Semantically enabling clinical decision support recommendations.

BACKGROUND: Clinical decision support systems have been widely deployed to guide healthcare decisions on patient diagnosis, treatment choices, and patient management through evidence-based recommendations. These recommendations are typically derived from clinical practice guidelines created by clinical specialties or healthcare organizations. Although there have been many different technical approaches to encoding guideline recommendations into decision support systems, much of the previous work has not focused on enabling system generated recommendations through the formalization of changes in a guideline, the provenance of a recommendation, and applicability of the evidence. Prior work indicates that healthcare providers may not find that guideline-derived recommendations always meet their needs for reasons such as lack of relevance, transparency, time pressure, and applicability to their clinical practice. RESULTS: We introduce several semantic techniques that model diseases based on clinical practice guidelines, provenance of the guidelines, and the study cohorts they are based on to enhance the capabilities of clinical decision support systems. We have explored ways to enable clinical decision support systems with semantic technologies that can represent and link to details in related items from the scientific literature and quickly adapt to changing information from the guidelines, identifying gaps, and supporting personalized explanations. Previous semantics-driven clinical decision systems have limited support in all these aspects, and we present the ontologies and semantic web based software tools in three distinct areas that are unified using a standard set of ontologies and a custom-built knowledge graph framework: (i) guideline modeling to characterize diseases, (ii) guideline provenance to attach evidence to treatment decisions from authoritative sources, and (iii) study cohort modeling to identify relevant research publications for complicated patients. CONCLUSIONS: We have enhanced existing, evidence-based knowledge by developing ontologies and software that enables clinicians to conveniently access updates to and provenance of guidelines, as well as gather additional information from research studies applicable to their patients' unique circumstances. Our software solutions leverage many well-used existing biomedical ontologies and build upon decades of knowledge representation and reasoning work, leading to explainable results.

Informing clinical assessment by contextualizing post-hoc explanations of risk prediction models in type-2 diabetes.

Medical experts may use Artificial Intelligence (AI) systems with greater trust if these are supported by 'contextual explanations' that let the practitioner connect system inferences to their context of use. However, their importance in improving model usage and understanding has not been extensively studied. Hence, we consider a comorbidity risk prediction scenario and focus on contexts regarding the patients' clinical state, AI predictions about their risk of complications, and algorithmic explanations supporting the predictions. We explore how relevant information for such dimensions can be extracted from Medical guidelines to answer typical questions from clinical practitioners. We identify this as a question answering (QA) task and employ several state-of-the-art Large Language Models (LLM) to present contexts around risk prediction model inferences and evaluate their acceptability. Finally, we study the benefits of contextual explanations by building an end-to-end AI pipeline including data cohorting, AI risk modeling, post-hoc model explanations, and prototyped a visual dashboard to present the combined insights from different context dimensions and data sources, while predicting and identifying the drivers of risk of Chronic Kidney Disease (CKD) - a common type-2 diabetes (T2DM) comorbidity. All of these steps were performed in deep engagement with medical experts, including a final evaluation of the dashboard results by an expert medical panel. We show that LLMs, in particular BERT and SciBERT, can be readily deployed to extract some relevant explanations to support clinical usage. To understand the value-add of the contextual explanations, the expert panel evaluated these regarding actionable insights in the relevant clinical setting. Overall, our paper is one of the first end-to-end analyses identifying the feasibility and benefits of contextual explanations in a real-world clinical use case. Our findings can help improve clinicians' usage of AI models.

Knowledge Extraction of Cohort Characteristics in Research Publications.

When healthcare providers review the results of a clinical trial study to understand its applicability to their practice, they typically analyze how well the characteristics of the study cohort correspond to those of the patients they see. We have previously created a study cohort ontology to standardize this information and make it accessible for knowledge-based decision support. The extraction of this information from research publications is challenging, however, given the wide variance in reporting cohort characteristics in a tabular representation. To address this issue, we have developed an ontology-enabled knowledge extraction pipeline for automatically constructing knowledge graphs from the cohort characteristics found in PDF-formatted research papers. We evaluated our approach using a training and test set of 41 research publications and found an overall accuracy of 83.3% in correctly assembling the knowledge graphs. Our research provides a promising approach for extracting knowledge more broadly from tabular information in research publications.