A nonparametric Bayesian method of translating machine learning scores to probabilities in clinical decision support

BMC Bioinformatics

Methodology Article

K. Bretonnel Cohen¹  Ulya Bayram²  Brian Connolly²  Daniel Santel²  John Pestian² 

[1] Computational Bioscience Program, University of Colorado School of Medicine, Denver, CO, USA;Department of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Ave., MLC 7024, 45229-3039, Cincinnati, OH, USA;

关键词: Statistics;    Nonparametric;    Bayesian;    Calibration;    Machine learning;   

DOI  :  10.1186/s12859-017-1736-3

 received in 2017-04-07, accepted in 2017-06-22,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundProbabilistic assessments of clinical care are essential for quality care. Yet, machine learning, which supports this care process has been limited to categorical results. To maximize its usefulness, it is important to find novel approaches that calibrate the ML output with a likelihood scale. Current state-of-the-art calibration methods are generally accurate and applicable to many ML models, but improved granularity and accuracy of such methods would increase the information available for clinical decision making.This novel non-parametric Bayesian approach is demonstrated on a variety of data sets, including simulated classifier outputs, biomedical data sets from the University of California, Irvine (UCI) Machine Learning Repository, and a clinical data set built to determine suicide risk from the language of emergency department patients.ResultsThe method is first demonstrated on support-vector machine (SVM) models, which generally produce well-behaved, well understood scores. The method produces calibrations that are comparable to the state-of-the-art Bayesian Binning in Quantiles (BBQ) method when the SVM models are able to effectively separate cases and controls. However, as the SVM models’ ability to discriminate classes decreases, our approach yields more granular and dynamic calibrated probabilities comparing to the BBQ method. Improvements in granularity and range are even more dramatic when the discrimination between the classes is artificially degraded by replacing the SVM model with an ad hoc k-means classifier.ConclusionsThe method allows both clinicians and patients to have a more nuanced view of the output of an ML model, allowing better decision making. The method is demonstrated on simulated data, various biomedical data sets and a clinical data set, to which diverse ML methods are applied. Trivially extending the method to (non-ML) clinical scores is also discussed.

【 授权许可】

CC BY   
© The Author(s). 2017

【 图 表 】

Fig. 3