Research Article: Cardiovascular disease risk prediction using automated machine learning: A prospective study of 423,604 UK Biobank participants

Date Published: May 15, 2019

Publisher: Public Library of Science

Author(s): Ahmed M. Alaa, Thomas Bolton, Emanuele Di Angelantonio, James H. F. Rudd, Mihaela van der Schaar, Katriina Aalto-Setala.


Identifying people at risk of cardiovascular diseases (CVD) is a cornerstone of preventative cardiology. Risk prediction models currently recommended by clinical guidelines are typically based on a limited number of predictors with sub-optimal performance across all patient groups. Data-driven techniques based on machine learning (ML) might improve the performance of risk predictions by agnostically discovering novel risk predictors and learning the complex interactions between them. We tested (1) whether ML techniques based on a state-of-the-art automated ML framework (AutoPrognosis) could improve CVD risk prediction compared to traditional approaches, and (2) whether considering non-traditional variables could increase the accuracy of CVD risk predictions.

Using data on 423,604 participants without CVD at baseline in UK Biobank, we developed a ML-based model for predicting CVD risk based on 473 available variables. Our ML-based model was derived using AutoPrognosis, an algorithmic tool that automatically selects and tunes ensembles of ML modeling pipelines (comprising data imputation, feature processing, classification and calibration algorithms). We compared our model with a well-established risk prediction algorithm based on conventional CVD risk factors (Framingham score), a Cox proportional hazards (PH) model based on familiar risk factors (i.e, age, gender, smoking status, systolic blood pressure, history of diabetes, reception of treatments for hypertension and body mass index), and a Cox PH model based on all of the 473 available variables. Predictive performances were assessed using area under the receiver operating characteristic curve (AUC-ROC). Overall, our AutoPrognosis model improved risk prediction (AUC-ROC: 0.774, 95% CI: 0.768-0.780) compared to Framingham score (AUC-ROC: 0.724, 95% CI: 0.720-0.728, p < 0.001), Cox PH model with conventional risk factors (AUC-ROC: 0.734, 95% CI: 0.729-0.739, p < 0.001), and Cox PH model with all UK Biobank variables (AUC-ROC: 0.758, 95% CI: 0.753-0.763, p < 0.001). Out of 4,801 CVD cases recorded within 5 years of baseline, AutoPrognosis was able to correctly predict 368 more cases compared to the Framingham score. Our AutoPrognosis model included predictors that are not usually considered in existing risk prediction models, such as the individuals’ usual walking pace and their self-reported overall health rating. Furthermore, our model improved risk prediction in potentially relevant sub-populations, such as in individuals with history of diabetes. We also highlight the relative benefits accrued from including more information into a predictive model (information gain) as compared to the benefits of using more complex models (modeling gain). Our AutoPrognosis model improves the accuracy of CVD risk prediction in the UK Biobank population. This approach performs well in traditionally poorly served patient subgroups. Additionally, AutoPrognosis uncovered novel predictors for CVD disease that may now be tested in prospective studies. We found that the “information gain” achieved by considering more risk factors in the predictive model was significantly higher than the “modeling gain” achieved by adopting complex predictive models.

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Globally, cardiovascular disease (CVD) remains the leading cause of morbidity and mortality [1]. Current clinical guidelines for primary prevention of CVD emphasize the need to identify asymptomatic patients who may benefit from preventive action (e.g., initiation of statin therapy [2]) based on their predicted risk [3–6]. Different guidelines recommend different algorithms for risk prediction. For example, the 2010 American College of Cardiology/American Heart Association (ACC/AHA) guideline [7] recommended use of Framingham Risk Score [4], whereas the 2016 European guidelines recommended use of the Systematic Coronary Risk Evaluation (SCORE) algorithm [8]. In the UK, the current National Institute for Health and Care Excellence (NICE) guidelines recommend use of the QRISK2 score to guide the initiation of lipid lowering therapies [9, 10].

In this large prospective cohort study, we developed a ML model based on the AutoPrognosis framework for predicting CVD events in asymptomatic individuals. The model was built using data for more than 400,000 UK Biobank participants, with over 450 variables for each participant. Our study conveys several key messages. First, AutoPrognosis significantly improved the accuracy of CVD risk prediction compared to well-established scoring systems based on conventional risk factors and currently recommended by primary prevention guidelines (Framingham score). Second, AutoPrognosis was able to agnostically discover new predictors of CVD risk. Among the discovered predictors were non-laboratory variables that can be collected relatively easily via questionnaires, such as the individuals’ self-reported health ratings and usual walking pace. Third, AutoPrognosis uncovered complex interaction effects between different characteristics of an individual, which led to recognition of risk predictors that are specific to certain sub-populations for whom existing guidelines were providing unreliable predictions.




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