Treatment recommendations within Clinical Practice Guidelines (CPGs) are largely based on findings from clinical trials and case studies, referred to here as research studies, that are often based on highly selective clinical populations, referred to here as study cohorts. When medical practitioners apply CPG recommendations, they need to understand how well their patient population matches the characteristics of those in the study cohort, and thus are confronted with the challenges of locating the study cohort information and making an analytic comparison. To address these challenges, we develop an ontology-enabled prototype system, which exposes the population descriptions in research studies in a declarative manner, with the ultimate goal of allowing medical practitioners to better understand the applicability and generalizability of treatment recommendations. We build a Study Cohort Ontology (SCO) to encode the vocabulary of study population descriptions, that are often reported in the first table in the published work, thus they are often referred to as Table 1. We leverage the well-used Semanticscience Integrated Ontology (SIO) for defining property associations between classes. Further, we model the key components of Table 1s, i.e., collections of study subjects, subject characteristics, and statistical measures in RDF knowledge graphs. We design scenarios for medical practitioners to perform population analysis, and generate cohort similarity visualizations to determine the applicability of a study population to the clinical population of interest. Our semantic approach to make study populations visible, by standardized representations of Table 1s, allows users to quickly derive clinically relevant inferences about study populations.
Translation-based embedding models have gained significant attention in link prediction tasks for knowledge graphs. TransE is the primary model among translation-based embeddings and is well-known for its low complexity and high efficiency. Therefore, most of the earlier works have modified the score function of the TransE approach in order to improve the performance of link prediction tasks. Nevertheless, proven theoretically and experimentally, the performance of TransE strongly depends on the loss function. Margin Ranking Loss (MRL) has been one of the earlier loss functions which is widely used for training TransE. However, the scores of positive triples are not necessarily enforced to be sufficiently small to fulfill the translation from head to tail by using relation vector (original assumption of TransE). To tackle this problem, several loss functions have been proposed recently by adding upper bounds and lower bounds to the scores of positive and negative samples. Although highly effective, previously developed models suffer from an expansion in search space for a selection of the hyperparameters (in particular the upper and lower bounds of scores) on which the performance of the translation-based models is highly dependent. In this paper, we propose a new loss function dubbed Adaptive Margin Loss (AML) for training translation-based embedding models. The formulation of the proposed loss function enables an adaptive and automated adjustment of the margin during the learning process. Therefore, instead of obtaining two values (upper bound and lower bound), only the center of a margin needs to be determined. During learning, the margin is expanded automatically until it converges. In our experiments on a set of standard benchmark datasets including Freebase and WordNet, the effectiveness of AML is confirmed for training TransE on link prediction tasks.