| { |
| "within.lasso": { |
| "auroc": 0.9503968253968255, |
| "auprc": 0.9537083978980874, |
| "brier": 0.09780938831091726, |
| "sensitivity_at_spec90": 0.873015873015873, |
| "specificity_at_sens90": 0.8548387096774194, |
| "n": 250, |
| "prevalence": 0.504, |
| "auroc_ci95": [ |
| 0.9246015745007681, |
| 0.9740303379416283 |
| ] |
| }, |
| "within.gbm": { |
| "auroc": 0.8972094214029698, |
| "auprc": 0.9088239565472542, |
| "brier": 0.14035917875148912, |
| "sensitivity_at_spec90": 0.7142857142857143, |
| "specificity_at_sens90": 0.6290322580645161, |
| "n": 250, |
| "prevalence": 0.504, |
| "auroc_ci95": [ |
| 0.8586741551459294, |
| 0.9322244623655914 |
| ] |
| }, |
| "within.targeted": { |
| "auroc": 0.9139784946236559, |
| "auprc": 0.9239706329613951, |
| "brier": 0.12130136959989281, |
| "sensitivity_at_spec90": 0.753968253968254, |
| "specificity_at_sens90": 0.6854838709677419, |
| "n": 250, |
| "prevalence": 0.504, |
| "auroc_ci95": [ |
| 0.8787090373783922, |
| 0.9436795954941117 |
| ] |
| }, |
| "within.multimodal": { |
| "auroc": 0.9567332309267793, |
| "auprc": 0.9589696832413457, |
| "brier": 0.09072201619977514, |
| "sensitivity_at_spec90": 0.8888888888888888, |
| "specificity_at_sens90": 0.8870967741935484, |
| "n": 250, |
| "prevalence": 0.504, |
| "auroc_ci95": [ |
| 0.933173323092678, |
| 0.9761952764976959 |
| ] |
| }, |
| "within.clinical_only": { |
| "auroc": 0.6690988223246288, |
| "auprc": 0.6859693850230023, |
| "brier": 0.22678546064067975, |
| "sensitivity_at_spec90": 0.2698412698412698, |
| "specificity_at_sens90": 0.18548387096774194, |
| "n": 250, |
| "prevalence": 0.504 |
| }, |
| "external.lasso": { |
| "auroc": 0.9423728813559322, |
| "auprc": 0.738482943780696, |
| "brier": 0.4649400820862006, |
| "sensitivity_at_spec90": 0.8, |
| "specificity_at_sens90": 0.864406779661017, |
| "n": 192, |
| "prevalence": 0.078125, |
| "auroc_ci95": [ |
| 0.8805743879472693, |
| 0.9864406779661017 |
| ] |
| }, |
| "external.gbm": { |
| "auroc": 0.9212806026365348, |
| "auprc": 0.5820216624108571, |
| "brier": 0.28547947784607763, |
| "sensitivity_at_spec90": 0.8666666666666667, |
| "specificity_at_sens90": 0.6666666666666666, |
| "n": 192, |
| "prevalence": 0.078125, |
| "auroc_ci95": [ |
| 0.8418079096045198, |
| 0.9834274952919021 |
| ] |
| }, |
| "selected_panel": [ |
| { |
| "probe": "cg_ZNF345_2", |
| "gene": "ZNF345", |
| "coef": 0.7035181247656423 |
| }, |
| { |
| "probe": "cg_TFPI2_1", |
| "gene": "TFPI2", |
| "coef": 0.5380634042743031 |
| }, |
| { |
| "probe": "cg_VIM_1", |
| "gene": "VIM", |
| "coef": 0.478083363737724 |
| }, |
| { |
| "probe": "cg_CCNA1_3", |
| "gene": "CCNA1", |
| "coef": 0.4403272227367819 |
| }, |
| { |
| "probe": "cg_TAC1_1", |
| "gene": "TAC1", |
| "coef": 0.4207556722110058 |
| }, |
| { |
| "probe": "cg_VIM_2", |
| "gene": "VIM", |
| "coef": 0.3264920743253056 |
| }, |
| { |
| "probe": "cg_TFPI2_2", |
| "gene": "TFPI2", |
| "coef": 0.3120380728741678 |
| }, |
| { |
| "probe": "cg_NELL1_1", |
| "gene": "NELL1", |
| "coef": 0.3008969535191267 |
| }, |
| { |
| "probe": "cg_VIM_3", |
| "gene": "VIM", |
| "coef": 0.27840107854419205 |
| }, |
| { |
| "probe": "cg_CCNA1_2", |
| "gene": "CCNA1", |
| "coef": 0.18589863770343062 |
| }, |
| { |
| "probe": "bg_01511", |
| "gene": "background", |
| "coef": -0.15830800052901345 |
| }, |
| { |
| "probe": "cg_ZNF345_1", |
| "gene": "ZNF345", |
| "coef": 0.14178484941506977 |
| }, |
| { |
| "probe": "bg_01691", |
| "gene": "background", |
