├── DataPreparation ├── CovariatesDataGenerator │ ├── CovariatesGenerator │ │ ├── Biofluids.py │ │ ├── Demographic.py │ │ ├── DiseaseHistory.py │ │ ├── FamilyHistory.py │ │ ├── Lifestyle.py │ │ ├── Lifestyle_Diet.py │ │ ├── Lifestyle_PA.py │ │ ├── Lifestyle_Social.py │ │ ├── MedicationHistory.py │ │ └── PhysicalMeasurements.py │ └── CovaritesPreprocessing.py ├── PRO_Data_Preprocessing │ ├── S0_ReadRawOlinkData.py │ ├── S1_ProteomicsQC.py │ └── S2_ProteoImputation.py └── TargetGenerator │ ├── S0_Target_Info_Generator.py │ ├── S1_Outcomes_Generator │ ├── A_Infection.py │ ├── C_Cancer.py │ ├── D_Blood.py │ ├── E_Endocrine.py │ ├── F_Mental_Behavior.py │ ├── G_Nervous.py │ ├── H_Eye_Ear.py │ ├── I_Circulatory.py │ ├── J_Respiratory.py │ ├── K_Digestive.py │ ├── L_Skin.py │ ├── M_Musculoskeletal.py │ ├── N_Genitourinary.py │ └── X_Death.py │ └── S2_TargetPreprocessor.py ├── Figures ├── Figure2 │ ├── KM_Plot.py │ └── QPlot.py ├── Figure3 │ ├── DataGenerator.py │ ├── Forest_Base.R │ ├── Forest_PANEL.R │ └── Forest_Serum.R ├── Figure4 │ ├── BarPlot.R │ ├── Heatmap.R │ ├── s1_FeatureImportanceRanking.py │ ├── s2_SelectTopProteins.py │ └── s3_CoxHR.py ├── Figure5 │ ├── Cancer.R │ └── Dementia.R └── Figure6 │ ├── Calibrations.py │ └── NetBenefit.py ├── ModelTraining ├── CPH │ ├── C-index │ │ ├── AgeSex.py │ │ ├── PANEL.py │ │ ├── ProRS.py │ │ ├── ProRS_AgeSex.py │ │ ├── ProRS_PANEL.py │ │ ├── ProRS_SERUM.py │ │ └── SERUM.py │ └── PredictedRisk │ │ ├── AgeSex.py │ │ ├── PANEL.py │ │ ├── ProRS.py │ │ ├── ProRS_AgeSex.py │ │ ├── ProRS_PANEL.py │ │ └── ProRS_raw.py └── ProResNet │ ├── ResNet.py │ └── SharedHead.py ├── README.md ├── Tables ├── sTable1 │ └── sTable1.py ├── sTable2 │ ├── sTable2_1.py │ ├── sTable2_2.py │ └── sTable2_3.py ├── sTable3 │ └── sTable3.py ├── sTable4 │ ├── sTable4_age.py │ └── sTable4_gender_ttest.py ├── sTable5 │ └── sTable5.py ├── sTable6 │ ├── sTable6_10yrs.py │ ├── sTable6_5yrs.py │ ├── sTable6_all.py │ ├── sTable6_over10yrs.py │ └── sTable_combine.py ├── sTable7 │ ├── sTable7_AgeSex.py │ ├── sTable7_PANEL.py │ ├── sTable7_Serum.py │ └── sTable7_univariate.py ├── sTable8 │ └── sTable8.py └── sTable9 │ └── sTable9.py ├── Utility ├── DelongTest.py ├── Evaluation_Utilities.py ├── FocalLoss.py ├── Processing_Utilities.py └── Training_Utilities.py └── src ├── Logo.png ├── ProNNet.png ├── Study_Flowchart.png └── Train-Evaluation.png /DataPreparation/CovariatesDataGenerator/CovariatesGenerator/Biofluids.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jasonHKU0907/FutureHealthProteomicPrediction/HEAD/DataPreparation/CovariatesDataGenerator/CovariatesGenerator/Biofluids.py -------------------------------------------------------------------------------- /DataPreparation/CovariatesDataGenerator/CovariatesGenerator/Demographic.py: -------------------------------------------------------------------------------- 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