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Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling.

ABSTRACT: We review some of the latest approaches to analysing cardiac electrophysiology data using machine learning and predictive modelling. Cardiac arrhythmias, particularly atrial fibrillation, are a major global healthcare challenge. Treatment is often through catheter ablation, which involves the targeted localised destruction of regions of the myocardium responsible for initiating or perpetuating the arrhythmia. Ablation targets are either anatomically defined, or identified based on their functional properties as determined through the analysis of contact intracardiac electrograms acquired with increasing spatial density by modern electroanatomic mapping systems. While numerous quantitative approaches have been investigated over the past decades for identifying these critical curative sites, few have provided a reliable and reproducible advance in success rates. Machine learning techniques, including recent deep-learning approaches, offer a potential route to gaining new insight from this wealth of highly complex spatio-temporal information that existing methods struggle to analyse. Coupled with predictive modelling, these techniques offer exciting opportunities to advance the field and produce more accurate diagnoses and robust personalised treatment. We outline some of these methods and illustrate their use in making predictions from the contact electrogram and augmenting predictive modelling tools, both by more rapidly predicting future states of the system and by inferring the parameters of these models from experimental observations.

SUBMITTER: Cantwell CD

PROVIDER: S-EPMC6334203 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature

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Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling.

Cantwell Chris D CD Mohamied Yumnah Y Tzortzis Konstantinos N KN Garasto Stef S Houston Charles C Chowdhury Rasheda A RA Ng Fu Siong FS Bharath Anil A AA Peters Nicholas S NS

Computers in biology and medicine 20181018

We review some of the latest approaches to analysing cardiac electrophysiology data using machine learning and predictive modelling. Cardiac arrhythmias, particularly atrial fibrillation, are a major global healthcare challenge. Treatment is often through catheter ablation, which involves the targeted localised destruction of regions of the myocardium responsible for initiating or perpetuating the arrhythmia. Ablation targets are either anatomically defined, or identified based on their function ...[more]

PMID: 30442428

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Project description:Streptococcus pneumoniae is a human pathogen that is a major cause of infant mortality. Identifying the pneumococcal serotype is an important step in monitoring the impact of vaccines used to protect against disease. Genomic microarrays provide an effective method for molecular serotyping. Previously we developed an empirical Bayesian model for the classification of serotypes from a molecular serotyping array. With only few samples available, a model driven approach was the only option. In the meanwhile, several thousand samples have been made available to us, providing an opportunity to investigate serotype classification by machine learning methods, which could complement the Bayesian model.We compare the performance of the original Bayesian model with two machine learning algorithms: Gradient Boosting Machines and Random Forests. We present our results as an example of a generic strategy whereby a preliminary probabilistic model is complemented or replaced by a machine learning classifier once enough data are available. Despite the availability of thousands of serotyping arrays, a problem encountered when applying machine learning methods is the lack of training data containing mixtures of serotypes; due to the large number of possible combinations. Most of the available training data comprises samples with only a single serotype. To overcome the lack of training data we implemented an iterative analysis, creating artificial training data of serotype mixtures by combining raw data from single serotype arrays.With the enhanced training set the machine learning algorithms out perform the original Bayesian model. However, for serotypes currently lacking sufficient training data the best performing implementation was a combination of the results of the Bayesian Model and the Gradient Boosting Machine. As well as being an effective method for classifying biological data, machine learning can also be used as an efficient method for revealing subtle biological insights, which we illustrate with an example.

Project description:ObjectiveWe aimed to develop and validate a predictive machine learning (ML) model for cardiac surgery associated with acute kidney injury (CSA-AKI) based on a multicenter randomized control trial (RCT) and a Medical Information Mart for Intensive Care-IV (MIMIC-IV) dataset.MethodsThis was a subanalysis from a completed RCT approved by the Ethics Committee of Fuwai Hospital in Beijing, China (NCT03782350). Data from Fuwai Hospital were randomly assigned, with 80% for the training dataset and 20% for the testing dataset. The data from three other centers were used for the external validation dataset. Furthermore, the MIMIC-IV dataset was also utilized to validate the performance of the predictive model. The area under the receiver operating characteristic curve (ROC-AUC), the precision-recall curve (PR-AUC), and the calibration brier score were applied to evaluate the performance of the traditional logistic regression (LR) and eleven ML algorithms. Additionally, the Shapley Additive Explanations (SHAP) interpreter was used to explain the potential risk factors for CSA-AKI.ResultA total of 6495 eligible patients undergoing cardiopulmonary bypass (CPB) were eventually included in this study, 2416 of whom were from Fuwai Hospital (Beijing), for model development, 562 from three other cardiac centers in China, and 3517 from the MIMICIV dataset, were used, respectively, for external validation. The CatBoostClassifier algorithms outperformed other models, with excellent discrimination and calibration performance for the development, as well as the MIMIC-IV, datasets. In addition, the CatBoostClassifier achieved ROC-AUCs of 0.85, 0.67, and 0.77 and brier scores of 0.14, 0.19, and 0.16 in the testing, external, and MIMIC-IV datasets, respectively. Moreover, the utmost important risk factor, the N-terminal brain sodium peptide (NT-proBNP), was confirmed by the LASSO method in the feature section process. Notably, the SHAP explainer identified that the preoperative blood urea nitrogen level, prothrombin time, serum creatinine level, total bilirubin level, and age were positively correlated with CSA-AKI; preoperative platelets level, systolic and diastolic blood pressure, albumin level, and body weight were negatively associated with CSA-AKI.ConclusionsThe CatBoostClassifier algorithms outperformed other ML models in the discrimination and calibration of CSA-AKI prediction cardiac surgery with CPB, based on a multicenter RCT and MIMIC-IV dataset. Moreover, the preoperative NT-proBNP level was confirmed to be strongly related to CSA-AKI.

Dataset Information

Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling.

Publications

Rethinking multiscale cardiac electrophysiology with machine learning and predictive modelling.

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