├── .gitignore ├── .gitmodules ├── LICENSE ├── LocalEnv.py.template ├── README.md ├── TestCDSS.py ├── medinfo ├── __init__.py ├── analysis │ ├── AccuracyPerTopItems.py │ ├── BaseAnalysis.py │ ├── BatchTTests.py │ ├── CalibrationHistogram.py │ ├── CalibrationPlot.py │ ├── CombineScoreOutcomeFiles.py │ ├── ConcatenateDataFiles.py │ ├── Const.py │ ├── Env.py │ ├── MergeJoinDataFiles.py │ ├── ROCPlot.py │ ├── RankSimilarity.py │ ├── RegressionAnalysis.py │ ├── SQLQueryDataFile.py │ ├── Util.py │ ├── __init__.py │ └── test │ │ ├── Const.py │ │ ├── TestAccuracyPerTopItems.py │ │ ├── TestBatchTTests.py │ │ ├── TestCalibrationPlot.py │ │ ├── TestConcatenateDataFiles.py │ │ ├── TestMergeJoinDataFiles.py │ │ ├── TestROCPlot.py │ │ ├── TestSQLQueryDataFile.py │ │ ├── Util.py │ │ └── __init__.py ├── common │ ├── Const.py │ ├── Env.py │ ├── IteratorFactory.py │ ├── ProcessManager.py │ ├── StatsUtil.py │ ├── Util.py │ ├── __init__.py │ ├── support │ │ ├── awaitProcess.py │ │ ├── clean.py │ │ └── sleeper.py │ └── test │ │ ├── Const.py │ │ ├── TestStatsUtil.py │ │ ├── Util.py │ │ └── __init__.py ├── cpoe │ ├── AssociationAnalysis.py │ ├── Const.py │ ├── DataManager.py │ ├── DecayingWindows.py │ ├── Env.py │ ├── ItemRecommender.py │ ├── OrderSetRecommender.py │ ├── TopicModel.py │ ├── TopicModelRecommender.py │ ├── TripleAssociationAnalysis.py │ ├── Util.py │ ├── __init__.py │ ├── analysis │ │ ├── BaseCPOEAnalysis.py │ │ ├── Const.py │ │ ├── Env.py │ │ ├── OrderSetRecommenderClassificationAnalysis.py │ │ ├── OrderSetUsageAnalysis.py │ │ ├── OutcomePredictionAnalysis.py │ │ ├── PreparePatientItems.py │ │ ├── RecommendationClassificationAnalysis.py │ │ ├── RecommendationRankingTrendAnalysis.py │ │ ├── TopicModelAnalysis.py │ │ ├── Util.py │ │ ├── __init__.py │ │ ├── associationQuery.sql │ │ └── test │ │ │ ├── Const.py │ │ │ ├── TestOrderSetRecommendationClassificationAnalysis.py │ │ │ ├── TestOrderSetUsageAnalysis.py │ │ │ ├── TestOutcomePredictionAnalysis.py │ │ │ ├── TestPreparePatientItems.py │ │ │ ├── TestRecommendationClassificationAnalysis.py │ │ │ ├── TestRecommendationRankingTrendAnalysis.py │ │ │ ├── TestTopicModelAnalysis.py │ │ │ ├── Util.py │ │ │ └── __init__.py │ ├── cpoeSim │ │ ├── Const.py │ │ ├── SimManager.py │ │ ├── __init__.py │ │ ├── analysis │ │ │ ├── CPOETrackerAnalysis-walkthrough.ipynb │ │ │ ├── CPOETrackerAnalysis.py │ │ │ ├── __init__.py │ │ │ ├── make_usage_report.py │ │ │ └── sampleQueries.sql │ │ ├── cpoeSim.md │ │ ├── simdata │ │ │ ├── Readme.md │ │ │ ├── cpoeSim.sql │ │ │ ├── createClinicalItemTable.py │ │ │ ├── dumpSimTables.sh │ │ │ ├── extraClinicalItems.sql │ │ │ ├── prepCPOESimulationData.py │ │ │ ├── restoreSimTables.sh │ │ │ ├── revertSimTables.sh │ │ │ ├── sim_grading_key.dump.sql │ │ │ ├── sim_note.dump.sql │ │ │ ├── sim_note_type.dump.sql │ │ │ ├── sim_order_result_map.dump.sql │ │ │ ├── sim_patient.dump.sql │ │ │ ├── sim_patient_order.dump.sql │ │ │ ├── sim_patient_state.dump.sql │ │ │ ├── sim_result.dump.sql │ │ │ ├── sim_state.dump.sql │ │ │ ├── sim_state_result.dump.sql │ │ │ ├── sim_state_transition.dump.sql │ │ │ └── sim_user.dump.sql │ │ └── test │ │ │ ├── Const.py │ │ │ ├── TestMakeUsageReport.py │ │ │ ├── TestSimManager.py │ │ │ ├── TestSimManagerGrading.py │ │ │ ├── Util.py │ │ │ └── __init__.py │ └── test │ │ ├── Const.py │ │ ├── TestAssociationAnalysis.py │ │ ├── TestDataManager.py │ │ ├── TestDecayingWindows.py │ │ ├── TestItemRecommender.py │ │ ├── TestOrderSetRecommender.py │ │ ├── TestTopicModel.py │ │ ├── TestTripleAssociationAnalysis.py │ │ ├── Util.py │ │ └── __init__.py ├── dataconversion │ ├── Const.py │ ├── DataExtractor.py │ ├── Env.py │ ├── FeatureExtractor.py │ ├── FeatureMatrix.py │ ├── FeatureMatrixFactory.py │ ├── FeatureMatrixIO.py │ ├── FeatureMatrixTransform.py │ ├── ProviderRotationConversion.py │ ├── ResidentScheduleFormat.py │ ├── STRIDEAccessLogConversion.py │ ├── STRIDECultureMicroConversion.py │ ├── STRIDEDemographicsConversion.py │ ├── STRIDEDxListConversion.py │ ├── STRIDEOrderMedConversion.py │ ├── STRIDEOrderProcConversion.py │ ├── STRIDEOrderResultsConversion.py │ ├── STRIDETreatmentTeamConversion.py │ ├── Util.py │ ├── __init__.py │ ├── cohorts.py │ ├── constants.py │ ├── featurizers.py │ ├── mapdata │ │ ├── 2018_I10gem.tab.gz │ │ ├── 2018_I9gem.tab.gz │ │ ├── CharlsonComorbidity-ICD10.tab │ │ ├── CharlsonComorbidity-ICD9CM.tab │ │ ├── ClinicalItems.IVAntibiotics.tab │ │ ├── ClinicalItems.POAntibiotics.tab │ │ ├── IVAntibiotics.Names.tab │ │ ├── LabResultMap.tab.gz │ │ ├── Medication.IVFluids.tab │ │ ├── POAntibiotic.Names.tab │ │ ├── TreatmentTeamGroups.tab │ │ ├── TreatmentTeamGroups_UCSF.tab │ │ ├── ahrq_ccsr.diagnosis_code.tab.gz │ │ ├── ahrq_ccsr.procedure_code.tab.gz │ │ ├── ahrq_citation.txt │ │ └── icd_gems_citation.txt │ ├── starr_conv │ │ ├── STARRDemographicsConversion.py │ │ ├── STARROrderMedConversion.py │ │ ├── STARROrderProcConversion.py │ │ ├── STARRTreatmentTeamConversion.py │ │ ├── STARRUtil.py │ │ ├── __init__.py │ │ └── test │ │ │ ├── TestSTARRDemographicsConversion.py │ │ │ ├── TestSTARROrderMedConversion.py │ │ │ ├── TestSTARROrderProcConversion.py │ │ │ ├── TestSTARRTreatmentTeamConversion.py │ │ │ └── __init__.py │ ├── support │ │ ├── __init__.py │ │ ├── extractExcelSheets.py │ │ └── patchHeader.py │ ├── test │ │ ├── Const.py │ │ ├── EventDigraphTestData.py │ │ ├── FMTransformTestData.py │ │ ├── FeatureMatrixIOTestData.py │ │ ├── FeatureMatrixTestData.py │ │ ├── TestDataExtractor.py │ │ ├── TestFeatureMatrixFactory.py │ │ ├── TestFeatureMatrixIO.py │ │ ├── TestFeatureMatrixTransform.py │ │ ├── TestProviderRotationConversion.py │ │ ├── TestResidentScheduleFormat.py │ │ ├── TestSTRIDEAccessLogConversion.py │ │ ├── TestSTRIDECultureMicroConversion.py │ │ ├── TestSTRIDEDemographicsConversion.py │ │ ├── TestSTRIDEDxListConversion.py │ │ ├── TestSTRIDEOrderMedConversion.py │ │ ├── TestSTRIDEOrderProcConversion.py │ │ ├── TestSTRIDEOrderResultsConversion.py │ │ ├── TestSTRIDETreatmentTeamConversion.py │ │ ├── UMichFeatureMatrixTestData.py │ │ ├── Util.py │ │ ├── __init__.py │ │ ├── test-matrix-no-header.tab │ │ └── test-matrix-with-header.tab │ └── trainers.py ├── db │ ├── Const.py │ ├── DBUtil.py │ ├── Env.py │ ├── Model.py │ ├── ResultsFormatter.py │ ├── Util.py │ ├── __init__.py │ ├── bigquery │ │ ├── __init__.py │ │ ├── bigQueryUtil.py │ │ └── test │ │ │ ├── __init__.py │ │ │ └── test_bigQueryUtil.py │ ├── definition │ │ ├── cpoeSimulation.sql │ │ ├── cpoeStats.sql │ │ └── opiodrx.sql │ ├── support │ │ ├── commonQueries.sql │ │ ├── deleteCategoryItems.py │ │ ├── dumpAccessTables.bat │ │ ├── dumpAccessTables.sh │ │ ├── dumpCPOESimulationTables.bat │ │ ├── dumpCPOETables.bat │ │ ├── dumpCPOETables.sh │ │ ├── dumpOpioidPCPTables.bat │ │ ├── restoreAccessTables.bat │ │ ├── restoreAccessTables.sh │ │ ├── restoreCPOESimulationTables.bat │ │ ├── restoreCPOETables.sh │ │ └── syncDatabaseTable.py │ └── test │ │ ├── Const.py │ │ ├── TestDBUtil.py │ │ ├── TestResultsFormatter.py │ │ ├── Util.py │ │ └── __init__.py ├── geography │ ├── ChloroplethGenerator.py │ ├── Const.py │ ├── ZIPCodeMapping.txt │ ├── ZIP_COUNTY_122019.csv.gz │ ├── __init__.py │ └── bp03mr20.csv ├── ml │ ├── BifurcatedSupervisedClassifier.py │ ├── ClassifierAnalyzer.py │ ├── ClassifierPipeline.py │ ├── Const.py │ ├── FeatureSelector.py │ ├── ListPredictor.py │ ├── Predictor.py │ ├── PredictorAnalyzer.py │ ├── Regressor.py │ ├── RegressorAnalyzer.py │ ├── SupervisedClassifier.py │ ├── SupervisedLearner.py │ ├── SupervisedLearner_Class.py │ ├── SupervisedLearner_System.py │ ├── SupervisedLearner_Utils.py │ ├── SupervisedLearningPipeline.py │ ├── __init__.py │ ├── pytorch_models.py │ └── test │ │ ├── ClassifierAnalyzerTestData.py │ │ ├── FeatureSelectorTestData.py │ │ ├── PredictorAnalyzerTestData.py │ │ ├── RegressorAnalyzerTestData.py │ │ ├── SupervisedLearnerTestData.py │ │ ├── SupervisedLearningTestData.py │ │ ├── TestBifurcatedSupervisedClassifier.py │ │ ├── TestClassifierAnalyzer.py │ │ ├── TestFeatureSelector.py │ │ ├── TestPredictorAnalyzer.py │ │ ├── TestRegressor.py │ │ ├── TestRegressorAnalyzer.py │ │ ├── TestSupervisedClassifier.py │ │ ├── TestSupervisedLearner.py │ │ ├── __init__.py │ │ ├── expected-linear-predictor.report │ │ └── expected-list-predictor.report ├── sequenceanalysis │ ├── CountRepeatNormals.py │ ├── SequenceAnalyzer.py │ ├── __init__.py │ └── test │ │ ├── TestCountRepeatNormals.py │ │ ├── TestSequenceAnalyzer.py │ │ └── __init__.py ├── textanalysis │ ├── AVSParse.py │ ├── BaseTextAnalysis.py │ ├── Const.py │ ├── Env.py │ ├── Util.py │ ├── __init__.py │ ├── stylesBasic.css │ ├── stylesGrey.css │ ├── test │ │ ├── Const.py │ │ ├── TestAVSParse.py │ │ ├── Util.py │ │ └── __init__.py │ └── textAnalysis.js └── web │ ├── __init__.py │ ├── cgibin │ ├── BaseWeb.py │ ├── Const.py │ ├── Env.py │ ├── Links.py │ ├── Options.py │ ├── Util.py │ ├── __init__.py │ ├── admin │ │ ├── BaseAdminWeb.py │ │ ├── DBUtilWeb.htm │ │ ├── DBUtilWeb.psp │ │ ├── DBUtilWeb.py │ │ ├── DebugWeb.py │ │ └── __init__.py │ ├── cgi2psp.py │ ├── cpoe │ │ ├── BaseCPOEWeb.py │ │ ├── ItemRecommenderWeb.htm │ │ ├── ItemRecommenderWeb.py │ │ ├── PatientCareFrame.htm │ │ ├── PatientCareFrame.js │ │ ├── PatientCareFrame.py │ │ ├── SimSetup.htm │ │ ├── SimSetup.py │ │ ├── Track.js │ │ ├── __init__.py │ │ └── dynamicdata │ │ │ ├── ActiveOrders.htm │ │ │ ├── ActiveOrders.py │ │ │ ├── BaseDynamicData.py │ │ │ ├── ClinicalItemData.htm │ │ │ ├── ClinicalItemData.py │ │ │ ├── ItemRecommendationTable.htm │ │ │ ├── ItemRecommendationTable.py │ │ │ ├── NewOrders.htm │ │ │ ├── NewOrders.py │ │ │ ├── NotesReview.htm │ │ │ ├── NotesReview.py │ │ │ ├── OrderSetSearch.htm │ │ │ ├── OrderSetSearch.py │ │ │ ├── RelatedOrders.htm │ │ │ ├── RelatedOrders.py │ │ │ ├── ResultsReview.htm │ │ │ ├── ResultsReview.py │ │ │ └── __init__.py │ ├── errorTemplate.htm │ └── errorTemplate.py │ ├── index.htm │ ├── resource │ ├── ajax-loader.gif │ ├── calendar.gif │ ├── calendarPopup.htm │ ├── cancelIcon.svg │ ├── dateHelper.js │ ├── errorReport.eml │ ├── graphIcon.png │ ├── jquery-1.11.3.js │ ├── magnify.gif │ ├── requestParam.js │ ├── stylesBasic.css │ ├── stylesBlue.css │ ├── stylesGrey.css │ └── toolkit.js │ └── tools │ ├── AcidBaseAnalysis.htm │ ├── Antibiogram │ ├── AntibiogramTable.htm │ ├── VAMC Wilkes Barre - Antibiogram FY17.xlsx │ ├── VAPAabgm2016Report FINAL4-14-17.pdf │ ├── antibiogramControls.js │ ├── antibiogramData.js │ ├── antibiogramStyles.css │ ├── melt.py │ ├── notes.xlsx │ ├── test.tsv │ └── testOut.tsv │ ├── Hyponatremia.htm │ ├── OpioidEquivalentDosing.htm │ ├── countdownTimer.htm │ ├── formatTemplates.py │ ├── kiosk │ ├── feedFrame.htm │ ├── image.img.full.high.jpg │ ├── index.htm │ ├── logoControl.htm │ ├── sleep.bat │ └── wake.bat │ ├── lib │ ├── Color.js │ └── toolkit.js │ └── medTemplates.htm ├── scripts ├── Archive │ ├── BMT_hyperglycemia │ │ ├── .RData │ │ ├── .Rhistory │ │ ├── ADT_BMT_pts.sql │ │ ├── BGs_BMT_pts.sql │ │ ├── BMT_A1c.sql │ │ ├── BMT_age.sql │ │ ├── BMT_and_DM_distinct.sql │ │ ├── BMT_dx_pts.sql │ │ ├── BMT_gender.sql │ │ ├── BMT_med_freq.sql │ │ ├── BMT_primary_TT.sql │ │ ├── BMT_steroid_orders.sql │ │ ├── BMTpts_given_steroids.sql │ │ ├── BMTpts_ordered_for_insulin.sql │ │ ├── TT_ADT_join_BMTmatching.sql │ │ ├── count_pt_enc_BMTprimary.sql │ │ ├── inpatient_BG_labs.sql │ │ ├── insulin_orders_BMT.sql │ │ ├── pts_on_ISS.sql │ │ ├── readme.md │ │ ├── recieved_insulin_BMTpts │ │ ├── recieved_insulin_BMTpts.sql │ │ ├── sql_query_R.R │ │ └── steroids_IV_PO_query.sql │ ├── BloodBPA-FreeTextAnnotateTags │ │ ├── Readme.txt │ │ ├── TagMergeWorksheet.txt │ │ ├── agreementStats.txt │ │ ├── autoAnnotate.py │ │ ├── calcAgreementStats.py │ │ ├── compareTags.py │ │ ├── extractWordCounts.py │ │ ├── mergeTags.py │ │ ├── mergedTags.Daniel.txt │ │ ├── mergedTags.txt │ │ ├── sampleTags.Daniel.txt │ │ ├── sampleTags.txt │ │ ├── summarizeAnnotationTags.py │ │ ├── util.py │ │ └── wordTags.txt │ ├── CDSS │ │ ├── addSynonyms.sql │ │ ├── assocAnalysis.py │ │ ├── insertData.bat │ │ ├── insertData.sh │ │ ├── patchBPFlowsheet.py │ │ ├── populateOrderResultStats.py │ │ ├── prepareItems.bat │ │ ├── setupDataPreprocessingNotes.txt │ │ ├── setupNotes.txt │ │ └── testGenSim.py │ ├── ClinicNet │ │ ├── README.md │ │ ├── bootstrap.py │ │ ├── clinicnet_model │ │ │ └── utils │ │ │ │ ├── datagenerator.py │ │ │ │ └── generator_cache.ipynb │ │ ├── data_processing │ │ │ ├── add_dates.py │ │ │ ├── compute_stats.py │ │ │ ├── feature_selection.py │ │ │ ├── make_batches.py │ │ │ ├── make_order_set_responses.py │ │ │ ├── prep_batches.py │ │ │ └── stratify_data_by_time.py │ │ ├── plotPCA.ipynb │ │ ├── preprocessing │ │ │ ├── data_split.sh │ │ │ └── make_hdf5.py │ │ ├── run_clinicnet.py │ │ └── utils │ │ │ ├── pca.py │ │ │ └── summarize.py │ ├── ClinicalPredictionRules │ │ ├── ConditionMortalityMatrix.py │ │ └── ConditionMortalityPredictor.py │ ├── Covid19 CDC │ │ ├── cdc_tbl1.ipynb │ │ ├── coinfectionQuery.sql │ │ ├── git_export.sh │ │ ├── long_tbl.ipynb │ │ ├── long_tbl_grp.ipynb │ │ ├── long_tbl_grp_person.ipynb │ │ ├── new_tbl_adj.ipynb │ │ ├── notebook.tex │ │ └── prevalenceQueries.sql │ ├── DecayingWindows │ │ ├── AALoopMonth.py │ │ ├── AAOneMonth.py │ │ ├── CreatePatientList.py │ │ ├── StitchIDFiles.py │ │ ├── __init__.py │ │ ├── addConstraints.sql │ │ ├── commitFromFile.py │ │ └── dropConstraints.sql │ ├── DeepLearningRecommender │ │ ├── ClinicLSTM.ipynb │ │ ├── ClinicNet.ipynb │ │ ├── FeatureMatrix.py │ │ ├── FeatureMatrixFactory.py │ │ ├── ReadMe.md │ │ ├── create_batches.py │ │ ├── feature_cols.txt │ │ ├── human_authored_baseline.ipynb │ │ ├── load_and_format_data.py │ │ ├── makeMatrix.py │ │ ├── response_variables.csv │ │ └── rnn_data_wrapper.py │ ├── DiabetesSecondLineTherapy │ │ ├── OptumSampleQueries.sql │ │ ├── STARRSampleQueries.sql │ │ ├── TruvenMarketscanMedicareSupplementalSampleQueries.sql │ │ └── TruvenMarketscanSampleQueries.sql │ ├── DiabeticsAtStanford │ │ ├── blood_glucose_partialquery.sql │ │ ├── pts_on_ISS.sql │ │ ├── pullBMTteams.sql │ │ └── readme │ ├── ExpertsVsEveryone │ │ ├── Matching_Function.Rmd │ │ ├── insertUpdates.sh │ │ ├── pipeline │ │ │ ├── Figures │ │ │ │ ├── generate_plots.sh │ │ │ │ ├── matching_parse.py │ │ │ │ └── plot_input.py │ │ │ ├── Matching │ │ │ │ ├── clean_data.py │ │ │ │ ├── extractData_modified.py │ │ │ │ ├── extract_age.py │ │ │ │ ├── matching.Rmd │ │ │ │ └── remap_ids.py │ │ │ ├── Miscellananeous │ │ │ │ ├── extract_diagnosis_codes.py │ │ │ │ └── extract_unmatched_patient_cohorts.py │ │ │ ├── README.txt │ │ │ ├── Training │ │ │ │ ├── get_predictions.py │ │ │ │ ├── run_association.sh │ │ │ │ └── stratify.py │ │ │ ├── everyone_patients_matched_remapped_excluding_ordersets.csv │ │ │ └── everyone_patients_with_ordersets.csv │ │ ├── referenceData │ │ │ ├── SetupReferenceData.txt │ │ │ ├── candidateOrders.tab │ │ │ ├── generateWorksheetData.py │ │ │ ├── item_collection.update.tab │ │ │ ├── item_collection_item.diagnosisLink.update.tab │ │ │ ├── item_collection_item.referenceOrders.update.tab │ │ │ ├── oldReferenceConversion.py │ │ │ ├── oldReferences.tab │ │ │ ├── orderSetQueries.txt │ │ │ ├── scratchNotes.txt │ │ │ └── updateReferenceData.py │ │ └── scripts │ │ │ ├── Figures │ │ │ ├── generate_plots.sh │ │ │ ├── matching_parse.py │ │ │ └── plot_input.py │ │ │ ├── Matching │ │ │ ├── clean_data.py │ │ │ ├── extractData_modified.py │ │ │ ├── extract_age.py │ │ │ ├── matching.Rmd │ │ │ └── remap_ids.py │ │ │ ├── Miscellananeous │ │ │ ├── extract_diagnosis_codes.py │ │ │ └── extract_unmatched_patient_cohorts.py │ │ │ ├── README.txt │ │ │ └── Training │ │ │ ├── get_predictions.py │ │ │ ├── run_association.sh │ │ │ └── stratify.py │ ├── Ferritin │ │ ├── extractData.py │ │ ├── extractionNotes.txt │ │ ├── formatData.py │ │ ├── machineLearn.py │ │ ├── plotAssociations.py │ │ ├── plotDistributions.py │ │ └── scratch.py │ ├── GlucoseControl │ │ ├── 1filterPatient.py │ │ ├── 2constructFeatures.py │ │ ├── 3regression.py │ │ ├── 4classification.py │ │ ├── README.md │ │ └── queries.sql │ ├── HighMortalityVsLowMortalityVsCrowd │ │ ├── BetterThanExpectedEvaluation │ │ │ ├── Better_Than_Expected_Evaluation_Line_Plot.ipynb │ │ │ ├── aggregate_evaluation_metrics.py │ │ │ ├── evaluate_association_models_recommended_items_against_verify_items.py │ │ │ ├── evaluate_ordersets_against_verify_items.py │ │ │ ├── extract_better_than_expected_patients.py │ │ │ ├── extract_mortality_unbinned.py │ │ │ ├── join_probs_mortality_delta.py │ │ │ └── prepare_query_and_verify_items.py │ │ ├── BuildExpectedMortalityPredictor │ │ │ ├── compute_observed_vs_expected_mortality.py │ │ │ ├── mortality_predictor.Rmd │ │ │ └── remap_ids_mortality_probs.py │ │ ├── ExtractPatientFeatureMatrix │ │ │ ├── clean_data.py │ │ │ ├── extract_admission_discharge_flow.py │ │ │ ├── extract_age.py │ │ │ ├── extract_diagnosis_codes.py │ │ │ ├── extract_encounter_data.py │ │ │ ├── extract_last_recorded_admission_diagnosis.py │ │ │ ├── extract_mortality.py │ │ │ ├── extract_physician_patient_map.py │ │ │ ├── extract_treatment_team.py │ │ │ └── reorder_data.py │ │ ├── Miscellaneous │ │ │ ├── compute_observed_vs_expected_mortalityORreadmission.py │ │ │ ├── extract_30_day_readmissions.py │ │ │ ├── extract_lengths_of_stay.py │ │ │ └── mortality_or_readmission_predictor.Rmd │ │ ├── PropensityScoreMatching │ │ │ ├── extract_unmatched_patients.py │ │ │ ├── matching.Rmd │ │ │ └── remap_ids_matching.py │ │ └── README │ ├── ICUDNR │ │ ├── RAnalysis │ │ │ ├── DNR_aug.sas │ │ │ ├── Example.FeatureMatrixProcessing.R │ │ │ ├── Step.10.DataLoading.R │ │ │ ├── Step.20.Demographics.R │ │ │ ├── Step.30.Imputation-Amelia.R │ │ │ ├── Step.40.CoxRegression.R │ │ │ └── timedep_cox.R │ │ ├── extractData.py │ │ ├── formatData.py │ │ ├── simulateData.py │ │ └── summaryStats.py │ ├── LabTestAnalysis │ │ ├── __init__.py │ │ ├── images │ │ │ └── sb_pipeline.png │ │ ├── lab_statistics │ │ │ ├── JAMANetworkOpen │ │ │ │ ├── Appendix Figures.ipynb │ │ │ │ ├── Appendix Tables.ipynb │ │ │ │ ├── Figure 1.ipynb │ │ │ │ ├── Figure 2.ipynb │ │ │ │ ├── Figure 3.ipynb │ │ │ │ ├── Figure 4.ipynb │ │ │ │ ├── JAMA_config.py │ │ │ │ ├── Table 1.ipynb │ │ │ │ └── statistical_analysis.ipynb │ │ │ ├── LabResultMap.csv │ │ │ ├── __init__.py │ │ │ ├── clinical_data.py │ │ │ ├── customDBUtil.py │ │ │ ├── data_consistency │ │ │ │ └── report │ │ │ ├── data_repeat_component_descriptive │ │ │ │ ├── base_names.csv │ │ │ │ ├── global_stats.csv │ │ │ │ ├── global_stats_null_filled.csv │ │ │ │ └── result_ids.csv │ │ │ ├── data_repeat_lab_descriptive │ │ │ │ ├── global_stats.csv │ │ │ │ └── proc_codes.csv │ │ │ ├── data_summary_stats │ │ │ │ ├── CLAB2018v1.csv │ │ │ │ ├── UCSF.csv │ │ │ │ ├── UMich_component.csv │ │ │ │ ├── UMich_panel.csv │ │ │ │ ├── billing_codes.csv │ │ │ │ ├── chargemaster.csv.gz │ │ │ │ ├── component_cnts.txt │ │ │ │ ├── components.csv │ │ │ │ ├── item_counts.csv │ │ │ │ ├── labs.csv │ │ │ │ ├── labs_charges_volumes.csv │ │ │ │ ├── labs_charges_volumes_modified.xlsx │ │ │ │ └── potential_matches.csv │ │ │ ├── repeat_component_descriptive.py │ │ │ ├── repeat_lab_descriptive.py │ │ │ ├── stats_database.py │ │ │ ├── stats_utils.py │ │ │ ├── summary_stats.py │ │ │ ├── test_repeat_component_descriptive.py │ │ │ └── test_summary_stats.py │ │ ├── machine_learning │ │ │ ├── LabChangeBatchDriver.py │ │ │ ├── LabChangePerformanceReport.Rmd │ │ │ ├── LabChangePredictionPipeline.py │ │ │ ├── LabComponentMap.tab │ │ │ ├── LabNormalityPredictionPipeline.py │ │ │ ├── LabResultMap.tab │ │ │ ├── __init__.py │ │ │ ├── data_conversion │ │ │ │ ├── map_UCSF_component_raw2code.csv │ │ │ │ ├── map_UCSF_panel_raw2code.csv │ │ │ │ ├── map_UMich_component_raw2code.csv │ │ │ │ ├── map_UMich_panel_raw2code.csv │ │ │ │ ├── map_component.csv │ │ │ │ ├── map_component_code2description.csv │ │ │ │ ├── map_cormobidity.csv │ │ │ │ ├── map_panel.csv │ │ │ │ ├── map_panel_code2description.csv │ │ │ │ ├── map_team.csv │ │ │ │ └── map_vitals.csv │ │ │ ├── extra │ │ │ │ ├── LABFER.txt │ │ │ │ ├── LABSPLAC.txt │ │ │ │ ├── LABTSH.txt │ │ │ │ ├── cols_labfer.csv │ │ │ │ ├── cols_labntbnp.csv │ │ │ │ ├── cols_labsplac.csv │ │ │ │ └── cols_labtsh.csv │ │ │ ├── extraction │ │ │ │ ├── FeatureMatrixChangeLabels.py │ │ │ │ ├── LabChangeMatrix.py │ │ │ │ ├── LabNormalityMatrix.py │ │ │ │ ├── __init__.py │ │ │ │ ├── generateLabNormalityMatrices.py │ │ │ │ └── mapLabToResultCodes.py │ │ │ ├── helpful_scripts │ │ │ │ └── look_RF_structure.py │ │ │ ├── ml_utils.py │ │ │ ├── pipeline.py │ │ │ ├── pipelineResults.zip │ │ │ ├── pipelineResults │ │ │ │ ├── LABFER_ada_boost_n_estimators=10,_learning_rate=0.01.