Standardizing clinical predictive modeling : standardizing development, validation, and interpretation of clinical prediction models

An ever-increasing number of prediction models is published every year in different medical specialties. Prognostic or diagnostic in nature, these models support medical decision making by utilizing one or more items of patient data to predict outcomes of interest, such as mortality or disease progression. While different computer tools exist that support clinical predictive modeling, I observed that the state of the art is lacking in the extent to which the needs of research clinicians are addressed. When it comes to model development, current support tools either 1) target specialist data engineers, requiring advanced coding skills, or 2) cater to a general-purpose audience, therefore not addressing the specific needs of clinical researchers. Furthermore, barriers to data access across institutional silos, cumbersome model reproducibility and extended experiment-to-result times significantly hampers validation of existing models. Similarly, without access to interpretable explanations, which allow a given model to be fully scrutinized, acceptance of machine learning approaches will remain limited. Adequate tool support, i.e., a software artifact more targeted at the needs of clinical modeling, can help mitigate the challenges identified with respect to model development, validation and interpretation. To this end, I conducted interviews with modeling practitioners in health care to better understand the modeling process itself and ascertain in what aspects adequate tool support could advance the state of the art. The functional and non-functional requirements identified served as the foundation for a software artifact that can be used for modeling outcome and risk prediction in health research. To establish the appropriateness of this approach, I implemented a use case study in the Nephrology domain for acute kidney injury, which was validated in two different hospitals. Furthermore, I conducted user evaluation to ascertain whether such an approach provides benefits compared to the state of the art and the extent to which clinical practitioners could benefit from it. Finally, when updating models for external validation, practitioners need to apply feature selection approaches to pinpoint the most relevant features, since electronic health records tend to contain several candidate predictors. Building upon interpretability methods, I developed an explanation-driven recursive feature elimination approach. This method was comprehensively evaluated against state-of-the art feature selection methods. Therefore, this thesis' main contributions are three-fold, namely, 1) designing and developing a software artifact tailored to the specific needs of the clinical modeling domain, 2) demonstrating its application in a concrete case in the Nephrology context and 3) development and evaluation of a new feature selection approach applicable in a validation context that builds upon interpretability methods. In conclusion, I argue that appropriate tooling, which relies on standardization and parametrization, can support rapid model prototyping and collaboration between clinicians and data scientists in clinical predictive modeling.