Background: PubMed is designed to provide rapid, comprehensive retrieval of papers that discuss a given topic. However, because PubMed does not organize the search output further, it is difficult for users to grasp an overview of the retrieved literature according to non-topical dimensions, to drill-down to find individual articles relevant to a particular individual's need, or to browse the collection.
This paper presents a study of incorporating domain-specific knowledge (i.e., information about concepts and relationships between concepts in a certain domain) in an information retrieval (IR) system to improve its effectiveness in retrieving biomedical literature. The effects of different types of domain-specific knowledge in performance contribution are examined. Based on the TREC platform, we show that appropriate use of domainspecific knowledge in a proposed conceptual retrieval model yields about 23% improvement over the best reported result in passage retrieval in the Genomics Track of TREC 2006.
The Arrowsmith two-node search is a strategy that is designed to assist biomedical investigators in formulating and assessing scientific hypotheses. More generally, it allows users to identify biologically meaningful links between any two sets of articles A and C in PubMed, even when these share no articles or authors in common and represent disparate topics or disciplines. The key idea is to relate the two sets of articles via title words and phrases (B-terms) that they share. We have created a free, public web-based version of the two-node search tool (http://arrowsmith.psych.uic.edu), have described its development and implementation, and have presented analyses of individual two-node searches. In this paper, we provide an updated tutorial intended for end-users, that covers the use of the tool for a variety of potential scientific use case scenarios. For example, one can assess a recent experimental, clinical or epidemiologic finding that connects two disparate fields of inquiry --identifying likely mechanisms to explain the finding, and choosing promising follow-up lines of investigation. Alternatively, one can assess whether the existing scientific literature lends indirect support to a hypothesis posed by the user that has not yet been investigated. One can also employ two-node searches to search for novel hypotheses. Arrowsmith provides a service that cannot be carried out feasibly via standard PubMed searches or by other available text mining tools.
Gaussian elimination and LU factoring have been greatly studied from the algorithmic point of view, but much less from the point view of the best output format. In this paper, we give new output formats for fraction free LU factoring and for QR factoring. The formats and the algorithms used to obtain them are valid for any matrix system in which the entries are taken from an integral domain, not just for integer matrix systems. After discussing the new output format of LU factoring, the complexity analysis for the fraction free algorithm and fraction free output is given. Our new output format contains smaller entries than previously suggested forms, and it avoids the gcd computations required by some other partially fraction free computations. As applications of our fraction free algorithm and format, we demonstrate how to construct a fraction free QR factorization and how to solve linear systems within a given domain.
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