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Use of electronic health record data and machine learning to identify candidates for HIV pre-exposure prophylaxis: a modelling study.

ABSTRACT: BACKGROUND:The limitations of existing HIV risk prediction tools are a barrier to implementation of pre-exposure prophylaxis (PrEP). We developed and validated an HIV prediction model to identify potential PrEP candidates in a large health-care system. METHODS:Our study population was HIV-uninfected adult members of Kaiser Permanente Northern California, a large integrated health-care system, who were not yet using PrEP and had at least 2 years of previous health plan enrolment with at least one outpatient visit from Jan 1, 2007, to Dec 31, 2017. Using 81 electronic health record (EHR) variables, we applied least absolute shrinkage and selection operator (LASSO) regression to predict incident HIV diagnosis within 3 years on a subset of patients who entered the cohort in 2007-14 (development dataset), assessing ten-fold cross-validated area under the receiver operating characteristic curve (AUC) and 95% CIs. We compared the full model to simpler models including only men who have sex with men (MSM) status and sexually transmitted infection (STI) positivity, testing, and treatment. Models were validated prospectively with data from an independent set of patients who entered the cohort in 2015-17. We computed predicted probabilities of incident HIV diagnosis within 3 years (risk scores), categorised as low risk (<0·05%), moderate risk (0·05% to <0·20%), high risk (0·20% to <1·0%), and very high risk (?1·0%), for all patients in the validation dataset. FINDINGS:Of 3?750?664 patients in 2007-17 (3?143?963 in the development dataset and 606?701 in the validation dataset), there were 784 incident HIV cases within 3 years of baseline. The LASSO procedure retained 44 predictors in the full model, with an AUC of 0·86 (95% CI 0·85-0·87) for incident HIV cases in 2007-14. Model performance remained high in the validation dataset (AUC 0·84, 0·80-0·89). The full model outperformed simpler models including only MSM status and STI positivity. For the full model, flagging 13?463 (2·2%) patients with high or very high HIV risk scores in the validation dataset identified 32 (38·6%) of the 83 incident HIV cases, including 32 (46·4%) of 69 male cases and none of the 14 female cases. The full model had equivalent sensitivity by race whereas simpler models identified fewer black than white HIV cases. INTERPRETATION:Prediction models using EHR data can identify patients at high risk of HIV acquisition who could benefit from PrEP. Future studies should optimise EHR-based HIV risk prediction tools and evaluate their effect on prescription of PrEP. FUNDING:Kaiser Permanente Community Benefit Research Program and the US National Institutes of Health.

SUBMITTER: Marcus JL

PROVIDER: S-EPMC7152802 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Use of electronic health record data and machine learning to identify candidates for HIV pre-exposure prophylaxis: a modelling study.

Marcus Julia L JL Hurley Leo B LB Krakower Douglas S DS Alexeeff Stacey S Silverberg Michael J MJ Volk Jonathan E JE

The lancet. HIV 20190705 10

<h4>Background</h4>The limitations of existing HIV risk prediction tools are a barrier to implementation of pre-exposure prophylaxis (PrEP). We developed and validated an HIV prediction model to identify potential PrEP candidates in a large health-care system.<h4>Methods</h4>Our study population was HIV-uninfected adult members of Kaiser Permanente Northern California, a large integrated health-care system, who were not yet using PrEP and had at least 2 years of previous health plan enrolment wi ...[more]

