Approaches to developing clinically useful Bayesian risk prediction models


Type
Thesis
Change log
Authors
Karapanagiotis, Solon  ORCID logo  https://orcid.org/0000-0003-4460-2073
Abstract

Prediction of the presence of disease (diagnosis) or an event in the future course of disease (prognosis) becomes increasingly important in the current era of personalised medicine. Both tasks (diagnosis and prognosis) are supported using (risk) prediction models. Such models usually combine multiple variables by using different statistical and/or machine learning approaches. Recent advances in prediction models have improved diagnostic and prognostic accuracy, in some cases surpassing the performance of clinicians. However, evidence is lacking that deployment of these models has improved care and patient outcomes. That is, their clinical usefulness is debatable. One barrier to demonstrating such improvement is the basis used to evaluate their performance. In this thesis, we explore methods for developing (building and evaluating) risk prediction models, in an attempt to create clinically useful models.

We start by introducing a few commonly used metrics to evaluate the predictive performance of prediction models. We then show that a model with good predictive performance is not enough to guarantee clinical usefulness. A well performing model can be clinically useless, and a poor model valuable. Following recent line of work, we adopt a decision theoretic approach for model evaluation that allows us to determine whether the model would change medical decisions and, if so, whether the outcome of interest would improve as a result.

We then apply this approach to investigate the clinical usefulness of including information about circulating tumour DNA (ctDNA) when predicting response to treatment in metastatic breast cancer. ctDNA has been proposed as a promising approach to assess response to treatment. We show that incorporating trajectories of circulating tumour DNA results in a clinically useful model and can improve clinical decisions.

However, an inherit limitation to the decision theoretic approach (and related ones) is that model building and evaluation are done independently. During training, the prediction model is agnostic of the clinical consequences from its use. That is, the prediction model is agnostic of its (clinical) purpose, e.g., which type of classification error is more costly (i.e., undesirable).

We address this shortcoming by introducing Tailored Bayes (TB), a novel Bayesian inference framework which “tailors” model fitting to optimise predictive performance with respect to unbalanced misclassification costs. In both simulated and real-world applications, we find our approach to perform favourably in comparison to standard Bayesian methods.

We then move to extend the framework to situations where a large number of (potentially irrelevant) variables are measured. Such high-dimensional settings represent a ubiquitous challenge in modern scientific research. We introduce a sparse TB framework for variable selection and find that TB favours smaller models (with fewer variables) compared to standard Bayesian methods, whilst performing better or no worse. This pattern was seen both in simulated and real data. In addition, we show the relative importance of the variables changes when we consider unbalanced misclassification costs.

Description
Date
2021-04-14
Advisors
Rueda, Oscar
Newcombe, Paul
Keywords
Tailored Bayesian methods, Bayesian inference, misclassification costs,, binary classification, breast cancer, risk prediction models, circulating tumour DNA
Qualification
Doctor of Philosophy (PhD)
Awarding Institution
University of Cambridge