A New Biomedical Passage Retrieval Framework for Laboratory Medicine: Leveraging Domain-specific Ontology, Multilevel PRF, and Negation Differential Weighting

Abstract

Clinical decision support (CDS) search is performed to retrieve key medical literature that can assist the practice of medical experts by offering appropriate medical information relevant to the medical case in hand. In this paper, we present a novel CDS search framework designed for passage retrieval from biomedical textbooks in order to support clinical decision-making using laboratory test results. The framework utilizes two unique characteristics of the textual reports derived from the test results, which are syntax variation and negation information. The proposed framework consists of three components: domain ontology, index repository, and query processing engine. We first created a domain ontology to resolve syntax variation by applying the ontology to detect medical concepts from the test results with language translation. We then preprocessed and performed indexing of biomedical textbooks recommended by clinicians for passage retrieval. We finally built the query-processing engine tailored for CDS, including translation, concept detection, query expansion, pseudo-relevance feedback at the local and global levels, and ranking with differential weighting of negation information. To evaluate the effectiveness of the proposed framework, we followed the standard information retrieval evaluation procedure. An evaluation dataset was created, including 28,581 textual reports for 30 laboratory test results and 56,228 passages from widely used biomedical textbooks, recommended by clinicians. Overall, our proposed passage retrieval framework, GPRF-NEG, outperforms the baseline by 36.2, 100.5, and 69.7 percent for MRR, R-precision, and Precision at 5, respectively. Our study results indicate that the proposed CDS search framework specifically designed for passage retrieval of biomedical literature represents a practically viable choice for clinicians as it supports their decision-making processes by providing relevant passages extracted from the sources that they prefer to refer to, with improved performances.