PMID: 31285183

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Project description:BackgroundHIV pre-exposure prophylaxis (PrEP) is effective but underused, in part because clinicians do not have the tools to identify PrEP candidates. We developed and validated an automated prediction algorithm that uses electronic health record (EHR) data to identify individuals at increased risk for HIV acquisition.MethodsWe used machine learning algorithms to predict incident HIV infections with 180 potential predictors of HIV risk drawn from EHR data from 2007-15 at Atrius Health, an ambulatory group practice in Massachusetts, USA. We included EHRs of all patients aged 15 years or older with at least one clinical encounter during 2007-15. We used ten-fold cross-validated area under the receiver operating characteristic curve (cv-AUC) with 95% CIs to assess the model's performance at identifying individuals with incident HIV and patients independently prescribed PrEP by clinicians. The best-performing model was validated prospectively with 2016 data from Atrius Health and externally with 2011-16 data from Fenway Health, a community health centre specialising in sexual health care in Boston (MA, USA). We calculated HIV risk scores (ie, probability of an incident HIV diagnosis) for every HIV-uninfected patient not on PrEP during 2007-15 at Atrius Health and assessed the distribution of scores for thresholds to determine possible candidates for PrEP in the three study cohorts.FindingsWe included 1 155 966 Atrius Health patients from 2007-15 (150 [<0·1%] patients with incident HIV) in our development cohort, 537 257 Atrius Health patients in 2016 (16 [<0·1%] with incident HIV) in our prospective validation cohort, and 33 404 Fenway Health patients from 2011-16 (423 [1·3%] with incident HIV) in our external validation cohort. The best-performing algorithm was obtained with least absolute shrinkage and selection operator (LASSO) and had a cv-AUC of 0·86 (95% CI 0·82-0·90) for identification of incident HIV infections in the development cohort, 0·91 (0·81-1·00) on prospective validation, and 0·77 (0·74-0·79) on external validation. The LASSO model successfully identified patients independently prescribed PrEP by clinicians at Atrius Health in 2016 (cv-AUC 0·93, 95% CI 0·90-0·96) or Fenway Health (0·79, 0·78-0·80). HIV risk scores increased steeply at the 98th percentile. Using this score as a threshold, we prospectively identified 9515 (1·8%) of 536 384 patients at Atrius Health in 2016 and 4385 (15·3%) of 28 702 Fenway Health patients as potential PrEP candidates.InterpretationAutomated algorithms can efficiently identify patients at increased risk for HIV acquisition. Integrating these models into EHRs to alert providers about patients who might benefit from PrEP could improve prescribing and prevent new HIV infections.FundingHarvard University Center for AIDS Research, Providence/Boston Center for AIDS Research, Rhode Island IDeA-CTR, the National Institute of Mental Health, and the US Centers for Disease Control and Prevention.

Project description:BACKGROUND:Systemic sclerosis (SSc) is a rare disease with studies limited by small sample sizes. Electronic health records (EHRs) represent a powerful tool to study patients with rare diseases such as SSc, but validated methods are needed. We developed and validated EHR-based algorithms that incorporate billing codes and clinical data to identify SSc patients in the EHR. METHODS:We used a de-identified EHR with over 3 million subjects and identified 1899 potential SSc subjects with at least 1 count of the SSc ICD-9 (710.1) or ICD-10-CM (M34*) codes. We randomly selected 200 as a training set for chart review. A subject was a case if diagnosed with SSc by a rheumatologist, dermatologist, or pulmonologist. We selected the following algorithm components based on clinical knowledge and available data: SSc ICD-9 and ICD-10-CM codes, positive antinuclear antibody (ANA) (titer ??1:80), and a keyword of Raynaud's phenomenon (RP). We performed both rule-based and machine learning techniques for algorithm development. Positive predictive values (PPVs), sensitivities, and F-scores (which account for PPVs and sensitivities) were calculated for the algorithms. RESULTS:PPVs were low for algorithms using only 1 count of the SSc ICD-9 code. As code counts increased, the PPVs increased. PPVs were higher for algorithms using ICD-10-CM codes versus the ICD-9 code. Adding a positive ANA and RP keyword increased the PPVs of algorithms only using ICD billing codes. Algorithms using ??3 or ??4 counts of the SSc ICD-9 or ICD-10-CM codes and ANA positivity had the highest PPV at 100% but a low sensitivity at 50%. The algorithm with the highest F-score of 91% was ??4 counts of the ICD-9 or ICD-10-CM codes with an internally validated PPV of 90%. A machine learning method using random forests yielded an algorithm with a PPV of 84%, sensitivity of 92%, and F-score of 88%. The most important feature was RP keyword. CONCLUSIONS:Algorithms using only ICD-9 codes did not perform well to identify SSc patients. The highest performing algorithms incorporated clinical data with billing codes. EHR-based algorithms can identify SSc patients across a healthcare system, enabling researchers to examine important outcomes.

