├── .gitignore ├── LICENSE ├── README.md ├── data └── Brain_Integ.mat ├── examples ├── Bayesian_Optimization.py ├── CostFunction.py ├── ModelAnalysis.py └── Run.py ├── requirements.txt ├── results ├── Gradients.gct ├── Gradients.rnk ├── Heatmap.pdf ├── KM.10p_CNVArm.pdf ├── KM.10q_CNVArm.pdf ├── KM.CDKN2A_CNV.pdf ├── KM.IDH1_Mut.pdf ├── KM.IDH2_Mut.pdf ├── KM.IGFBP2_Protein.pdf ├── KM.PTEN_CNV.pdf ├── KM.SMARCA4_Mut.pdf ├── KM.age_at_initial_pathologic_diagnosis_Clinical.pdf ├── KM.histological_type-Is-untreated primary (de novo) gbm_Clinical.pdf ├── PairedScatter.Feature.pdf ├── PairedScatter.Gradient.pdf ├── RankedBox.pdf ├── c_index_list.mat └── glioma_integ_model ├── setup.py └── survivalnet ├── __init__.py ├── analysis ├── FeatureAnalysis.py ├── PathwayAnalysis.py ├── ReadGMT.py ├── RiskCluster.py ├── RiskCohort.py ├── Visualization.py ├── WriteGCT.py ├── WriteRNK.py └── __init__.py ├── model ├── DropoutHiddenLayer.py ├── HiddenLayer.py ├── Model.py ├── RiskLayer.py ├── SparseDenoisingAutoencoder.py └── __init__.py ├── optimization ├── BFGS.py ├── EarlyStopping.py ├── GDLS.py ├── Optimization.py ├── SurvivalAnalysis.py └── __init__.py └── train.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathologyDataScience/SurvivalNet/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathologyDataScience/SurvivalNet/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/PathologyDataScience/SurvivalNet/HEAD/README.md -------------------------------------------------------------------------------- /data/Brain_Integ.mat: 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