| "coef": 0.13350253242783736 |
| }, |
| { |
| "probe": "bg_01367", |
| "gene": "background", |
| "coef": 0.12902553267595554 |
| }, |
| { |
| "probe": "bg_01532", |
| "gene": "background", |
| "coef": -0.12201077014600044 |
| }, |
| { |
| "probe": "bg_00290", |
| "gene": "background", |
| "coef": -0.1101334005361793 |
| }, |
| { |
| "probe": "bg_00733", |
| "gene": "background", |
| "coef": 0.10831257522986705 |
| }, |
| { |
| "probe": "bg_00105", |
| "gene": "background", |
| "coef": -0.10737308224671371 |
| }, |
| { |
| "probe": "bg_00509", |
| "gene": "background", |
| "coef": 0.10623849312332573 |
| }, |
| { |
| "probe": "bg_00686", |
| "gene": "background", |
| "coef": -0.09256552909242247 |
| }, |
| { |
| "probe": "bg_00994", |
| "gene": "background", |
| "coef": 0.08975507656339371 |
| }, |
| { |
| "probe": "bg_01544", |
| "gene": "background", |
| "coef": -0.0880138674460795 |
| }, |
| { |
| "probe": "bg_00140", |
| "gene": "background", |
| "coef": 0.08341806735469658 |
| }, |
| { |
| "probe": "bg_00641", |
| "gene": "background", |
| "coef": -0.08049141437016215 |
| }, |
| { |
| "probe": "bg_00080", |
| "gene": "background", |
| "coef": -0.07966493645195764 |
| } |
| ], |
| "gbm_top_features": [ |
| { |
| "probe": "cg_ZNF345_2", |
| "gene": "ZNF345", |
| "importance": 0.44761625569077046 |
| }, |
| { |
| "probe": "cg_CCNA1_3", |
| "gene": "CCNA1", |
| "importance": 0.3919606170447708 |
| }, |
| { |
| "probe": "cg_TFPI2_1", |
| "gene": "TFPI2", |
| "importance": 0.33921190341330115 |
| }, |
| { |
| "probe": "cg_VIM_1", |
| "gene": "VIM", |
| "importance": 0.2951477251550466 |
| }, |
| { |
| "probe": "cg_TAC1_1", |
| "gene": "TAC1", |
| "importance": 0.2890054574210354 |
| }, |
| { |
| "probe": "cg_TFPI2_2", |
| "gene": "TFPI2", |
| "importance": 0.25664946466597705 |
| }, |
| { |
| "probe": "cg_VIM_3", |
| "gene": "VIM", |
| "importance": 0.1199790025149959 |
| }, |
| { |
| "probe": "cg_NELL1_1", |
| "gene": "NELL1", |
| "importance": 0.11122904068379584 |
| }, |
| { |
| "probe": "cg_CCNA1_2", |
| "gene": "CCNA1", |
| "importance": 0.11077148485183563 |
| }, |
| { |
| "probe": "cg_CCNA1_1", |
| "gene": "CCNA1", |
| "importance": 0.10342810589743917 |
| }, |
| { |
| "probe": "cg_SST_1", |
| "gene": "SST", |
| "importance": 0.09712306979141481 |
| }, |
| { |
| "probe": "bg_00924", |
| "gene": "background", |
| "importance": 0.09479481971948106 |
| }, |
| { |
| "probe": "cg_VIM_2", |
| "gene": "VIM", |
| "importance": 0.09407314074850304 |
| }, |
| { |
| "probe": "bg_00771", |
| "gene": "background", |
| "importance": 0.08693690495060578 |
| }, |
| { |
| "probe": "cg_ZNF345_1", |
| "gene": "ZNF345", |
| "importance": 0.08437516401768441 |
| }, |
| { |
| "probe": "bg_01581", |
| "gene": "background", |
| "importance": 0.07109450882190814 |
| }, |
| { |
| "probe": "bg_00944", |
| "gene": "background", |
| "importance": 0.039676060837992425 |
| }, |
| { |
| "probe": "bg_00757", |
| "gene": "background", |
| "importance": 0.03689797391343528 |
| }, |
| { |
| "probe": "bg_01281", |
| "gene": "background", |
| "importance": 0.034912264438296474 |
| }, |
| { |
| "probe": "bg_00720", |
| "gene": "background", |
| "importance": 0.0338130151909994 |
| } |
| ], |
| "_summary": { |
| "discovery_cohort": "GSE81334_like", |
| "external_cohort": "GSE104707_like", |
| "n_discovery": 250, |
| "n_external": 192, |
| "n_probes_after_qc": 2074, |
| "n_samples_dropped_qc": 18, |
| "discovery_prevalence": 0.504, |
| "external_prevalence": 0.078125 |
| } |
| } |