Project description:Electronic health records (EHRs) have given rise to large and complex databases of medical information that have the potential to become powerful tools for clinical research. However, differences in coding systems and the detail and accuracy of the information within EHRs can vary across institutions. This makes it challenging to identify subpopulations of patients and limits the widespread use of multi-institutional databases. In this study, we leveraged machine learning to identify patterns in medication usage among hospitalized pediatric patients receiving renal replacement therapy and created a predictive model that successfully differentiated between intermittent (iHD) and continuous renal replacement therapy (CRRT) hemodialysis patients. We trained six machine learning algorithms (logistical regression, Naïve Bayes, k-nearest neighbor, support vector machine, random forest, and gradient boosted trees) using patient records from a multi-center database (n = 533) and prescribed medication ingredients (n = 228) as features to discriminate between the two hemodialysis types. Predictive skill was assessed using a 5-fold cross-validation, and the algorithms showed a range of performance from 0.7 balanced accuracy (logistical regression) to 0.86 (random forest). The two best performing models were further tested using an independent single-center dataset and achieved 84-87% balanced accuracy. This model overcomes issues inherent within large databases and will allow us to utilize and combine historical records, significantly increasing population size and diversity within both iHD and CRRT populations for future clinical studies. Our work demonstrates the utility of using medications alone to accurately differentiate subpopulations of patients in large datasets, allowing codes to be transferred between different coding systems. This framework has the potential to be used to distinguish other subpopulations of patients where discriminatory ICD codes are not available, permitting more detailed insights and new lines of research.

Project description:ObjectiveElectronic health records (EHR) offer medical and pharmacogenomics research unprecedented opportunities to identify and classify patients at risk. EHRs are collections of highly inter-dependent records that include biological, anatomical, physiological, and behavioral observations. They comprise a patient's clinical phenome, where each patient has thousands of date-stamped records distributed across many relational tables. Development of EHR computer-based phenotyping algorithms require time and medical insight from clinical experts, who most often can only review a small patient subset representative of the total EHR records, to identify phenotype features. In this research we evaluate whether relational machine learning (ML) using inductive logic programming (ILP) can contribute to addressing these issues as a viable approach for EHR-based phenotyping.MethodsTwo relational learning ILP approaches and three well-known WEKA (Waikato Environment for Knowledge Analysis) implementations of non-relational approaches (PART, J48, and JRIP) were used to develop models for nine phenotypes. International Classification of Diseases, Ninth Revision (ICD-9) coded EHR data were used to select training cohorts for the development of each phenotypic model. Accuracy, precision, recall, F-Measure, and Area Under the Receiver Operating Characteristic (AUROC) curve statistics were measured for each phenotypic model based on independent manually verified test cohorts. A two-sided binomial distribution test (sign test) compared the five ML approaches across phenotypes for statistical significance.ResultsWe developed an approach to automatically label training examples using ICD-9 diagnosis codes for the ML approaches being evaluated. Nine phenotypic models for each ML approach were evaluated, resulting in better overall model performance in AUROC using ILP when compared to PART (p=0.039), J48 (p=0.003) and JRIP (p=0.003).DiscussionILP has the potential to improve phenotyping by independently delivering clinically expert interpretable rules for phenotype definitions, or intuitive phenotypes to assist experts.ConclusionRelational learning using ILP offers a viable approach to EHR-driven phenotyping.

