248eb28c..a451f118744b4b53c96cd966cacc59e214994e0d 100644 --- a/ebrains/diagnosis_group/config.yaml +++ b/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 diff --git a/ebrains/idh_status/config.yaml b/ebrains/idh_status/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..cfe5b03d0e34f70ad3dc790be38bc8b69b4960db --- /dev/null +++ b/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 diff --git a/hancook/OS_treatment_rdc/config.yaml b/hancook/OS_treatment_rdc/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..6fb67b4e5e469e6b696ee402fc07ff7f1ce71f77 --- /dev/null +++ b/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 diff --git a/hancook/grading_SCC_Conventional_Keratinizing/config.yaml b/hancook/grading_SCC_Conventional_Keratinizing/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..a084cc096b3fb46ac3adafe242150e53bd51bb24 --- /dev/null +++ b/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 diff --git a/hancook/grading_SCC_Conventional_NonKeratinizing/config.yaml b/hancook/grading_SCC_Conventional_NonKeratinizing/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..7296484f162cd77a6a77d5f3d593db0e9b96147c --- /dev/null +++ b/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 diff --git a/hancook/lymphovascular_invasion_L/config.yaml b/hancook/lymphovascular_invasion_L/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..18a13b6481d4387455cab726789d3911aaede285 --- /dev/null +++ b/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 diff --git a/hancook/perineural_invasion_Pn/config.yaml b/hancook/perineural_invasion_Pn/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ab46139dc1a3bb94c61f476491d0000e6475cba1 --- /dev/null +++ b/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 diff --git a/hancook/primarily_metastasis/config.yaml b/hancook/primarily_metastasis/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..ee690c3886428401fede3be64144a8abab1d7cc2 --- /dev/null +++ b/hancook/primarily_metastasis/config.yaml @@ -0,0 +1,12 @@ +datasets: +- hancook +extra_cols: [] +label_dict: + 0: Primary + 1: Metastasis +metrics: +- macro-ovr-auc +num_samples: 676 +sample_col: case_id +task_col: primarily_metastasis +task_type: classification diff --git a/hancook/primary_tumor_site/config.yaml b/hancook/primary_tumor_site/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..9f82d289db11ce863ac9748ed1fc465290babdaa --- /dev/null +++ b/hancook/primary_tumor_site/config.yaml @@ -0,0 +1,14 @@ +datasets: +- hancook +extra_cols: [] +label_dict: + 0: Oral Cavity + 1: Hypopharynx + 2: Larynx + 3: Oropharynx +metrics: +- bacc +num_samples: 696 +sample_col: case_id +task_col: primary_tumor_site +task_type: classification diff --git a/hancook/vascular_invasion_V/config.yaml b/hancook/vascular_invasion_V/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..755c2eb864c5d051b4f2b617377dea544bca8ca6 --- /dev/null +++ b/hancook/vascular_invasion_V/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: vascular_invasion_V +task_type: classification diff --git a/herroi/response/config.yaml b/herroi/response/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..49a8343c7a1ce6250447f7ad6c2a3602cc078e0e --- /dev/null +++ b/herroi/response/config.yaml @@ -0,0 +1,14 @@ +datasets: + - herroi + +task_col: response +extra_cols: [] +task_type: classification +metrics: + - macro-ovr-auc +label_dict: + 0: negative + 1: positive + +sample_col: slide_id +num_samples: 85 diff --git a/imp/grade/config.yaml b/imp/grade/config.yaml index 9199ffb66186fbb6f51af230cce4bc1615df42df..c0dc4d81ad70dfde64509f8834b457136dc80a32 100644 --- a/imp/grade/config.yaml +++ b/imp/grade/config.yaml @@ -7,9 +7,9 @@ task_type: classification metrics: - weighted_kappa label_dict: - 0: "Non-neoplastic" - 1: "Low-grade lesions" - 2: "High-grade lesions" + 0: "0 (non-neoplastic)" + 1: "1 (low-grade)" + 2: "2 (high-grade)" sample_col: slide_id num_samples: 5333 diff --git a/panda/isup_grade/config.yaml b/panda/isup_grade/config.yaml index 69c367c16b4513a5bc63219e63b754f10ddc04ce..82d61e658ab363c8eba72006a5d22c35b7cf58e8 100644 --- a/panda/isup_grade/config.yaml +++ b/panda/isup_grade/config.yaml @@ -7,12 +7,12 @@ 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 + 0: 0 + 1: 1 + 2: 2 + 3: 3 + 4: 4 + 5: 5 sample_col: slide_id num_samples: 9555 diff --git a/ucla_lung/progression_regression/config.yaml b/ucla_lung/progression_regression/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..5d9544ebd3bd73d0daa90d3a6b8a3faacb25d907 --- /dev/null +++ b/ucla_lung/progression_regression/config.yaml @@ -0,0 +1,12 @@ +datasets: +- ucla_lung +extra_cols: [] +label_dict: + 0: regression + 1: progression +metrics: +- macro-ovr-auc +num_samples: 112 +sample_col: case_id +task_col: progression_regression +task_type: classification diff --git a/visiomel/relapse_noprev_melanoma/config.yaml b/visiomel/relapse_noprev_melanoma/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..bbe85891c309118978c11ddf66265984c4f72b42 --- /dev/null +++ b/visiomel/relapse_noprev_melanoma/config.yaml @@ -0,0 +1,12 @@ +datasets: +- visiomel +extra_cols: [] +label_dict: + 0: negative + 1: positive +metrics: +- macro-ovr-auc +num_samples: 584 +sample_col: case_id +task_col: relapse_noprev_melanoma +task_type: classification diff --git a/visiomel/relapse_overall/config.yaml b/visiomel/relapse_overall/config.yaml new file mode 100644 index 0000000000000000000000000000000000000000..511438211cd123982555b0e999f7158fcac10d70 --- /dev/null +++ b/visiomel/relapse_overall/config.yaml @@ -0,0 +1,12 @@ +datasets: +- visiomel +extra_cols: [] +label_dict: + 0: negative + 1: positive +metrics: +- macro-ovr-auc +num_samples: 1341 +sample_col: case_id +task_col: relapse_overall +task_type: classification