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Evaluation is a major driving force in advancing the state of the art in language technologies. In particular, methods for automatically assessing the quality of machine output is the preferred method for measuring progress, provided that these metrics have been validated against human judgments. Following recent developments in the automatic evaluation of(More)
This paper represents a continuation of research into the retrieval and annotation of textual genomics documents (both MEDLINE ® citations and full text articles) for the purpose of satisfying biologists' real information needs. The overall approach taken here for both the ad hoc retrieval and categorization tasks within the TREC genomics track in 2005 was(More)
We describe a natural language processing system (Enhanced SemRep) to identify core assertions on pharmacogenomics in Medline citations. Extracted information is represented as semantic predications covering a range of relations relevant to this domain. The specific relations addressed by the system provide greater precision than that achievable with(More)
The ability to accurately model the content structure of text is important for many natural language processing applications. This paper describes experiments with generative models for analyzing the discourse structure of medical abstracts , which generally follow the pattern of " introduction " , " methods " , " results " , and " conclusions ". We(More)
We present a methodology that automatically selects indexing algorithms for each heading in Medical Subject Headings (MeSH), National Library of Medicine's vocabulary for indexing MEDLINE. While manually comparing indexing methods is manageable with a limited number of MeSH headings, a large number of them make automation of this selection desirable.(More)
OBJECTIVES We analyzed the extent to which comparative effectiveness research (CER) organizations share terms for designs, analyzed coverage of CER designs in Medical Subject Headings (MeSH) and Emtree, and explored whether scientists use CER design terms. METHODS We developed local terminologies (LTs) and a CER design terminology by extracting terms in(More)
The combination of recent developments in question-answering research and the availability of unparalleled resources developed specifically for automatic semantic processing of text in the medical domain provides a unique opportunity to explore complex question answering in the domain of clinical medicine. This article presents a system designed to satisfy(More)
This article describes the algorithms implemented in the Essie search engine that is currently serving several Web sites at the National Library of Medicine. Essie is a phrase-based search engine with term and concept query expansion and probabilistic relevancy ranking. Essie's design is motivated by an observation that query terms are often conceptually(More)
Despite its intuitive appeal, the hypothesis that retrieval at the level of "concepts" should outperform purely term-based approaches remains unverified empirically. In addition, the use of "knowledge" has not consistently resulted in performance gains. After identifying possible reasons for previous negative results, we present a novel framework for(More)