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=10,_learning_rate=0.1.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=10,_learning_rate=1.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=100,_learning_rate=0.01.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=100,_learning_rate=0.1.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=100,_learning_rate=1.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=50,_learning_rate=0.01.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=50,_learning_rate=0.1.eps │ │ │ │ ├── LABFER_ada_boost_n_estimators=50,_learning_rate=1.eps │ │ │ │ ├── LABFER_decision_tree_max_depth=20.eps │ │ │ │ ├── LABFER_decision_tree_max_depth=5.eps │ │ │ │ ├── LABFER_decision_tree_max_depth=50.eps │ │ │ │ ├── LABFER_gaussian_naive_bayes.eps │ │ │ │ ├── LABFER_logistic_regression_c=0.1.eps │ │ │ │ ├── LABFER_logistic_regression_c=1.0.eps │ │ │ │ ├── LABFER_logistic_regression_c=10.0.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=10,_max_depth=10.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=10,_max_depth=15.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=10,_max_depth=5.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=30,_max_depth=10.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=30,_max_depth=15.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=30,_max_depth=5.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=5,_max_depth=10.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=5,_max_depth=15.eps │ │ │ │ ├── LABFER_random_forest_n_estimators=5,_max_depth=5.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=10,_learning_rate=0.01.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=10,_learning_rate=0.1.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=10,_learning_rate=1.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=100,_learning_rate=0.01.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=100,_learning_rate=0.1.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=100,_learning_rate=1.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=50,_learning_rate=0.01.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=50,_learning_rate=0.1.eps │ │ │ │ ├── LABNTBNP_ada_boost_n_estimators=50,_learning_rate=1.eps │ │ │ │ ├── LABNTBNP_decision_tree_max_depth=20.eps │ │ │ │ ├── LABNTBNP_decision_tree_max_depth=5.eps │ │ │ │ ├── LABNTBNP_decision_tree_max_depth=50.eps │ │ │ │ ├── LABNTBNP_gaussian_naive_bayes.eps │ │ │ │ ├── LABNTBNP_logistic_regression_c=0.1.eps │ │ │ │ ├── LABNTBNP_logistic_regression_c=1.0.eps │ │ │ │ ├── LABNTBNP_logistic_regression_c=10.0.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=10,_max_depth=10.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=10,_max_depth=15.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=10,_max_depth=5.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=30,_max_depth=10.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=30,_max_depth=15.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=30,_max_depth=5.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=5,_max_depth=10.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=5,_max_depth=15.eps │ │ │ │ ├── LABNTBNP_random_forest_n_estimators=5,_max_depth=5.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=10,_learning_rate=0.01.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=10,_learning_rate=0.1.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=10,_learning_rate=1.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=100,_learning_rate=0.01.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=100,_learning_rate=0.1.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=100,_learning_rate=1.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=50,_learning_rate=0.01.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=50,_learning_rate=0.1.eps │ │ │ │ ├── LABSPLAC_ada_boost_n_estimators=50,_learning_rate=1.eps │ │ │ │ ├── LABSPLAC_decision_tree_max_depth=20.eps │ │ │ │ ├── LABSPLAC_decision_tree_max_depth=5.eps │ │ │ │ ├── LABSPLAC_decision_tree_max_depth=50.eps │ │ │ │ ├── LABSPLAC_gaussian_naive_bayes.eps │ │ │ │ ├── LABSPLAC_logistic_regression_c=0.1.eps │ │ │ │ ├── LABSPLAC_logistic_regression_c=1.0.eps │ │ │ │ ├── LABSPLAC_logistic_regression_c=10.0.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=10,_max_depth=10.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=10,_max_depth=15.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=10,_max_depth=5.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=30,_max_depth=10.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=30,_max_depth=15.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=30,_max_depth=5.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=5,_max_depth=10.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=5,_max_depth=15.eps │ │ │ │ ├── LABSPLAC_random_forest_n_estimators=5,_max_depth=5.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=10,_learning_rate=0.01.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=10,_learning_rate=0.1.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=10,_learning_rate=1.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=100,_learning_rate=0.01.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=100,_learning_rate=0.1.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=100,_learning_rate=1.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=50,_learning_rate=0.01.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=50,_learning_rate=0.1.eps │ │ │ │ ├── LABTSH_ada_boost_n_estimators=50,_learning_rate=1.eps │ │ │ │ ├── LABTSH_decision_tree_max_depth=20.eps │ │ │ │ ├── LABTSH_decision_tree_max_depth=5.eps │ │ │ │ ├── LABTSH_decision_tree_max_depth=50.eps │ │ │ │ ├── LABTSH_gaussian_naive_bayes.eps │ │ │ │ ├── LABTSH_logistic_regression_c=0.1.eps │ │ │ │ ├── LABTSH_logistic_regression_c=1.0.eps │ │ │ │ ├── LABTSH_logistic_regression_c=10.0.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=10,_max_depth=10.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=10,_max_depth=15.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=10,_max_depth=5.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=30,_max_depth=10.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=30,_max_depth=15.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=30,_max_depth=5.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=5,_max_depth=10.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=5,_max_depth=15.eps │ │ │ │ ├── LABTSH_random_forest_n_estimators=5,_max_depth=5.eps │ │ │ │ ├── accuracy_f1_scores.txt │ │ │ │ ├── logistic_regression.eps │ │ │ │ └── topKPrecision.py │ │ │ ├── pipelineResults_median_imputation.zip │ │ │ ├── pipelineResults_zero_imputation.zip │ │ │ ├── prepareData.py │ │ │ ├── prepareData_NonSTRIDE.py │ │ │ ├── processData.py │ │ │ ├── repeated_labs_charges_volumes.csv │ │ │ ├── try_Keras.py │ │ │ ├── utils_UCSF.py │ │ │ └── utils_UMich.py │ │ ├── multisite_mapping │ │ │ ├── map_component.tab │ │ │ ├── map_cormobidity.tab │ │ │ ├── map_standalone.tab │ │ │ ├── map_team.tab │ │ │ └── map_vitals.tab │ │ ├── report │ │ │ ├── JAMAopenNetwork.py │ │ │ ├── LNPP-repro-steps.md │ │ │ ├── LabNormalityReport.py │ │ │ ├── __init__.py │ │ │ └── data_inspector.py │ │ └── test │ │ │ ├── TestDataCreator.py │ │ │ ├── TestLabNormalityMatrix_UMich.py │ │ │ └── __init__.py │ ├── OpioidRx │ │ ├── compositeAssociations.py │ │ ├── dataNotes.txt │ │ ├── extractData.py │ │ ├── extractionNotes.longitudinal.txt │ │ ├── extractionNotes.txt │ │ ├── logisticRegression.R │ │ ├── machineLearn.py │ │ ├── preprocessData.py │ │ ├── problemAssociations.py │ │ ├── problemListAssociations.txt │ │ ├── setupNotes.txt │ │ └── webScraping │ │ │ ├── buprenorphinePhysicians.6.htm │ │ │ ├── buprenorphinePrescriberDownloader.py │ │ │ └── buprenorphinePrescriberScraper.py │ ├── PressGaney │ │ ├── Step.10.DataLoadingRegression.R │ │ └── Step.20.LogisticRegressionFormatOutput.R │ ├── ResidentLogs │ │ ├── pagerWordCounts.py │ │ └── stopWords.txt │ ├── ResidentRotationEHRUsage │ │ ├── Code │ │ │ ├── .RData │ │ │ ├── .Rhistory │ │ │ ├── .ipynb_checkpoints │ │ │ │ └── Daily EHR Time Spent Analysis Should We Filter-checkpoint.ipynb │ │ │ ├── compute_number_ehr_actions_per_24hour_cycle.py │ │ │ ├── compute_summary_stats.py │ │ │ └── generate_usage_spreadsheet.py │ │ ├── Data │ │ │ ├── Medical_Student_EHR_Use_Provider_Level.xlsx │ │ │ ├── ehr_action_categories.csv │ │ │ ├── ehr_action_descriptions.tsv │ │ │ ├── rotations.csv │ │ │ └── usage_spreadsheet.csv │ │ └── README │ ├── SepsisICU │ │ ├── exampleDates.py │ │ ├── extractData.py │ │ └── formatData.py │ ├── SimulationRecommender │ │ ├── Clinical Recommender Pipeline .ipynb │ │ ├── RecommenderPipeline │ │ │ ├── readme.md │ │ │ └── syncPipeline │ │ │ │ ├── UnitTests │ │ │ │ ├── CPOETrackerAnalysis.py │ │ │ │ ├── clinicalRecommenderGradingTests.py │ │ │ │ ├── clinicalRecommenderTests.py │ │ │ │ ├── configuration.py │ │ │ │ ├── helper.py │ │ │ │ ├── oneClick.py │ │ │ │ ├── readme.md │ │ │ │ ├── tables_figures.R │ │ │ │ ├── tables_figures_part2.R │ │ │ │ ├── tracker_script.py │ │ │ │ ├── tracker_script_v4.py │ │ │ │ ├── tracker_script_v5.py │ │ │ │ └── unique_grading.R │ │ │ │ └── readme.md │ │ ├── UserTestingNotes.txt │ │ ├── interview_script.md │ │ ├── parser.R │ │ ├── readme.md │ │ ├── simDataReader.py │ │ ├── simTest.md │ │ └── simulateCases.py │ ├── TSI_prediction │ │ └── TSI_Prediction_scripts.sql │ └── TopicModelsVsOrderSets │ │ ├── orderSetsUsed.py │ │ ├── patchAdHocOrderSet.py │ │ ├── step10.preparePatientItems.py │ │ ├── step110.prepareOrderSetItems.py │ │ ├── step130.orderSetTopicModelAnalysis.py │ │ ├── step140.orderSetAssociationAnalysis.py │ │ ├── step150.orderSetUsage.py │ │ ├── step170.collateResults.py │ │ ├── step180.formatResults.py │ │ ├── step185.formatResults.TimeMatched.py │ │ ├── step20.buildTopicModel.py │ │ ├── step30.topicModelAnalysis.py │ │ ├── step40.associationAnalysis.py │ │ ├── step50.orderSetUsage.py │ │ ├── stepXX.quickTest.py │ │ └── testGenSim.py ├── AuditLog │ ├── MooreMeeting │ │ └── July10.md │ ├── ct_head.R │ ├── general_inpatient_population_diagnosis.sql │ ├── mlSplitScript.py │ ├── pipeline.R │ ├── readme.md │ ├── sql_scripts │ │ └── ct_head.sql │ ├── strokeOrder.R │ ├── stroke_cohort.sql │ └── stroke_cohort_summary.R ├── BPA_Analysis │ ├── BPA_AlertAnalysis_Demgraphics.ipynb │ ├── BPA_AlertAnalysis_ICUTransferRate │ ├── BPA_AlertAnalysis_Paper_Demographics.ipynb │ ├── BPA_EncounterAnalysis_ReadmissionRateDiscrepancies │ ├── BPA_EncounterAnalysis_ReadmissionRateOrders │ ├── BPA_EncounterAnalysis_ReadmissionRateUpdated │ └── README.md ├── BloodCulturePrediction │ ├── EmpiricZosynBloodCultureOrganisms.sql │ ├── EmpiricZosynBloodCultureSusceptibility.sql │ ├── LabCultureMatrix.py │ └── SampleDataFigures.xlsx ├── Blood_Culture_Stewardship │ ├── Adult │ │ ├── Apply_Fabre_Fit_Notes_LLM.ipynb │ │ ├── BloodCultStewardship-AddingEDNotes.ipynb │ │ ├── BloodCultStewardshipCohort_Creation_StructureEHR.ipynb │ │ ├── Extract_Relevent_Chunk.ipynb │ │ ├── Fit_Notes_LLM_BloodCulture_Classification_NoFabre-COT.ipynb │ │ ├── Fit_Notes_LLM_BloodCulture_Classification_NoFabre.ipynb │ │ ├── ModelDevelopment_StructuredEHRData_LR.ipynb │ │ ├── ModelDevelopment_StructuredEHRData_PointingSystem.ipynb │ │ ├── Notes_With_EHR_LLM_Classification.ipynb │ │ └── README.md │ ├── Adult_refactor │ │ ├── BloodCultStewardship-AddingEDNotes.ipynb │ │ ├── BloodCultStewardshipCohort_Creation_StructureEHR.ipynb │ │ ├── Extract_Relevent_Chunk.ipynb │ │ ├── Fit_Notes_LLM_BloodCulture_Classification_NoFabre.ipynb │ │ ├── ModelDevelopment_StructuredEHRData_LR.ipynb │ │ ├── ModelDevelopment_StructuredEHRData_PointingSystem.ipynb │ │ ├── README.md │ │ └── src │ │ │ ├── Plain_Python_Baseline │ │ │ └── classify.py │ │ │ └── physician_label_aggregate │ │ │ └── dedup_result.ipynb │ ├── BloodCultStewardship.ipynb │ ├── Notes_With_EHR_LLM_Classification.ipynb │ ├── PEDs │ │ ├── ModelDev │ │ │ ├── Extract_Embeding_STELLA.py │ │ │ ├── ModelDevelopment.ipynb │ │ │ └── README.md │ │ ├── README.md │ │ └── StudyCohort │ │ │ ├── DataExtraction-PEDs-SIRS.ipynb │ │ │ ├── DataExtraction.ipynb │ │ │ └── README.md │ ├── README.md │ └── SimpleDecisionRuleInterpretation.sql ├── ClinicalDocumentationIntegrity │ ├── SampleDischargeSummary.txt │ ├── SampleRCC.txt │ └── SecureGPTSampleCodingDialog.txt ├── DevWorkshop │ ├── AWSDevEnvironment │ │ ├── ExampleQueryApp.py │ │ ├── batchDriver.py │ │ └── batchDriver.sh │ ├── DevWorkshopR │ │ ├── 02_unit_testing.R │ │ ├── command_line01.R │ │ ├── command_line02.R │ │ ├── markup_python_R.Rmd │ │ ├── mtcars2.csv │ │ ├── readme.md │ │ ├── unit_testing.R │ │ ├── unit_testing_a.R │ │ ├── unit_testing_b.R │ │ └── unit_testing_c.R │ ├── FHIR │ │ ├── fhir_endpoints.md │ │ └── fhir_fun.py │ ├── GithubWorkshop │ │ ├── github_workshop.txt │ │ ├── group_signature_1.txt │ │ ├── group_signature_2.txt │ │ ├── group_signature_3.txt │ │ ├── group_signature_4.txt │ │ ├── group_signature_5.txt │ │ ├── group_signature_6.txt │ │ ├── group_signature_7.txt │ │ └── group_signature_8.txt │ ├── GoogleCloudPlatform │ │ ├── ExampleQueryApp.py │ │ ├── batchDriver.py │ │ ├── batchDriver.sh │ │ ├── log │ │ │ └── placeholder.txt │ │ ├── moreExamples │ │ │ ├── auth_cloud.py │ │ │ ├── auth_quiver.py │ │ │ ├── batch │ │ │ │ ├── cloud_driver.sh │ │ │ │ ├── cloud_log.sh │ │ │ │ ├── cloud_read.py │ │ │ │ ├── cloud_write.py │ │ │ │ └── generateDriverScript.py │ │ │ ├── readme.md │ │ │ ├── requirements.txt │ │ │ └── sleep_loop.py │ │ └── results │ │ │ └── placeholder.txt │ ├── PredictiveModelling │ │ ├── predictive-modelling-workshop-solution.ipynb │ │ └── predictive-modelling-workshop.ipynb │ ├── Public_Data_Release_Guide.md │ ├── ROC-power │ │ ├── .vscode │ │ │ ├── launch.json │ │ │ └── settings.json │ │ ├── LICENSE │ │ ├── P3D │ │ │ ├── LICENSE │ │ │ ├── P3D.ipynb │ │ │ ├── Procfile │ │ │ ├── README.md │ │ │ ├── compare_auc_delong_xu.py │ │ │ ├── requirements.txt │ │ │ └── runtime.txt │ │ ├── README.md │ │ ├── bivariate_normal │ │ │ ├── compare_auc_delong_xu.py │ │ │ ├── contour.py │ │ │ ├── interactive_contours.ipynb │ │ │ └── interactive_contours.py │ │ ├── bootstrap.jpeg │ │ ├── data_and_models.pkl │ │ ├── data_gen.ipynb │ │ ├── data_mod.csv │ │ ├── de_long.R │ │ ├── final_mlp.pkl │ │ ├── final_models.pkl │ │ ├── final_rf.pkl │ │ ├── fit_models.ipynb │ │ ├── from_pairs │ │ │ ├── pair_power.ipynb │ │ │ └── pair_power.py │ │ ├── index.html │ │ ├── p3d.png │ │ ├── p3d_cropped.png │ │ ├── pilot.csv │ │ ├── roc_power.ipynb │ │ ├── shinyapp │ │ │ ├── basic-app │ │ │ │ ├── app.py │ │ │ │ ├── compare_auc_delong_xu.py │ │ │ │ ├── rsconnect-python │ │ │ │ │ └── basic-app.json │ │ │ │ ├── stats.py │ │ │ │ ├── stats2.py │ │ │ │ └── three_panel.py │ │ │ ├── collins │ │ │ │ ├── app.py │ │ │ │ ├── rsconnect-python │ │ │ │ │ └── collins.json │ │ │ │ └── stat_custom.py │ │ │ └── pilot │ │ │ │ ├── app.py │ │ │ │ ├── compare_auc_delong_xu.py │ │ │ │ ├── pilot.csv │ │ │ │ ├── rsconnect-python │ │ │ │ └── pilot.json │ │ │ │ └── three_panel_pilot.py │ │ └── speedboot.py │ ├── ReadMe.AWSDevEnvironment.txt │ ├── ReadMe.Git.BasicVersionControl.txt │ ├── ReadMe.GoogleCloud-BigQuery-VPC.txt │ ├── ReadMe.GoogleCloudDevEnvironment.txt │ ├── ReadMe.LLaMAsetup.md │ ├── ReadMe.PHSDataAccess.txt │ ├── ReadMe.PivotCharts.txt │ ├── ReadMe.PowerCalculationSimulation.txt │ ├── ReadMe.SQLQuery.txt │ ├── ReadMe.TestFirstDev.txt │ ├── STARR-OMOP │ │ ├── StarterNotes.txt │ │ ├── WorkshopNotes.01.txt │ │ ├── WorkshopNotes.02.txt │ │ └── WorkshopNotes.03.txt │ ├── UnitTesting │ │ ├── ApplicationModule.py │ │ ├── TestApplicationModule.py │ │ ├── UnitTesting.R │ │ └── __init__.py │ ├── causal_inference │ │ ├── README.md │ │ ├── correlation_causation.png │ │ ├── cow.png │ │ ├── tuto.html │ │ └── tuto.ipynb │ ├── cosmos-onboarding.md │ ├── llm-api │ │ ├── agnostic_evaluator_models.py │ │ ├── openaimodels_1.png │ │ ├── openaimodels_2.png │ │ └── phi-llm-api-python.md │ ├── open-weight-llms.md │ ├── sampleData │ │ ├── abstractLines.txt │ │ ├── abstracts.parser.py │ │ ├── abstracts.xml │ │ ├── labBaseDisplayNameLookup.tsv │ │ └── labConsecutiveNormalStats.tsv │ ├── sandbox │ │ ├── TestFile.txt │ │ ├── bootstrapTest.py │ │ └── jonc101.testfile.txt │ ├── screening │ │ ├── associationStats │ │ │ ├── AssociationStatsExample.py │ │ │ ├── PartD_Prescriber_PUF_NPI_DRUG_15.sample.zip │ │ │ └── TestAssociationStatsExample.py │ │ ├── parsing │ │ │ ├── ParsingExample.py │ │ │ └── TestParsingExample.py │ │ └── sqlQuery │ │ │ ├── SQLQueryExample.py │ │ │ ├── TestSQLQueryExample.py │ │ │ └── chinook.db │ ├── statsSimCalc │ │ ├── powerCalculation.R │ │ ├── powerCalculation.examples.R │ │ └── rocBootstrap.R │ └── survival_analysis │ │ └── survival_analysis_workshop_R.Rmd ├── Discharge_Sum │ ├── ExtractDischargeSummaryInfo.py │ ├── database_extraction │ │ ├── clean_notes.py │ │ ├── export.py │ │ ├── export_from_final_df.py │ │ └── pivoted_notes.py │ ├── export.py │ ├── format_prefill.py │ ├── google_app_scripts │ │ ├── collect_responses.gs │ │ ├── copy_template_form.gs │ │ ├── get_note_links.gs │ │ ├── get_note_links2.gs │ │ ├── new_prefill.gs │ │ ├── populate_forms.gs │ │ └── resart_all.gs │ ├── google_spreadsheet │ │ ├── better_query.txt │ │ └── query.py │ ├── llm │ │ ├── ExtractDischargeSummaryInfo.py │ │ ├── h_face.py │ │ ├── keras_hub_test.py │ │ ├── prefill_with_llm.py │ │ └── search_clean_notes.py │ └── pivoted_notes.py ├── ER_Infection │ ├── README.md │ ├── SQL │ │ ├── Featurize │ │ │ ├── Feature_Sequence.sql │ │ │ └── feature_counts_long.sql │ │ ├── Refactored │ │ │ ├── abx_orders_given_and_stopped.sql │ │ │ ├── abx_orders_given_and_stopped_2_weeks.sql │ │ │ ├── abx_orders_given_and_stopped_include_oral.sql │ │ │ ├── abx_orders_within_24_hrs.sql │ │ │ ├── abx_orders_within_24_hrs_incude_oral.sql │ │ │ ├── abx_orders_within_2_weeks.sql │ │ │ ├── abx_types.sql │ │ │ ├── cohort_not_infected_rules.sql │ │ │ ├── culture_orders_within_24_hrs.sql │ │ │ ├── culture_types.sql │ │ │ ├── final_cohort_table.sql │ │ │ └── mar_was_given.sql │ │ ├── abx_ast_long.sql │ │ ├── abx_cohort_mar_interm.sql │ │ ├── abx_cohort_not_censored_label.sql │ │ ├── abx_cohort_not_censored_no_kids.sql │ │ ├── abx_cohort_not_censored_no_kids_no_prior.sql │ │ ├── abx_culture_orders_within_4_hours.sql │ │ ├── abx_include.sql │ │ ├── abx_include_exclude_cultures.sql │ │ ├── abx_mar_action_was_given_flag.sql │ │ ├── abx_med_orders_given_and_stopped_info.sql │ │ ├── abx_med_orders_within_last_4_hours.sql │ │ ├── abx_not_infected_csns.sql │ │ ├── abx_organism_and_ast_report_freq.sql │ │ ├── abx_temp_14_day_orders.sql │ │ ├── positive_urine_cultures_outpatient.sql │ │ └── positive_urine_cultures_with_abx_info.sql │ └── notebooks │ │ ├── decision_alg │ │ ├── Allocation Distribution Figure.ipynb │ │ ├── Antibiotic Sweep Plots.ipynb │ │ ├── DecisionAnalysis.py │ │ ├── Integer Programming Including Not Infected.ipynb │ │ ├── Integer Programming.ipynb │ │ └── integer_programming.py │ │ ├── demo │ │ └── Demo Personalized Antibiogram Linear Programming.ipynb │ │ ├── eda │ │ ├── Abx_Start_and_Stop.ipynb │ │ └── PositiveCultures.ipynb │ │ ├── featurizing │ │ ├── bin_features.ipynb │ │ ├── bin_labs_vitals.ipynb │ │ ├── bin_labs_vitals.py │ │ ├── to_sparse.py │ │ ├── to_sparse_ast.ipynb │ │ └── to_sparse_c.ipynb │ │ ├── figure_and_tabels │ │ ├── Classier Results Table Bucket 1.ipynb │ │ ├── Culture Result Times.ipynb │ │ ├── Figure 2 Abx Selection Patterns.ipynb │ │ ├── IPW vs NOT AUROC Estimates.ipynb │ │ ├── Table Feature Types And Counts.ipynb │ │ ├── Table Misses by bug.ipynb │ │ ├── Table1.ipynb │ │ ├── Table2 Top Bugs.ipynb │ │ ├── figure2.sql │ │ ├── sweep_plots.py │ │ ├── table1.sql │ │ └── table2.sql │ │ ├── labelling │ │ ├── AST_Processing.ipynb │ │ └── fill_in_rules.py │ │ ├── mit_data_analysis │ │ ├── CheckDrPerformance.ipynb │ │ ├── linear_programming.py │ │ └── train_models_mit.py │ │ └── modeling │ │ ├── FeatureMatrix.py │ │ ├── Train Censored Model.ipynb │ │ ├── batch_driver.sh │ │ └── train_model.py ├── GoogleCloud │ ├── BQ │ │ ├── BigQueryConnect.py │ │ ├── BigQueryConnect_py2.py │ │ ├── __init__.py │ │ ├── ahrq │ │ │ ├── ahrq_citation.txt │ │ │ ├── create_ahrq.sh │ │ │ ├── create_ahrq_table.py │ │ │ ├── upload_ahrq.py │ │ │ └── upload_ahrq_diag.py │ │ ├── alert_upload.py │ │ ├── auth_cloud.py │ │ ├── google_auth.R │ │ ├── load_stride_tables.py │ │ ├── lpch │ │ │ ├── date_utc_change.sql │ │ │ ├── directory_flowsheet_setup.sh │ │ │ ├── preprocess_flowsheet.py │ │ │ ├── preprocess_upload_flowsheet.py │ │ │ ├── upload_lpch_clinical_note_meta.py │ │ │ ├── upload_lpch_demographics.py │ │ │ ├── upload_lpch_diagnosis.py │ │ │ ├── upload_lpch_drg_code.py │ │ │ ├── upload_lpch_lab_result.py │ │ │ ├── upload_lpch_mar.py │ │ │ ├── upload_lpch_ndc_code.py │ │ │ ├── upload_lpch_order_med.py │ │ │ ├── upload_lpch_path_report.py │ │ │ ├── upload_lpch_procedure.py │ │ │ ├── upload_lpch_radiology_meta.py │ │ │ ├── upload_new_date_column.py │ │ │ └── upload_template.py │ │ ├── readme.md │ │ ├── requirements.txt │ │ ├── shc │ │ │ ├── directory_shc_setup.sh │ │ │ ├── preprocess_shc_order_proc.py │ │ │ └── upload_shc_order_proc.py │ │ ├── test │ │ │ ├── check_row_counts.py │ │ │ ├── testBigQueryConnect.py │ │ │ └── testSTARRDemo.py │ │ ├── upload_alert_history.py │ │ ├── upload_alerts_orders.py │ │ ├── upload_alt_com_action.py │ │ ├── upload_alt_drug_allergy.py │ │ └── upload_culture_sensitivity.py │ ├── Sheets │ │ ├── sheets_to_df.py │ │ └── test_sheets_to_df.py │ ├── StrokeCohort │ │ ├── ministudy.sql │ │ ├── readme.md │ │ └── stroke_aggregate.R │ ├── __init__.py │ ├── cloud_sdk │ │ └── readme.md │ ├── readme.md │ └── specialty_referral │ │ ├── cardiology_referral.sql │ │ ├── cardiology_referral_script.R │ │ ├── gastroenterology_referral.sql │ │ ├── gastroenterology_referral_script.R │ │ ├── nested_referral_script.R │ │ └── readme.md ├── Heme-Stamp │ ├── README.md │ ├── __init__.py │ ├── cosmos.py │ ├── deploy.py │ ├── generateEmail.py │ ├── orderInfo.py │ ├── order_action.py │ └── train_model.py ├── InpatientDiabetes │ ├── BigQuery Access.ipynb │ ├── Data_Getting.ipynb │ ├── Inpatient diabetes cohort │ ├── Inpatientdiabetesreadme.md │ ├── TDD prediction │ │ ├── Except_pts_TT_ICU_vs_ADT_ICU.sql │ │ ├── Patients_with_TxTeam_as_ICU.sql │ │ ├── TDD cohort │ │ ├── TDD_insulin.sql │ │ └── TDD_subqueries.sql │ ├── TDD_insulin.sql │ ├── TDD_subqueries.sql │ ├── flowsheetglucoses.sql │ ├── inpt_glucose_labs.sql │ ├── inpt_subQ_insulin.sql │ └── inpt_weight.sql ├── InpatientVariability │ ├── clinicalFeatures.R │ ├── clinicalFeatures.sql │ ├── cohortSelection.sql │ ├── comorbiditiesOnAdmission.sql │ ├── hospitalLengthOfStayVariability.sql │ ├── inptCostVar_lm_v1.R │ ├── lacticAcidosisOnAdmission.sql │ ├── objectiveFeatures.sql │ ├── objectiveFindings.R │ ├── obsAdmitMismatch.sql │ └── readme.txt ├── InpatientVariabilityUpdate │ ├── Explorations │ │ ├── 0.1 DRG burden.sql │ │ ├── 0.2 GI hospitalization checks.sql │ │ ├── 0.3 Link cost data.sql │ │ ├── 0.4 Cost sanity checks [DRAFT] │ │ ├── 0.5 Extractor merge checks │ │ └── readme.txt │ ├── Master file.ipynb │ └── readme.txt ├── KFREReferralRate │ ├── AUROC_initial code_AC.R │ ├── Notes.txt │ └── referral_gaps.sql ├── LabCulturePrediction │ ├── AntiBiogramMatrix.py │ ├── AntiBiogramPredictionPipeline.py │ ├── DecisionMakingClass │ │ ├── SQL │ │ │ ├── DemographicFeatures.sql │ │ │ ├── DxFeatures.sql │ │ │ ├── ImagingFeatures.sql │ │ │ ├── LabFeatures.sql │ │ │ ├── MedFeatures.sql │ │ │ ├── MicrobiologyOrderFeatures.sql │ │ │ └── ProcedureFeatures.sql │ │ ├── UtilityModel.py │ │ ├── batch_driver.sh │ │ ├── cohort_queries.py │ │ ├── cost_analysis.py │ │ ├── feature_engineering.py │ │ ├── label_generation.py │ │ ├── predictive_models.py │ │ └── run_experiments.py │ ├── LabCultureMatrix.py │ ├── LabCulturePredictionPipeline.py │ ├── MRSAMatrix.py │ ├── MRSAPredictionPipeline.py │ ├── PersonalizedAntibiogramMatrix.py │ ├── PersonalizedAntibiogramPredictionPipeline.py │ ├── README.md │ ├── SusceptibilityPredictionPipeline.py │ ├── Susceptibility_Feature_Names.csv │ └── __init__.py ├── Labogram │ ├── labRepeatSummaryStats.sql │ ├── labogram.ipynb │ ├── labogram_2022-04-19.csv │ ├── labogram_2022-04-19_ci.csv │ └── unit_test_results.csv ├── Manoj_AntibioticPrediction │ ├── AMIA_models_antibiotic_susceptibility.Rmd │ ├── AMIA_revision_logreg_imputed.Rmd │ ├── antibiotic_susceptibility_inference_rules.sql │ ├── antibiotics_in_next_24_hours.sql │ ├── dataset_generation_with_antibiotic_inference.sql │ └── test.Rmd ├── Monitoring_Induced_Feedback-main │ ├── Pickles │ │ └── results.pickle │ ├── README.md │ ├── data_generation.py │ ├── monitoring.py │ └── simulate.py ├── Moore_Stroke │ ├── Aspirin.sql │ ├── Demographics.sql │ ├── ExampleAccessLogJoin.sql │ ├── HistoryOfAfib.sql │ ├── Labels.sql │ ├── Moore_Stroke_Exploration.ipynb │ └── Vitals.sql ├── OUDTreatmentRetentionVSAttrition │ ├── SQL │ │ ├── externalValidation_extractRecords.sql │ │ ├── extractDemogs.sql │ │ ├── extractRecords.sql │ │ ├── featureSelection.sql │ │ └── table1.sql │ ├── Sanity Check │ │ ├── 29978050.csv │ │ ├── 30021837_demographics.csv │ │ ├── 30021837_eras.csv │ │ ├── 30021837_exposures.csv │ │ ├── 30153707_demographics.csv │ │ ├── 30153707_eras.csv │ │ ├── 30153707_exposures.csv │ │ ├── 30959303_demographics.csv │ │ ├── 30959303_eras.csv │ │ ├── 30959303_exposures.csv │ │ ├── Book1.xlsx │ │ └── example_patient_data.xlsx │ ├── WebApp │ │ ├── README.md │ │ ├── app.py │ │ ├── build.sh │ │ ├── models.py │ │ ├── requirements.txt │ │ ├── static │ │ │ ├── app.js │ │ │ └── style.css │ │ └── templates │ │ │ └── index.html │ ├── cohortConstruction.py │ ├── compare_roc_curves_all.py │ ├── externalValidation_cohortConstruction.py │ ├── llm_models │ │ ├── dev_setup_m42_multi_gpu_assertion.py │ │ ├── dev_setup_m42_multi_gpu_assertion_updated.py │ │ ├── med42_load.py │ │ └── med42_load_updated.py │ ├── main_ml_models.py │ ├── main_visualization.py │ ├── models │ │ ├── ml_models.py │ │ └── survival_pipeline.py │ ├── results │ │ ├── bar_xgb_original_test.png │ │ ├── beeswarm_xgb_original_test.png │ │ ├── lr_prediction_performance.csv │ │ ├── lr_results_report.csv │ │ ├── reapeated_testing │ │ │ ├── dict_report_lr_1.csv │ │ │ ├── dict_report_lr_10.csv │ │ │ ├── dict_report_lr_11.csv │ │ │ ├── dict_report_lr_12.csv │ │ │ ├── dict_report_lr_13.csv │ │ │ ├── dict_report_lr_14.csv │ │ │ ├── dict_report_lr_15.csv │ │ │ ├── dict_report_lr_16.csv │ │ │ ├── dict_report_lr_17.csv │ │ │ ├── dict_report_lr_18.csv │ │ │ ├── dict_report_lr_19.csv │ │ │ ├── dict_report_lr_2.csv │ │ │ ├── dict_report_lr_20.csv │ │ │ ├── dict_report_lr_21.csv │ │ │ ├── dict_report_lr_22.csv │ │ │ ├── dict_report_lr_23.csv │ │ │ ├── dict_report_lr_24.csv │ │ │ ├── dict_report_lr_25.csv │ │ │ ├── dict_report_lr_26.csv │ │ │ ├── dict_report_lr_27.csv │ │ │ ├── dict_report_lr_28.csv │ │ │ ├── dict_report_lr_29.csv │ │ │ ├── dict_report_lr_3.csv │ │ │ ├── dict_report_lr_30.csv │ │ │ ├── dict_report_lr_31.csv │ │ │ ├── dict_report_lr_32.csv │ │ │ ├── dict_report_lr_33.csv │ │ │ ├── dict_report_lr_34.csv │ │ │ ├── dict_report_lr_35.csv │ │ │ ├── dict_report_lr_36.csv │ │ │ ├── dict_report_lr_37.csv │ │ │ ├── dict_report_lr_38.csv │ │ │ ├── dict_report_lr_39.csv │ │ │ ├── dict_report_lr_4.csv │ │ │ ├── dict_report_lr_40.csv │ │ │ ├── dict_report_lr_41.csv │ │ │ ├── dict_report_lr_42.csv │ │ │ ├── dict_report_lr_43.csv │ │ │ ├── dict_report_lr_44.csv │ │ │ ├── dict_report_lr_45.csv │ │ │ ├── dict_report_lr_46.csv │ │ │ ├── dict_report_lr_47.csv │ │ │ ├── dict_report_lr_48.csv │ │ │ ├── dict_report_lr_49.csv │ │ │ ├── dict_report_lr_5.csv │ │ │ ├── dict_report_lr_50.csv │ │ │ ├── dict_report_lr_6.csv │ │ │ ├── dict_report_lr_7.csv │ │ │ ├── dict_report_lr_8.csv │ │ │ ├── dict_report_lr_9.csv │ │ │ ├── dict_report_rf_1.csv │ │ │ ├── dict_report_rf_10.csv │ │ │ ├── dict_report_rf_11.csv │ │ │ ├── dict_report_rf_12.csv │ │ │ ├── dict_report_rf_13.csv │ │ │ ├── dict_report_rf_14.csv │ │ │ ├── dict_report_rf_15.csv │ │ │ ├── dict_report_rf_16.csv │ │ │ ├── dict_report_rf_17.csv │ │ │ ├── dict_report_rf_18.csv │ │ │ ├── dict_report_rf_19.csv │ │ │ ├── dict_report_rf_2.csv │ │ │ ├── dict_report_rf_20.csv │ │ │ ├── dict_report_rf_21.csv │ │ │ ├── dict_report_rf_22.csv │ │ │ ├── dict_report_rf_23.csv │ │ │ ├── dict_report_rf_24.csv │ │ │ ├── dict_report_rf_25.csv │ │ │ ├── dict_report_rf_26.csv │ │ │ ├── dict_report_rf_27.csv │ │ │ ├── dict_report_rf_28.csv │ │ │ ├── dict_report_rf_29.csv │ │ │ ├── dict_report_rf_3.csv │ │ │ ├── dict_report_rf_30.csv │ │ │ ├── dict_report_rf_31.csv │ │ │ ├── dict_report_rf_32.csv │ │ │ ├── dict_report_rf_33.csv │ │ │ ├── dict_report_rf_34.csv │ │ │ ├── dict_report_rf_35.csv │ │ │ ├── dict_report_rf_36.csv │ │ │ ├── dict_report_rf_37.csv │ │ │ ├── dict_report_rf_38.csv │ │ │ ├── dict_report_rf_39.csv │ │ │ ├── dict_report_rf_4.csv │ │ │ ├── dict_report_rf_40.csv │ │ │ ├── dict_report_rf_41.csv │ │ │ ├── dict_report_rf_42.csv │ │ │ ├── dict_report_rf_43.csv │ │ │ ├── dict_report_rf_44.csv │ │ │ ├── dict_report_rf_45.csv │ │ │ ├── dict_report_rf_46.csv │ │ │ ├── dict_report_rf_47.csv │ │ │ ├── dict_report_rf_48.csv │ │ │ ├── dict_report_rf_49.csv │ │ │ ├── dict_report_rf_5.csv │ │ │ ├── dict_report_rf_50.csv │ │ │ ├── dict_report_rf_6.csv │ │ │ ├── dict_report_rf_7.csv │ │ │ ├── dict_report_rf_8.csv │ │ │ ├── dict_report_rf_9.csv │ │ │ ├── dict_report_xgb_1.csv │ │ │ ├── dict_report_xgb_10.csv │ │ │ ├── dict_report_xgb_11.csv │ │ │ ├── dict_report_xgb_12.csv │ │ │ ├── dict_report_xgb_13.csv │ │ │ ├── dict_report_xgb_14.csv │ │ │ ├── dict_report_xgb_15.csv │ │ │ ├── dict_report_xgb_16.csv │ │ │ ├── dict_report_xgb_17.csv │ │ │ ├── dict_report_xgb_18.csv │ │ │ ├── dict_report_xgb_19.csv │ │ │ ├── dict_report_xgb_2.csv │ │ │ ├── dict_report_xgb_20.csv │ │ │ ├── dict_report_xgb_21.csv │ │ │ ├── dict_report_xgb_22.csv │ │ │ ├── dict_report_xgb_23.csv │ │ │ ├── dict_report_xgb_24.csv │ │ │ ├── dict_report_xgb_25.csv │ │ │ ├── dict_report_xgb_26.csv │ │ │ ├── dict_report_xgb_27.csv │ │ │ ├── dict_report_xgb_28.csv │ │ │ ├── dict_report_xgb_29.csv │ │ │ ├── dict_report_xgb_3.csv │ │ │ ├── dict_report_xgb_30.csv │ │ │ ├── dict_report_xgb_31.csv │ │ │ ├── dict_report_xgb_32.csv │ │ │ ├── dict_report_xgb_33.csv │ │ │ ├── dict_report_xgb_34.csv │ │ │ ├── dict_report_xgb_35.csv │ │ │ ├── dict_report_xgb_36.csv │ │ │ ├── dict_report_xgb_37.csv │ │ │ ├── dict_report_xgb_38.csv │ │ │ ├── dict_report_xgb_39.csv │ │ │ ├── dict_report_xgb_4.csv │ │ │ ├── dict_report_xgb_40.csv │ │ │ ├── dict_report_xgb_41.csv │ │ │ ├── dict_report_xgb_42.csv │ │ │ ├── dict_report_xgb_43.csv │ │ │ ├── dict_report_xgb_44.csv │ │ │ ├── dict_report_xgb_45.csv │ │ │ ├── dict_report_xgb_46.csv │ │ │ ├── dict_report_xgb_47.csv │ │ │ ├── dict_report_xgb_48.csv │ │ │ ├── dict_report_xgb_49.csv │ │ │ ├── dict_report_xgb_5.csv │ │ │ ├── dict_report_xgb_50.csv │ │ │ ├── dict_report_xgb_6.csv │ │ │ ├── dict_report_xgb_7.csv │ │ │ ├── dict_report_xgb_8.csv │ │ │ ├── dict_report_xgb_9.csv │ │ │ ├── reapeated_testing_lr.csv │ │ │ ├── reapeated_testing_lr.xlsx │ │ │ ├── reapeated_testing_precisions_recalls_lr.csv │ │ │ ├── reapeated_testing_precisions_recalls_rf.csv │ │ │ ├── reapeated_testing_precisions_recalls_xgb.csv │ │ │ ├── reapeated_testing_rf.csv │ │ │ ├── reapeated_testing_rf.xlsx │ │ │ ├── reapeated_testing_xgb.csv │ │ │ └── reapeated_testing_xgb.xlsx │ │ ├── rf_feature_importance_concept_ids.png │ │ ├── rf_prediction_performance.csv │ │ ├── rf_results_report.csv │ │ ├── roc_curve_lr.png │ │ ├── roc_curve_rf.png │ │ ├── roc_curve_xgb.png │ │ └── xgb_prediction_performance.csv │ ├── saved_classical_ml_models │ │ ├── best_params_lr.csv │ │ ├── best_params_rf.csv │ │ ├── best_params_xgb.csv │ │ ├── lr_hyperparameters.csv │ │ ├── predictions_lr.csv │ │ ├── predictions_rf.csv │ │ ├── predictions_xgb.csv │ │ ├── rf_hyperparameters.csv │ │ └── xgb_hyperparameters.csv │ ├── shap │ │ └── shap.py │ ├── survival_models │ │ ├── column_mapping.py │ │ ├── pipeline_survival.py │ │ ├── synthetic_data_generate.py │ │ └── synthetic_survival_data.csv │ └── unit_test.py ├── OrderSetStats │ └── orderser_stats.sql ├── OrdersetExpectedVsReality │ ├── Code │ │ ├── STEP1A_get_orderset_usage_instances.py │ │ ├── STEP1B_define_orders_in_ordersets.py │ │ ├── STEP2A_count_co_occurring_orders_not_in_orderset.py │ │ ├── STEP2B_compute_co_occurring_statistics.py │ │ ├── STEP2C_compute_median_ordering_prob_cutoffs.py │ │ ├── STEP2D_filter_co_occurring_orders.py │ │ ├── STEP3A_find_order_ids_associated_with_ordersets.py │ │ ├── STEP3B_count_co_occurring_orders_already_in_orderset.py │ │ └── STEP3C_filter_a_la_carte_orders.py │ └── Data │ │ ├── orderset_ordering_probabilities.csv │ │ └── retraction_spreadsheet.csv ├── OutpatientLabPrediction │ └── OutpatientAutomatedMLCode.ipynb ├── OutpatientReferral │ ├── ChatGPT.CustomInstructions.txt │ ├── TemplatePromptEngineeringTests.txt │ ├── __init__.py │ ├── data_config.py │ ├── data_utils.py │ ├── eConsult_frequent_meds.sql │ ├── encounterCohortDescription.sql │ ├── encounterCohortItemAssociation.sql │ ├── entNasalCongestionReferralCohort.sql │ ├── mapping │ │ ├── EConsult.SmartText.Endrocrinology.txt │ │ └── icd10_categories.csv │ ├── notes.md │ ├── optumQueries.sql │ ├── queries.py │ ├── sampleQueries.sql │ ├── specialtyReferralEncounterCohortDefinitions.sql │ └── topSpecialtyOrders.sql ├── PADScreening │ └── vascularPADcohort.sql ├── PedsLabUtil │ ├── STARR-Data-Dictionary.pdf │ ├── analysis_lradt.ipynb │ ├── analysis_lradt_icu.ipynb │ ├── data │ │ ├── group_lab_name_counts.csv │ │ ├── group_lab_name_counts_icu.csv │ │ ├── labdtq.csv │ │ ├── labdtq_icu.csv │ │ ├── labstab.csv │ │ ├── labstab_icu.csv │ │ ├── labstab_melted.csv │ │ ├── labstabcnts.csv │ │ └── labstabcnts_icu.csv │ ├── explore_lab_result.ipynb │ ├── explore_lradt.ipynb │ ├── explore_lradt_acc.ipynb │ ├── figures_cic.ipynb │ ├── query_log_2021-09-25.txt │ ├── query_lradt_20210927.ipynb │ ├── query_lradt_20211025.ipynb │ └── query_lradt_icu_20211027.ipynb ├── SubstanceUseRelapseNLP │ └── sampleQueries.sql ├── UrineCulture │ ├── notebooks │ │ └── suspected-uti-cohort-eda.ipynb │ └── sql │ │ └── antibiogram.sql ├── WayfindingInfoGathering │ └── erVisitPrimaryDiagnosisNoteConcepts.sql ├── __init__.py ├── algorithm_ranking_analysis │ └── ranking_friedman_nemenyi.py ├── antibiotic-susceptibility │ ├── AIM2 │ │ ├── HttpTriggerInference │ │ │ ├── EmpricABX.py │ │ │ ├── README.md │ │ │ ├── __init__.py │ │ │ ├── cosmos.py │ │ │ └── feature_engineering.py │ │ ├── README.md │ │ ├── TimetriggerActivepopulation │ │ │ ├── __init__.py │ │ │ └── function.json │ │ └── utils │ │ │ ├── README.md │ │ │ ├── cosmos.py │ │ │ └── utils.py │ ├── Aim 1a │ │ ├── CPT_ICD10PCS_mapping.csv │ │ ├── Labs.sql │ │ ├── Microbial_Resistance.sql │ │ ├── Preganacy-posetive-test.sql │ │ ├── README.md │ │ ├── README.txt │ │ ├── Vitals.sql │ │ ├── abx_class_exposure.sql │ │ ├── abx_subtype_exposure.sql │ │ ├── comorbidity_step2.ipynb │ │ ├── microbiology_cultures_adi_scores.sql │ │ ├── microbiology_cultures_cohort_query.sql │ │ ├── microbiology_cultures_comorbidity_step1.sql │ │ ├── microbiology_cultures_demographics.sql │ │ ├── microbiology_cultures_nursing_home_visits.sql │ │ ├── microbiology_cultures_pregnancy.sql │ │ ├── microbiology_cultures_prior_med.sql │ │ ├── microbiology_cultures_procedures_6mo.sql │ │ ├── microbiology_cultures_ward_info.sql │ │ ├── notes_query.sql │ │ ├── pediatrics_queries │ │ │ ├── microbiology_cultures_adi_scores_peds.sql │ │ │ ├── microbiology_cultures_antibiotic_class_exposure_peds.sql │ │ │ ├── microbiology_cultures_antibiotic_subtype_exposure_peds.sql │ │ │ ├── microbiology_cultures_cohort_peds_query.sql │ │ │ ├── microbiology_cultures_demographics_peds.sql │ │ │ └── microbiology_cultures_medication_exposure_peds.sql │ │ ├── prior_abx_class_subtype_lookup.sql │ │ ├── prior_infecting_organism.sql │ │ ├── susceptibility_inference_antibiotics_organisms.sql │ │ └── time-to-event-augmented-queries │ │ │ ├── Implied-susceptibility.sql │ │ │ ├── antibiotic_class_exposure.sql │ │ │ ├── antibiotic_subtype_exposure.sql │ │ │ ├── comorbidities.sql │ │ │ ├── medication_exposure.sql │ │ │ ├── microbial_resistance.sql │ │ │ ├── nursing_home_visits.sql │ │ │ ├── previous_infecting_organisms.sql │ │ │ └── prior_procedures.sql │ ├── Aim 3 │ │ └── README.txt │ ├── Aim 4 │ │ ├── AIM4 │ │ │ ├── .gitignore │ │ │ ├── Aim_4_Cohort_Flowchart_previous │ │ │ │ ├── Aim_4_Cohort_Flowchart_Final.key │ │ │ │ ├── Aim_4_Cohort_Flowchart_previous.001.png │ │ │ │ ├── Aim_4_Cohort_Flowchart_previous.002.png │ │ │ │ └── Aim_4_Figure.key │ │ │ ├── Embedding_Pilot_Exp │ │ │ │ ├── .gitignore │ │ │ │ ├── README_ENV.md │ │ │ │ ├── activate_env.sh │ │ │ │ ├── notebook │ │ │ │ │ ├── README.md │ │ │ │ │ ├── actual_error_checking.ipynb │ │ │ │ │ ├── automated_error_checking.py │ │ │ │ │ ├── config.py │ │ │ │ │ ├── data_explore.ipynb │ │ │ │ │ ├── data_explore_with_error_checking.ipynb │ │ │ │ │ ├── error_analysis.ipynb │ │ │ │ │ ├── evaluator_analysis_notebook.ipynb │ │ │ │ │ ├── example_config_usage.py │ │ │ │ │ └── huggingface_embedding.ipynb │ │ │ │ ├── requirements.txt │ │ │ │ ├── script │ │ │ │ │ ├── export_from_bigquery.py │ │ │ │ │ ├── query_logger.py │ │ │ │ │ └── update_ssh_ip.sh │ │ │ │ └── src │ │ │ │ │ ├── batch_runner.py │ │ │ │ │ ├── batch_runner_DSPy_.py │ │ │ │ │ ├── config │ │ │ │ │ ├── __init__.py │ │ │ │ │ └── config.py │ │ │ │ │ ├── llm │ │ │ │ │ ├── __init__.py │ │ │ │ │ ├── llm_client.py │ │ │ │ │ └── llm_models.py │ │ │ │ │ ├── main.py │ │ │ │ │ ├── main_DSPy.py │ │ │ │ │ ├── notebook │ │ │ │ │ ├── comparison_with_new_pipeline.ipynb │ │ │ │ │ ├── human_validation_results.ipynb │ │ │ │ │ ├── reformat.ipynb │ │ │ │ │ ├── reformat.py │ │ │ │ │ └── results_analysis_with_reference.ipynb │ │ │ │ │ └── util │ │ │ │ │ ├── DSPy_modules.py │ │ │ │ │ ├── DSPy_results_helpers.py │ │ │ │ │ ├── prompt_helper.py │ │ │ │ │ ├── pydantic_modules.py │ │ │ │ │ └── results_helper.py │ │ │ └── Notebook │ │ │ │ ├── Adult_ED_Cohort_no_allergy.ipynb │ │ │ │ ├── Adult_ED_Cohort_no_allergy_debug.ipynb │ │ │ │ ├── Adult_ED_Cohort_no_allergy_debug_outpatient.ipynb │ │ │ │ ├── Adult_ED_Cohort_no_allergy_present.ipynb │ │ │ │ ├── Adult_ED_Cohort_no_allergy_present.pdf │ │ │ │ ├── Adult_ED_Cohort_no_allergy_present_copy.ipynb │ │ │ │ ├── Cohort_analysis.ipynb │ │ │ │ ├── PEDs_ED_Cohort_no_allergy_debug.ipynb │ │ │ │ ├── PEDs_ED_Cohort_no_allergy_present.ipynb │ │ │ │ ├── antibiotic_stewardship_results_dev5.csv │ │ │ │ ├── antibiotic_stewardship_results_with_labels.csv │ │ │ │ └── imgs │ │ │ │ ├── Aim_4_Flowchart_Custom.pdf │ │ │ │ ├── Aim_4_Flowchart_Custom_peds.pdf │ │ │ │ ├── final_step.png.png │ │ │ │ ├── final_step_peds.png │ │ │ │ ├── oervall.png │ │ │ │ ├── step1-2.png │ │ │ │ ├── step1-2_peds.png │ │ │ │ ├── step3-1.png │ │ │ │ ├── step3-1_peds.png │ │ │ │ ├── step3-2.png │ │ │ │ ├── step3-2_peds.png │ │ │ │ ├── step3.png │ │ │ │ ├── step3_peds.png │ │ │ │ ├── step4-1.png │ │ │ │ ├── step4-1.png.png │ │ │ │ ├── step4-2.png │ │ │ │ ├── step4-2.png.png │ │ │ │ ├── step4-2_peds.png.png │ │ │ │ ├── step5.png │ │ │ │ ├── step5.png.png │ │ │ │ ├── step5_peds.png │ │ │ │ ├── step6.png │ │ │ │ ├── step6.png.png │ │ │ │ └── step6_peds.png │ │ ├── README.txt │ │ ├── aim4_base_cohort.sql │ │ ├── aim4_no_growth.sql │ │ ├── aim4_overtreatment.sql │ │ └── aim4_undertreatment.sql │ └── Aim1b │ │ ├── Datapreprocessing │ │ ├── DataPrepration_Inpatient_AllAbx.ipynb │ │ ├── DataPrepration_Outpatient_AllAbx.ipynb │ │ └── README.md │ │ ├── InPatients │ │ ├── DataPrepration_Inpatient_5ABX.ipynb │ │ └── README.md │ │ ├── ModelDevelopment │ │ ├── Aim_1b_ModelDevelopment_Inpatients.ipynb │ │ ├── Aim_1b_ModelDevelopment_Outpatients.ipynb │ │ └── README.md │ │ ├── README.md │ │ └── main2.py ├── cost_variability │ ├── SQL │ │ └── sql_scripts.sql │ ├── cost_variability.py │ ├── extract_descriptions.py │ ├── main_create_metadata.py │ ├── main_create_stationary.py │ ├── main_extract_codes.py │ ├── results │ │ ├── LASSO │ │ │ ├── LASSO_hyperparameters_all.csv │ │ │ ├── LASSO_hyperparameters_mir.csv │ │ │ ├── LASSO_hyperparameters_reg.csv │ │ │ ├── best_params_LASSO_all.csv │ │ │ ├── best_params_LASSO_mir.csv │ │ │ ├── best_params_LASSO_reg.csv │ │ │ ├── predictions_LASSO_all.csv │ │ │ ├── predictions_LASSO_mir.csv │ │ │ ├── predictions_LASSO_reg.csv │ │ │ ├── results_LASSO_all.csv │ │ │ ├── results_LASSO_mir.csv │ │ │ └── results_LASSO_reg.csv │ │ ├── LR │ │ │ ├── predictions_lr_all.csv │ │ │ ├── predictions_lr_mir.csv │ │ │ ├── predictions_lr_reg.csv │ │ │ ├── results_lr_all.csv │ │ │ ├── results_lr_mir.csv │ │ │ └── results_lr_reg.csv │ │ ├── XGB │ │ │ ├── best_params_xgb_all.csv │ │ │ ├── best_params_xgb_mir.csv │ │ │ ├── best_params_xgb_reg.csv │ │ │ ├── predictions_xgb_all.csv │ │ │ ├── predictions_xgb_mir.csv │ │ │ ├── predictions_xgb_reg.csv │ │ │ ├── results_xgb_all.csv │ │ │ ├── results_xgb_mir.csv │ │ │ ├── results_xgb_reg.csv │ │ │ ├── shap_beeswarm_all.png │ │ │ ├── shap_beeswarm_mir.png │ │ │ ├── shap_beeswarm_reg.png │ │ │ ├── xgb_all_feature_importance_.csv │ │ │ ├── xgb_hyperparameters_all.csv │ │ │ ├── xgb_hyperparameters_mir.csv │ │ │ ├── xgb_hyperparameters_reg.csv │ │ │ ├── xgb_mir_feature_importance_.csv │ │ │ └── xgb_reg_feature_importance_.csv │ │ ├── feature_scores_mir.csv │ │ ├── feature_scores_mir_descriptions.csv │ │ ├── feature_scores_reg.csv │ │ └── feature_scores_reg_descriptions.csv │ └── utils │ │ ├── create_metadata.py │ │ ├── create_stationary.py │ │ └── extract_codes.py ├── cost_variability_2024 │ ├── .vscode │ │ └── launch.json │ ├── cal_drg_to_cost.png │ └── scripts │ │ ├── Checks and visualizations.ipynb │ │ ├── Predicting costs using case mix index - CLEAN.ipynb │ │ ├── bigquerry_python_api.ipynb │ │ ├── clusterITE.py │ │ ├── cost_db.SQL │ │ ├── cost_pivot_drg_tab.py │ │ ├── diagnosis.ipynb │ │ ├── exploration.ipynb │ │ ├── feature_extraction.py │ │ ├── first_h_per_drg.py │ │ ├── fit_from_cost_pivot_drg.py │ │ ├── fit_from_drg.py │ │ ├── model_fit.py │ │ ├── model_fit_moe.py │ │ ├── pipeline │ │ ├── all_drg_to_all_plots.py │ │ ├── combine_tab.py │ │ ├── dat_to_conformal.py │ │ ├── drg_to_dat.py │ │ ├── drg_to_plot.py │ │ ├── export.yml │ │ ├── notes_py │ │ ├── pipeline.py │ │ ├── res_by_lo.py │ │ ├── res_by_or.py │ │ ├── res_or │ │ │ └── res_comb │ │ │ │ ├── res_comp_diag.csv │ │ │ │ ├── res_comp_med.csv │ │ │ │ ├── res_comp_medorderset.csv │ │ │ │ ├── res_comp_proc.csv │ │ │ │ └── res_comp_procorderset.csv │ │ └── res_p │ │ │ └── res_comb │ │ │ ├── res_comp_diag.csv │ │ │ ├── res_comp_med.csv │ │ │ ├── res_comp_medorderset.csv │ │ │ ├── res_comp_proc.csv │ │ │ └── res_comp_procorderset.csv │ │ └── pivot_features.py ├── critical_care_billing │ └── bigquery.sql ├── eConsult │ ├── Q&A_no_derm.sql │ ├── Recommender │ │ ├── .gitignore │ │ ├── Readme.md │ │ ├── phase_1 │ │ │ ├── Notebook │ │ │ │ └── phase_1_updated.ipynb │ │ │ ├── README.md │ │ │ ├── api │ │ │ │ ├── __init__.py │ │ │ │ ├── bigquery_api.py │ │ │ │ ├── bigquery_api_original.py │ │ │ │ ├── demo_api.sh │ │ │ │ ├── example_usage.py │ │ │ │ └── fastapi_app.py │ │ │ └── main.py │ │ └── requirements.txt │ ├── Recommender_Eval │ │ ├── README.md │ │ ├── configs │ │ │ └── base.yaml │ │ ├── data_split.py │ │ ├── generate_synthetic_data.py │ │ ├── note_embed │ │ │ ├── .env │ │ │ ├── README.md │ │ │ ├── requirements.txt │ │ │ └── scripts │ │ │ │ └── embed_notes.py │ │ └── run_experiment.py │ ├── eConsult-embeddings │ │ ├── .dockerignore │ │ ├── Dockerfile │ │ ├── README.md │ │ ├── api │ │ │ └── main.py │ │ ├── data │ │ │ ├── Allergy eConsult Checklists .txt │ │ │ ├── Allergy eConsult Checklists _extracted.txt │ │ │ ├── Cardiology eConsult Checklists.txt │ │ │ ├── Cardiology eConsult Checklists_extracted.txt │ │ │ ├── Chemical Dependency eConsult Checklists.txt │ │ │ ├── Chemical Dependency eConsult Checklists_extracted.txt │ │ │ ├── Dermatology eConsult Checklists.txt │ │ │ ├── Dermatology eConsult Checklists_extracted.txt │ │ │ ├── ENT eConsult Checklists.txt │ │ │ ├── ENT eConsult Checklists_extracted.txt │ │ │ ├── Endocrinology eConsult Checklists FINAL 4.19.22.txt │ │ │ ├── Endocrinology eConsult Checklists FINAL 4.19.22_extracted.txt │ │ │ ├── Gastroenterology eConsult Checklists.txt │ │ │ ├── Gastroenterology eConsult Checklists_extracted.txt │ │ │ ├── Gynecology eConsult Checklists.txt │ │ │ ├── Gynecology eConsult Checklists_extracted.txt │ │ │ ├── Hematology eConsult Checklists FINAL 9.7.22.txt │ │ │ ├── Hematology eConsult Checklists FINAL 9.7.22_extracted.txt │ │ │ ├── Hepatology Oncology eConsult Checklists.txt │ │ │ ├── Hepatology Oncology eConsult Checklists_extracted.txt │ │ │ ├── Infectious Disease eConsult Checklists_3.13.24.txt │ │ │ ├── Infectious Disease eConsult Checklists_3.13.24_extracted.txt │ │ │ ├── Interventional Pulmonology eConsult Checklists .txt │ │ │ ├── Interventional Pulmonology eConsult Checklists _extracted.txt │ │ │ ├── LGBTQ+ eConsult Checklists.txt │ │ │ ├── LGBTQ+ eConsult Checklists_extracted.txt │ │ │ ├── Nephrology eConsult Checklists.txt │ │ │ ├── Nephrology eConsult Checklists_extracted.txt │ │ │ ├── Neurology eConsult Checklists.txt │ │ │ ├── Neurology eConsult Checklists_extracted.txt │ │ │ ├── Oncology trial eConsult Checklists.txt │ │ │ ├── Oncology trial eConsult Checklists_extracted.txt │ │ │ ├── Orthopedics eConsult Checklists.txt │ │ │ ├── Orthopedics eConsult Checklists_extracted.txt │ │ │ ├── Pain Medicine eConsult Checklists.txt │ │ │ ├── Pain Medicine eConsult Checklists_extracted.txt │ │ │ ├── Psychiatry eConsult Checklists.txt │ │ │ ├── Psychiatry eConsult Checklists_extracted.txt │ │ │ ├── Pulmonology eConsult Checklists.txt │ │ │ ├── Pulmonology eConsult Checklists_extracted.txt │ │ │ ├── Rheumatology eConsult Checklists.txt │ │ │ ├── Rheumatology eConsult Checklists_extracted.txt │ │ │ ├── SHC Referral Templates Checklists compiled DRAFT.txt │ │ │ ├── SHC Referral Templates Checklists compiled DRAFT_extracted.txt │ │ │ ├── Sleep Medicine eConsult Checklists.txt │ │ │ ├── Sleep Medicine eConsult Checklists_extracted.txt │ │ │ ├── Urology eConsult Checklists.txt │ │ │ ├── Urology eConsult Checklists_extracted.txt │ │ │ └── json │ │ │ │ ├── allergy │ │ │ │ ├── allergy_anaphylaxis.json │ │ │ │ ├── allergy_angioedema.json │ │ │ │ ├── allergy_asthma.json │ │ │ │ ├── allergy_chronic_urticaria_or_hives.json │ │ │ │ ├── allergy_drug_allergy.json │ │ │ │ ├── allergy_food_allergy.json │ │ │ │ ├── allergy_immunodeficiency.json │ │ │ │ ├── allergy_other.json │ │ │ │ ├── allergy_rhinitis_and_environmental_allergies.json │ │ │ │ └── allergy_stinging_insect_allergy.json │ │ │ │ ├── cardiology │ │ │ │ ├── cardiology_abnormal_ekg.json │ │ │ │ ├── cardiology_arrhythmia_palpitations.json │ │ │ │ ├── cardiology_atrial_fibrillation_atrial_flutter.json │ │ │ │ ├── cardiology_bradycardia.json │ │ │ │ ├── cardiology_cardiac_imaging_stress_test_cac.json │ │ │ │ ├── cardiology_chest_pain.json │ │ │ │ ├── cardiology_coronary_artery_disease.json │ │ │ │ ├── cardiology_heart_failure.json │ │ │ │ ├── cardiology_hyperlipidemia.json │ │ │ │ ├── cardiology_hypertension.json │ │ │ │ ├── cardiology_other.json │ │ │ │ ├── cardiology_syncope.json │ │ │ │ └── cardiology_valvular_disease.json │ │ │ │ ├── chemical_dependency │ │ │ │ ├── chemical_dependency_alcohol.json │ │ │ │ ├── chemical_dependency_benzodiazepines.json │ │ │ │ ├── chemical_dependency_cannabis.json │ │ │ │ ├── chemical_dependency_opioids.json │ │ │ │ └── chemical_dependency_other.json │ │ │ │ ├── dermatology │ │ │ │ ├── dermatology_growth_lesion.json │ │ │ │ ├── dermatology_other.json │ │ │ │ └── dermatology_rash_dermatitis.json │ │ │ │ ├── endocrinology │ │ │ │ ├── endocrinology_adrenal_insufficiency.json │ │ │ │ ├── endocrinology_adrenal_mass.json │ │ │ │ ├── endocrinology_diabetes_mellitus.json │ │ │ │ ├── endocrinology_hyperaldosteronism.json │ │ │ │ ├── endocrinology_hypercalcemia.json │ │ │ │ ├── endocrinology_hyperparathyroidism.json │ │ │ │ ├── endocrinology_hyperprolactinemia.json │ │ │ │ ├── endocrinology_hyperthyroidism.json │ │ │ │ ├── endocrinology_hypothyroidism.json │ │ │ │ ├── endocrinology_osteoporosis.json │ │ │ │ ├── endocrinology_other.json │ │ │ │ ├── endocrinology_pituitary_mass.json │ │ │ │ ├── endocrinology_thyroid_nodule.json │ │ │ │ └── endocrinology_vitamin_d_deficiency.json │ │ │ │ ├── ent │ │ │ │ ├── ent_other.json │ │ │ │ ├── ent_sinusitis.json │ │ │ │ └── ent_tinnitus.json │ │ │ │ ├── gastroenterology │ │ │ │ ├── gastroenterology_abdominal_pain.json │ │ │ │ ├── gastroenterology_abnormal_abdominal_imaging.json │ │ │ │ ├── gastroenterology_abnormal_lfts_redirect.json │ │ │ │ ├── gastroenterology_alcohol_redirect.json │ │ │ │ ├── gastroenterology_anemia.json │ │ │ │ ├── gastroenterology_anormal_liver_imaging_redirect.json │ │ │ │ ├── gastroenterology_constipation.json │ │ │ │ ├── gastroenterology_diarrhea.json │ │ │ │ ├── gastroenterology_gerd_dyspepsia.json │ │ │ │ ├── gastroenterology_ibs.json │ │ │ │ ├── gastroenterology_nausea_vomiting.json │ │ │ │ └── gastroenterology_other.json │ │ │ │ ├── gynecology │ │ │ │ ├── gynecology_abnormal_pap_smear.json │ │ │ │ ├── gynecology_contraceptive_issues.json │ │ │ │ ├── gynecology_other.json │ │ │ │ └── gynecology_vaginitis.json │ │ │ │ ├── hematology │ │ │ │ ├── hematology_anemia.json │ │ │ │ ├── hematology_elevated_ferritin.json │ │ │ │ ├── hematology_isolated_erythrocytosis.json │ │ │ │ ├── hematology_isolated_leukocytosis.json │ │ │ │ ├── hematology_isolated_leukopenia.json │ │ │ │ ├── hematology_mgus_paraproteinemia.json │ │ │ │ ├── hematology_thrombocytopenia.json │ │ │ │ ├── hematology_thrombocytosis.json │ │ │ │ └── hematology_vte_thrombophilia.json │ │ │ │ ├── hepatology_oncology │ │ │ │ ├── hepatology_oncology_chemotherapy_immunotherapy_hepatotoxicity.json │ │ │ │ └── hepatology_oncology_other.json │ │ │ │ ├── infectious_disease │ │ │ │ ├── infectious_disease_cdi.json │ │ │ │ ├── infectious_disease_covid_positive_patients.json │ │ │ │ ├── infectious_disease_covid_vaccines_and_antibodies.json │ │ │ │ ├── infectious_disease_herpes_simplex.json │ │ │ │ ├── infectious_disease_hiv_prep.json │ │ │ │ ├── infectious_disease_immunizations_vaccinations_non_covid.json │ │ │ │ ├── infectious_disease_latent_tuberculosis.json │ │ │ │ ├── infectious_disease_lyme.json │ │ │ │ ├── infectious_disease_other.json │ │ │ │ ├── infectious_disease_parasites.json │ │ │ │ ├── infectious_disease_recurrent_skin_soft_tissue_infection_mrsa.json │ │ │ │ ├── infectious_disease_serologies.json │ │ │ │ ├── infectious_disease_simple_cystitis_uti_recurrent_uti.json │ │ │ │ └── infectious_disease_syphilis.json │ │ │ │ ├── interventional_pulmonology │ │ │ │ ├── interventional_pulmonology_pneumonitis_drug_induced.json │ │ │ │ ├── interventional_pulmonology_pulmonary_nodule.json │ │ │ │ └── interventional_pulmonology_unspecified.json │ │ │ │ ├── lgbtqplus │ │ │ │ ├── lgbtqplus_gender_health.json │ │ │ │ ├── lgbtqplus_other.json │ │ │ │ └── lgbtqplus_sexual_health.json │ │ │ │ ├── nephrology │ │ │ │ ├── nephrology_ckd.json │ │ │ │ ├── nephrology_creatinine_rise.json │ │ │ │ ├── nephrology_hematuria.json │ │ │ │ ├── nephrology_hyponatremia.json │ │ │ │ ├── nephrology_kidney_cysts.json │ │ │ │ ├── nephrology_other.json │ │ │ │ └── nephrology_proteinuria.json │ │ │ │ ├── neurology │ │ │ │ ├── neurology_abnormal_imaging_study.json │ │ │ │ ├── neurology_abnormal_movements_tremor.json │ │ │ │ ├── neurology_cognitive_impairment_memory_loss.json │ │ │ │ ├── neurology_headache.json │ │ │ │ ├── neurology_known_epilepsy.json │ │ │ │ ├── neurology_neuropathic_pain.json │ │ │ │ ├── neurology_other_sensory_symptoms.json │ │ │ │ ├── neurology_peripheral_neuropathy_distal_numbness.json │ │ │ │ ├── neurology_seizure_spell.json │ │ │ │ ├── neurology_stroke_cva.json │ │ │ │ └── neurology_vertigo_dizziness.json │ │ │ │ ├── oncology │ │ │ │ └── oncology_trial_eligibility.json │ │ │ │ ├── orthopedics │ │ │ │ ├── orthopedics_back_hip_pain.json │ │ │ │ ├── orthopedics_hand_wrist_pain.json │ │ │ │ ├── orthopedics_knee_pain.json │ │ │ │ ├── orthopedics_neck_pain.json │ │ │ │ ├── orthopedics_other.json │ │ │ │ └── orthopedics_shoulder_pain.json │ │ │ │ ├── pain_medicine │ │ │ │ ├── pain_medicine_abdominal_pelvic_genital_pain.json │ │ │ │ ├── pain_medicine_cancer_pain.json │ │ │ │ ├── pain_medicine_chronic_back_pain.json │ │ │ │ ├── pain_medicine_crps_rsd.json │ │ │ │ ├── pain_medicine_facial_pain.json │ │ │ │ ├── pain_medicine_fybromialgia_myofascial_diffuse_body_pain.json │ │ │ │ ├── pain_medicine_headache.json │ │ │ │ ├── pain_medicine_medication_review_recommendations.json │ │ │ │ ├── pain_medicine_neck_pain.json │ │ │ │ ├── pain_medicine_neuropathy_neuralgia_neuritis.json │ │ │ │ ├── pain_medicine_opioid_tapering.json │ │ │ │ ├── pain_medicine_other.json │ │ │ │ ├── pain_medicine_pain_psychology.json │ │ │ │ └── pain_medicine_persistent_post_op_pain.json │ │ │ │ ├── psychiatry │ │ │ │ ├── psychiatry_adhd.json │ │ │ │ ├── psychiatry_anxiety_depression.json │ │ │ │ ├── psychiatry_bipolar_disorder.json │ │ │ │ ├── psychiatry_other.json │ │ │ │ ├── psychiatry_psychiatric_diagnosis_clarification.json │ │ │ │ ├── psychiatry_psychiatric_medication_questions.json │ │ │ │ ├── psychiatry_psychiatric_resources.json │ │ │ │ └── psychiatry_substance_use_disorder.json │ │ │ │ ├── pulmonology │ │ │ │ ├── pulmonology_abnormal_imaging.json │ │ │ │ ├── pulmonology_abnormal_pfts.json │ │ │ │ ├── pulmonology_asthma.json │ │ │ │ ├── pulmonology_chronic_cough.json │ │ │ │ ├── pulmonology_copd.json │ │ │ │ ├── pulmonology_osa.json │ │ │ │ ├── pulmonology_other.json │ │ │ │ └── pulmonology_pulmonary_nodule.json │ │ │ │ ├── rheumatology │ │ │ │ ├── rheumatology_gout.json │ │ │ │ ├── rheumatology_inflammatory_back_pain.json │ │ │ │ ├── rheumatology_joint_pain.json │ │ │ │ ├── rheumatology_lupus.json │ │ │ │ ├── rheumatology_osteoarthritis.json │ │ │ │ ├── rheumatology_other.json │ │ │ │ ├── rheumatology_polymyalgia_rheumatica.json │ │ │ │ └── rheumatology_rheumatoid_arthritis.json │ │ │ │ ├── sleep_medicine │ │ │ │ ├── sleep_medicine_insomnia.json │ │ │ │ ├── sleep_medicine_osa.json │ │ │ │ ├── sleep_medicine_other.json │ │ │ │ ├── sleep_medicine_parasomnias.json │ │ │ │ └── sleep_medicine_rls.json │ │ │ │ └── urology │ │ │ │ ├── urology_dysuria.json │ │ │ │ ├── urology_ejaculatory_dysfunction_hematospermia.json │ │ │ │ ├── urology_microscopic_hematuria.json │ │ │ │ ├── urology_nocturia.json │ │ │ │ ├── urology_other.json │ │ │ │ ├── urology_overactive_bladder.json │ │ │ │ ├── urology_recurrent_uti.json │ │ │ │ ├── urology_renal_cyst.json │ │ │ │ ├── urology_testicular_pain.json │ │ │ │ └── urology_void_trial_catheter_questions.json │ │ ├── embeddings │ │ │ ├── embedding_generator.py │ │ │ └── extract_all_templates.py │ │ └── requirements.txt │ ├── eConsult_QA_NoDerm_NONULL_lab_orders.sql │ ├── eConsult_QA_NoDerm_NONULL_med_orders.sql │ ├── eConsult_QA_NoDerm_NONULL_proc_orders.sql │ └── econsult_qa_noderm_noteextraction.sql ├── hematology-recommender │ ├── .gitignore │ ├── README.md │ ├── data │ │ ├── __init__.py │ │ ├── define_cohort.sql │ │ ├── get_gold_standard.py │ │ └── organize_feats.py │ ├── train.py │ └── utils │ │ ├── __init__.py │ │ └── eval_utils.py ├── lab_prediction_pro │ ├── SmartAlert Low Value Labs Pilot │ │ └── SmartAlertQueryReview.sql │ ├── cbc_w_diff_pipeline.py │ ├── cohort_definitions.py │ ├── constants.py │ ├── datasets.py │ ├── driver.py │ ├── feature_extractors.py │ ├── featurizers.py │ ├── hemestamp_model_pipeline.py │ ├── pytorch_driver.py │ ├── pytorch_models.py │ ├── train.sh │ └── trainers.py ├── llm_assertion │ ├── README.md │ ├── helper_functions.py │ ├── run_dataset_ner.py │ ├── run_extraction.py │ ├── run_finetune_classifier.py │ ├── run_llm_assertion.py │ ├── run_llm_filter_cosine_sim_ner_output.py │ ├── run_ner_cosine_similarity.py │ └── run_umls_synonym_ner.py ├── model_performance_partitioning │ ├── driver.py │ └── partition.py └── specialty_recommender │ ├── Recommender.py │ ├── SpecialtyReferral_Recommender.ipynb │ ├── TableFigures.py │ ├── Util.py │ ├── V3_Item_Prevalence_RR.ipynb │ ├── V3_OMOP_Feature_Extraction.ipynb │ ├── V3_OMOP_Pediatric_Referral.ipynb │ └── schema.py ├── setup ├── BigQueryDataUpdateGuide.MD ├── installPythonLibraries.py ├── lpch_conversion.py ├── new_SHCdata_Organize_DateTime.ipynb ├── setup.sh ├── shc_lpch_conversions.md ├── webAppSetupNotes.txt └── windows.profile.bat └── stride ├── __init__.py ├── box ├── BoxClient.py ├── __init__.py ├── box-API.md └── test │ ├── TestBoxClient.py │ ├── __init__.py │ ├── box-download-test.txt │ ├── box-test-verify │ ├── box-download-test.txt │ └── box-test-subdirectory │ │ ├── box-download-test.txt │ │ └── box-upload-test.txt │ └── box-upload-test.txt ├── clinical_item ├── ClinicalItemDataLoader.py ├── __init__.py ├── clinical_item_tables.md └── psql │ ├── dump_clinical_item.sh │ ├── indices │ ├── build_indices.sh │ ├── clinical_item.indices.sql │ ├── clinical_item_association.indices.sql │ ├── clinical_item_category.indices.sql │ ├── item_collection_item.indices.sql │ ├── patient_item.indices.sql │ └── patient_item_collection_link.indices.sql │ ├── restore-clinical_item.md │ ├── restore_clinical_item.sh │ └── schemata │ ├── backup_link_patient_item.schema.sql │ ├── clinical_item.schema.sql │ ├── clinical_item_association.schema.sql │ ├── clinical_item_category.schema.sql │ ├── clinical_item_link.schema.sql │ ├── collection_type.schema.sql │ ├── data_cache.schema.sql │ ├── item_collection.schema.sql │ ├── item_collection_item.schema.sql │ ├── order_result_stat.schema.sql │ ├── patient_item.schema.sql │ └── patient_item_collection_link.schema.sql ├── core ├── StrideLoader.py ├── StrideLoaderParams.py ├── __init__.py └── test │ ├── TestStrideLoader.py │ ├── __init__.py │ ├── test_clean_data_file.csv │ └── test_raw_data_file.csv ├── dataExtract ├── main_lpch.txt └── main_shc.txt ├── psql ├── dump_stride.sh ├── indices │ ├── build_indices.sh │ ├── stride_adt.indices.sql │ ├── stride_chargemaster.indices.sql │ ├── stride_flowsheet.indices.sql │ ├── stride_medication_mpi.indices.sql │ ├── stride_note.indices.sql │ ├── stride_order_med.indices.sql │ ├── stride_order_proc.indices.sql │ ├── stride_order_results.indices.sql │ ├── stride_orderset_order_med.indices.sql │ ├── stride_orderset_order_proc.indices.sql │ ├── stride_patient.indices.sql │ └── stride_patient_encounter.indices.sql ├── restore_stride.sh └── schemata │ ├── stride_admit.schema.sql │ ├── stride_admit_vital.schema.sql │ ├── stride_adt.schema.sql │ ├── stride_chargemaster.schema.sql │ ├── stride_culture_micro.schema.sql │ ├── stride_drg.schema.sql │ ├── stride_dx_list.schema.sql │ ├── stride_flowsheet.schema.sql │ ├── stride_icd10_cm.schema.sql │ ├── stride_icd9_cm.schema.sql │ ├── stride_income.schema.sql │ ├── stride_insurance.schema.sql │ ├── stride_io_flowsheet.schema.sql │ ├── stride_mapped_meds.schema.sql │ ├── stride_medication_mpi.schema.sql │ ├── stride_note.schema.sql │ ├── stride_order_med.schema.sql │ ├── stride_order_medmixinfo.schema.sql │ ├── 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