save_name: "Cox_PFS"
target: "PFS"


#### Data paths + pre-processing for each modality (e.g. simple imputation)
clinical_data:
  clinical_file:  "data/clinicals.csv"
  imputation:
    numericals: [1, 3, 4, 13, 14, 15, 16, 17, 18, 19, -4]
    categoricals: [20, -5, -3]

radiomics_data:
  radiomics_file: "data/radiomics.csv"
  preprocessing:
    f_log_transform: ['TMTV', 'T_TMTV', 'N1_TMTV', 'N2_TMTV', 'N3_TMTV', 'M1a_TMTV', 'M1bc_TMTV']
  imputation:
    numericals: [2]
    categoricals: null

pathomics_data:
  pathomics_file: "data/pathomics.csv"
  imputation:
    numericals: [27, 28, 29, 31, 33, 35, 38, 40, 41, 43, 44, 45, 47, 48, 49, 52, 53, 54, 55, 56, 57, 58, 59, 60,
                  61, 62, 63, 64, 65, 66, 67, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130,
                  131, 132, 133]
    categoricals: null

RNA_data:
  RNA_file: "data/omics.csv"
  imputation:
    numericals: [32]
    categoricals: null


####  Define survival model + hyperparameters
survival_model:
  type: "Cox"
  args:
    n_alphas: 100
    alpha_min_ratio: 0.01
    l1_ratio: 0.5
#  type: "RF"
#  args:
#    max_features: "sqrt"
#    max_depth: 6


#### Define earlyfusion parameters (see multipit.multi_model.earlyfusion)
earlyfusion:
  n_repeats: 100
  seed: 3
  args:
    calibration: True # if True the fused model is calibrated with inner cross-validation
    balance_features: False # only availbale for classifier with 'feature_weight' parameter
    select_features: True # if True univariate feature selection is used as a pre-processing step
    threshold_select: null # minimum performance value for feature selection
    max_features: 40 # maximum number of features to select
    max_corr: 0.7 # maximum correlation threshold for feature selection
    n_jobs: 1


##### Additionnal parameters
parallelization: # number of jobs for dealing with several repeats in parallel (conflict with n_jobs of latefusion)
  n_jobs_repeats: 1

collect_thresholds: False # collect threshold that optimizes log-rank test on the training set