Many text mining applications in the biomedical domain benefit from automatic clustering of relational phrases into synonymous groups, since it alleviates the problem of spurious mismatches caused by the diversity of natural language expressions. Mos...
Document collections resulting from searches in the biomedical literature, for instance, in PubMed, are often so large that some organization of the returned information is necessary. Clustering is an efficient tool for organizing search results. To ...
BACKGROUND: Systems approaches to studying drug-side-effect (drug-SE) associations are emerging as an active research area for both drug target discovery and drug repositioning. However, a comprehensive drug-SE association knowledge base does not exi...
Journal of the American Medical Informatics Association : JAMIA
Feb 5, 2015
OBJECTIVE: For many literature review tasks, including systematic review (SR) and other aspects of evidence-based medicine, it is important to know whether an article describes a randomized controlled trial (RCT). Current manual annotation is not com...
INTRODUCTION: The ambiguity of biomedical abbreviations is one of the challenges in biomedical text mining systems. In particular, the handling of term variants and abbreviations without nearby definitions is a critical issue. In this study, we adopt...
OBJECTIVE: It is important to identify separate publications that report outcomes from the same underlying clinical trial, in order to avoid over-counting these as independent pieces of evidence.
BACKGROUND: Cluster randomized trials (CRTs) are becoming an increasingly important design. However, authors of CRTs do not always adhere to requirements to explicitly identify the design as cluster randomized in titles and abstracts, making retrieva...
BACKGROUND: Systematic and scoping literature searches are increasingly resource intensive. We present the results of a scoping review which combines the use of a novel artificial-intelligence-(AI)-assisted Medline search tool with two other 'traditi...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Jan 1, 2021
Sentence boundary detection (SBD) is a fundamental building block in the Natural Language Processing (NLP) pipeline. Incorrect SBD may impact subsequent processing stages resulting in decreased performance. In well-behaved corpora, a few simple rules...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 1, 2021
Grant support (GS) in the MEDLINE database refers to funding agencies and contract numbers. It is important for funding organizations to track their funding outcomes from the GS information. As such, how to accurately and automatically extract fundin...