Project description:ImportanceComparisons of antimicrobial use among hospitals are difficult to interpret owing to variations in patient case mix. Risk-adjustment strategies incorporating larger numbers of variables haves been proposed as a method to improve comparisons for antimicrobial stewardship assessments.ObjectiveTo evaluate whether variables of varying complexity and feasibility of measurement, derived retrospectively from the electronic health records, accurately identify inpatient antimicrobial use.Design, setting, and participantsRetrospective cohort study, using a 2-stage random forests machine learning modeling analysis of electronic health record data. Data were split into training and testing sets to measure model performance using area under the curve and absolute error. All adult and pediatric inpatient encounters from October 1, 2015, to September 30, 2017, at 2 community hospitals and 1 academic medical center in the Duke University Health System were analyzed. A total of 204 candidate variables were categorized into 4 tiers based on feasibility of measurement from the electronic health records.Main outcomes and measuresAntimicrobial exposure was measured at the encounter level in 2 ways: binary (ever or never) and number of days of therapy. Analyses were stratified by age (pediatric or adult), unit type, and antibiotic group.ResultsThe data set included 170 294 encounters and 204 candidate variables from 3 hospitals during the 3-year study period. Antimicrobial exposure occurred in 80 190 encounters (47%); 64 998 (38%) received 1 to 6 days of therapy, and 15 192 (9%) received 7 or more days of therapy. Two-stage models identified antimicrobial use with high fidelity (mean area under the curve, 0.85; mean absolute error, 1.0 days of therapy). Addition of more complex variables increased accuracy, with largest improvements occurring with inclusion of diagnosis information. Accuracy varied based on location and antibiotic group. Models underestimated the number of days of therapy of encounters with long lengths of stay.Conclusions and relevanceModels using variables derived from electronic health records identified antimicrobial exposure accurately. Future risk-adjustment strategies incorporating encounter-level information may make comparisons of antimicrobial use more meaningful for hospital antimicrobial stewardship assessments.

Project description:BACKGROUND:Stroke severity is an important predictor of patient outcomes and is commonly measured with the National Institutes of Health Stroke Scale (NIHSS) scores. Because these scores are often recorded as free text in physician reports, structured real-world evidence databases seldom include the severity. The aim of this study was to use machine learning models to impute NIHSS scores for all patients with newly diagnosed stroke from multi-institution electronic health record (EHR) data. METHODS:NIHSS scores available in the Optum© de-identified Integrated Claims-Clinical dataset were extracted from physician notes by applying natural language processing (NLP) methods. The cohort analyzed in the study consists of the 7149 patients with an inpatient or emergency room diagnosis of ischemic stroke, hemorrhagic stroke, or transient ischemic attack and a corresponding NLP-extracted NIHSS score. A subset of these patients (n?=?1033, 14%) were held out for independent validation of model performance and the remaining patients (n?=?6116, 86%) were used for training the model. Several machine learning models were evaluated, and parameters optimized using cross-validation on the training set. The model with optimal performance, a random forest model, was ultimately evaluated on the holdout set. RESULTS:Leveraging machine learning we identified the main factors in electronic health record data for assessing stroke severity, including death within the same month as stroke occurrence, length of hospital stay following stroke occurrence, aphagia/dysphagia diagnosis, hemiplegia diagnosis, and whether a patient was discharged to home or self-care. Comparing the imputed NIHSS scores to the NLP-extracted NIHSS scores on the holdout data set yielded an R2 (coefficient of determination) of 0.57, an R (Pearson correlation coefficient) of 0.76, and a root-mean-squared error of 4.5. CONCLUSIONS:Machine learning models built on EHR data can be used to determine proxies for stroke severity. This enables severity to be incorporated in studies of stroke patient outcomes using administrative and EHR databases.

Dataset Information

Use of electronic health record data and machine learning to identify candidates for HIV pre-exposure prophylaxis: a modelling study.

Publications

Use of electronic health record data and machine learning to identify candidates for HIV pre-exposure prophylaxis: a modelling study.

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