settings.yaml

outdir: 'output'
flexynesis: "flexynesis --hpo_patience 10 --variance_threshold 50 --num_workers 0 --disable_marker_finding --restrict_to_features /data/local/buyar/arcas/multiomics_integration/benchmarks/hallmarks_xcell_genes_names.txt"

tasks:
    ccle_vs_gdsc:
        url: 'https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/ccle_vs_gdsc.tgz'
        vars:
          #drugs with known targets in civic db and also found in both ccle and gdsc
          - 'target:Crizotinib'
          - 'target:Erlotinib'
          - 'target:Irinotecan'
          - 'target:Lapatinib'
          - 'target:Paclitaxel'
          - 'target:Palbociclib'
          - 'target:Selumetinib'
          - 'target:Sorafenib'
        data_types:
          - 'rna,cnv'
          - 'cnv'
          - 'rna'
        tools: 'GNN:GC,GNN:SAGE,GNN:GCN,DirectPred,supervised_vae,RandomForest,SVM'
        fusions:
            - intermediate
            - early
        min_features: 500
        features_top_percentile: 20
        finetuningSampleN: '0,100'
        hpo_iterations: 100
        early_stop_patience: 10
        log_transform: 'False'

    lgg_gbm:
        url: 'https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/lgggbm_tcga_pub_processed.tgz'
        vars: 
            - 'event:OS_STATUS time:OS_MONTHS'
        data_types: 
            - 'mut,cna'
            - 'mut'
            - 'cna' 
        tools: 'GNN:GC,GNN:SAGE,GNN:GCN,DirectPred,supervised_vae,RandomSurvivalForest' 
        fusions: 
            - early 
            - intermediate
        min_features: 500 
        features_top_percentile: 20
        hpo_iterations: 100
        finetuningSampleN: '0,100'
        early_stop_patience: 10
        log_transform: 'False'

    metabric:
        url: 'https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/brca_metabric_processed.tgz'
        vars: 
            - 'target:CHEMOTHERAPY'
            - 'target:CLAUDIN_SUBTYPE'
        data_types:
            - 'gex,cna'
            - 'gex'
            - 'cna' 
        tools: 'GNN:GC,GNN:SAGE,GNN:GCN,DirectPred,supervised_vae,MultiTripletNetwork,RandomForest,SVM' 
        fusions: 
            - early 
            - intermediate
        min_features: 500
        features_top_percentile: 20
        hpo_iterations: 100
        finetuningSampleN: '0,100'
        early_stop_patience: 10 
        log_transform: 'False'

    singlecell_bonemarrow:
        url: 'https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis-benchmark-datasets/singlecell_bonemarrow5K.tgz'
        vars:
            - 'target:celltype_l2'
            - 'target:celltype_l1'
        data_types:
            - 'RNA' 
        tools: 'GNN:GC,GNN:SAGE,GNN:GCN,DirectPred,supervised_vae,MultiTripletNetwork,RandomForest,SVM'
        fusions: 
            - intermediate
        min_features: 500
        features_top_percentile: 20
        hpo_iterations: 100
        finetuningSampleN: '0,100'
        early_stop_patience: 10 
        log_transform: 'False'