├── AD_Training ├── AD_10yrs │ ├── FSF.py │ ├── SHAP.py │ ├── s01_ad_10yrs_clf.py │ ├── s02_ad_10yrs_clf.py │ ├── s03_ad_10yrs_clf.py │ ├── s04_ad_10yrs_clf.py │ └── s05_ad_10yrs_clf.py ├── AD_5yrs │ ├── FSF.py │ ├── SHAP.py │ ├── s01_ad_5yrs_clf.py │ ├── s02_ad_5yrs_clf.py │ ├── s03_ad_5yrs_clf.py │ ├── s04_ad_5yrs_clf.py │ └── s05_ad_5yrs_clf.py ├── AD_full │ ├── FSF.py │ ├── SHAP.py │ ├── permutation.py │ ├── s01_ad_full_clf.py │ ├── s02_ad_full.py │ ├── s03_ad_full.py │ ├── s04_ad_clf.py │ └── s05_ad_full_clf.py ├── Deploy │ ├── Deploy_AD_10yrs.py │ ├── Deploy_AD_5yrs.py │ └── Deploy_AD_full.py ├── merge_features.py └── s02-1_dm_10yrs_permutation.py ├── DataGeneration ├── S01_stroke_combine.py ├── S02_prs_combine.py ├── S03_target_data_generation.py ├── S04_train_data_generation.py ├── S05_mannully_remove_features.py ├── S06_add_manual_features.py ├── SummaryStatistics.py └── Top_features.py ├── Deploy_Models ├── Calibrations │ ├── ad_10yrs.csv │ ├── ad_5yrs.csv │ ├── ad_all.csv │ ├── calibrations.csv │ ├── dm_10yrs.csv │ ├── dm_5yrs.csv │ └── dm_all.csv ├── isoreg_models │ ├── ad_10yrs │ │ ├── iso_mod1.rds │ │ ├── iso_mod2.rds │ │ ├── iso_mod3.rds │ │ ├── iso_mod4.rds │ │ └── iso_mod5.rds │ ├── ad_5yrs │ │ ├── iso_mod1.rds │ │ ├── iso_mod2.rds │ │ ├── iso_mod3.rds │ │ ├── iso_mod4.rds │ │ └── iso_mod5.rds │ ├── ad_all │ │ ├── iso_mod1.rds │ │ ├── iso_mod2.rds │ │ ├── iso_mod3.rds │ │ ├── iso_mod4.rds │ │ └── iso_mod5.rds │ ├── dm_10yrs │ │ ├── iso_mod1.rds │ │ ├── iso_mod2.rds │ │ ├── iso_mod3.rds │ │ ├── iso_mod4.rds │ │ └── iso_mod5.rds │ ├── dm_5yrs │ │ ├── iso_mod1.rds │ │ ├── iso_mod2.rds │ │ ├── iso_mod3.rds │ │ ├── iso_mod4.rds │ │ └── iso_mod5.rds │ └── dm_all │ │ ├── iso_mod1.rds │ │ ├── iso_mod2.rds │ │ ├── iso_mod3.rds │ │ ├── iso_mod4.rds │ │ └── iso_mod5.rds └── lgbm_models │ ├── lgb_mod1.rds │ ├── lgb_mod2.rds │ ├── lgb_mod3.rds │ ├── lgb_mod4.rds │ └── lgb_mod5.rds ├── Plots ├── AUC_AD_Age.py ├── AUC_AD_woHES.py ├── AUC_DM_Age.py ├── AUC_DM_woHES.py ├── Age_histograms.py ├── Calibration.py ├── Calibration_AD_Age.py ├── Calibration_AD_woHES.py ├── Calibration_DM_Age.py ├── Calibration_DM_woHES.py ├── Deploy │ ├── AUC_Deploy_AD2AD_woHES.py │ ├── AUC_Deploy_DM2AD_woHES.py │ ├── AUC_Deploy_DM2DM_woHES.py │ ├── Calibration_Deploy_AD2AD_woHES.py │ ├── Calibration_Deploy_DM2AD_woHES.py │ ├── Calibration_Deploy_DM2DM_woHES.py │ └── Calibrations_Results_DF.py ├── RiskScores │ ├── AUC_AD_RiskScores.py │ ├── AUC_AD_RiskScores_cali.py │ ├── AUC_AD_RiskScores_woUKB_cali.py │ ├── AUC_DM_RiskScores.py │ ├── AUC_DM_RiskScores_cali.py │ ├── AUC_DM_RiskScores_woUKB_cali.py │ ├── Calibration_AD_RiskScores_cali.py │ ├── Calibration_AD_RiskScores_uncali.py │ ├── Calibration_DM_RiskScores_cali.py │ ├── Calibration_DM_RiskScores_uncali.py │ ├── Calibration_woUKB_AD_RiskScores_cali.py │ ├── Calibration_woUKB_AD_RiskScores_cali1.py │ ├── Calibration_woUKB_AD_RiskScores_uncali.py │ ├── Calibration_woUKB_DM_RiskScores_cali.py │ └── Calibration_woUKB_DM_RiskScores_uncali.py ├── Test.py └── Years2Baseline.py ├── README.md ├── RiskScoreEvaluation ├── Evaluation │ ├── AD_full │ │ ├── ANU_ADRI.py │ │ ├── CAIDE_APOE_Score.py │ │ ├── CAIDE_APOE_cali.py │ │ ├── CAIDE_APOE_lm.py │ │ ├── CAIDE_woAPOE_Score.py │ │ ├── CAIDE_woAPOE_cali.py │ │ ├── CAIDE_woAPOE_lm.py │ │ ├── DRS_cali.py │ │ ├── DRS_lm.py │ │ ├── UKB_DRS_APOE_cali.py │ │ ├── UKB_DRS_APOE_lm.py │ │ ├── UKB_DRS_cali.py │ │ └── UKB_DRS_lm.py │ └── DM_full │ │ ├── ANU_ADRI.py │ │ ├── CAIDE_APOE_Score.py │ │ ├── CAIDE_APOE_cali.py │ │ ├── CAIDE_APOE_lm.py │ │ ├── CAIDE_woAPOE_Score.py │ │ ├── CAIDE_woAPOE_cali.py │ │ ├── CAIDE_woAPOE_lm.py │ │ ├── DRS_cali.py │ │ ├── DRS_lm.py │ │ ├── UKB_DRS_APOE_cali.py │ │ ├── UKB_DRS_APOE_lm.py │ │ ├── UKB_DRS_cali.py │ │ └── UKB_DRS_lm.py └── ScoresDataGeneration │ ├── ANU-ADRI_DataGeneration.py │ ├── CAIDE_APOE_DataGeneration.py │ ├── CAIDE_woAPOE_DataGeneration.py │ ├── DRS_DataGeneration.py │ └── UKB_DRS_DataGeneration.py ├── Utility ├── DelongTest.py ├── Evaluation_Utilities.py ├── FocalLoss.py ├── OneVsRestLightGBMWithCustomizedLoss.py ├── OrdinalClassifier.py ├── Processing_Utilities.py ├── Training_Utilities.py └── __pycache__ │ ├── DelongTest.cpython-39.pyc │ ├── Evaluation_Utilities.cpython-38.pyc │ ├── Evaluation_Utilities.cpython-39.pyc │ ├── FocalLoss.cpython-39.pyc │ ├── OneVsRestLightGBMWithCustomizedLoss.cpython-39.pyc │ ├── OrdinalClassifier.cpython-39.pyc │ ├── Processing_Utilities.cpython-38.pyc │ ├── Processing_Utilities.cpython-39.pyc │ ├── Training_Utilities.cpython-38.pyc │ └── Training_Utilities.cpython-39.pyc └── Web-ShinyApp-Develop └── app.R /AD_Training/AD_10yrs/FSF.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jasonHKU0907/UKB_DRP/HEAD/AD_Training/AD_10yrs/FSF.py -------------------------------------------------------------------------------- /AD_Training/AD_10yrs/SHAP.py: 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