Search (29 results, page 1 of 2)

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Abstract

Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures.

Date

22. 7.2006 14:40:10

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Abstract

SIBRIS (Sandwich Interactive Browsing and Ranking Information System) is an interactive text retrieval system which has been developed to support the browsing of library and product files at Pfizer Central Research, Sandwich, UK. Once an initial ranking has been produced, the system will allow the user to select any document displayed on the screen at any point during the browse and to use that as the basis for another search. Facilities have been included to enable the user to keep track of the browse and to facilitate backtracking, thus allowing the user to move away from the original query to wander in and out of different areas of interest.

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Abstract

This paper provides an introduction to genetic algorithms, a new approach to the investigation of computationally-intensive problems that may be insoluble using conventional, deterministic approaches. A genetic algorithm takes an initial set of possible starting solutions and then iteratively improves theses solutions using operators that are analogous to those involved in Darwinian evolution. The approach is illusrated by reference to several problems in information retrieval

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Abstract

This paper summarizes the historical development of the discipline that is now called 'chemoinformatics'. It shows how this has evolved, principally as a result of technological developments in chemistry and biology during the past decade, from long-established techniques for the modelling and searching of chemical molecules. A total of 30 papers, the earliest dating back to 1957, are briefly summarized to highlight some of the key publications and to show the development of the discipline.

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Abstract

Genetic algorithms are a class of non-deterministic algorithms that derive from Darwinian evolution and that provide good, though not necessarily optimal, solutions to combinatorial problems. We describe their application to the identification of characteristics that occur approximately equifrequently in a database, using two different methods for the creation of the chromosome data structures that lie at the heart of a genetic algortihm. Experiments with files of English and Turkish text suggest that the genetic algorithm developed here can produce results superior to those produced by existing non-deterministic algorithms; however, the results are inferior to those produced by an existing deterministic algorithm

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Abstract

Summarises the results to date of a continuing programme of research at Sheffield Univ. to investigate the use of nearest-neighbour retrieval algorithms for full text searching. Given a natural language query statement, the research methods result in a ranking of the paragraphs comprising a full text document in order of decreasing similarity with the query, where the similarity for each paragraph is determined by the number of keyword stems that it has in common with the query

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Abstract

This paper provides an over-view of 2, complementary approaches to the design and implementation of information retrieval systems. The first approach focuses on the algorithms and data structures that are needed to maximise the effectiveness and the efficiency of the searches that can be carried out on text databases, while the second adopts a cognitive approach that focuses on the role of the user and of the knowledge sources involved in information retrieval. The paper argues for an holistic view of information retrieval that is capable of encompassing both of these approaches

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Abstract

We have recently completed a survey of the operational use of hypertext-based information systems in academic, public and special libraries in the UK. A literatur search, questionnaire and both telephone and face-to-face interviews demonstrate that the principle application of hypertext systems is for the implementation of public-access point-of-information systems, which provide guidance to the users of local information resources. In this paper, we describe the principle issuse relating to the design and usage of these systems that were raised in the interviews and that we experienced when using the systems for ourselves. We then present a set of technical recommendations with the intention of helping the developers of future systems, with special attention being given to the need to develop effective methods for system evaluation

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Abstract

State of the art review of hypertext systems in use in UK libraries. Systems include public access point of information (POI) systems that provide guidance to users of local resources, and networked document retrieval systems, such as WWW, that enable users to access texts stored on machines linked by the Internet. Particular emphasis is placed on those systems that are produced inhouse by the libraries in which they are used. The review is based on a series of telephone or face to face interviews conducted with representatives of those organizations that a literature review and mailed questionnaire survey identified as current users of hypertext. Considers issues relating to system development and usability, and presents a set of appropriate guidelines for the designers of future systems. Concludes that: the principle application of hypertext systems in UK libraries is in the implementation of POI systems; that such development is most advanced in the academic sector; and that such development is set to increase in tandem with use of the WWW

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Abstract

In important stage in the process of retrieval of objects from a hypertext database is the creation of a set of inter-nodal links that are intended to represent the relationships existing between objects; this operation is often undertaken manually, just as index terms are often manually assigned to documents in a conventional retrieval system. Studies of conventional systems have suggested that a degree of consistency in the terms assigned to documents by indexers is positively associated with retrieval effectiveness. It is thus of interest to investigate the consistency of assignment of links in separate hypertext versions of the same full-text document, since a measure of agreement may be related to the subsequent utility of the resulting hypertext databases. The calculation of values indicating the degree of similarity between objects is a technique that has been widely used in the fields of textual and chemical information retrieval; in this paper we describe the application of arithmetic coefficients and topological indices to the measurement of the degree of similarity between the sets of inter-nodal links in hypertext databases. We publish the results of a study in which several different of links are inserted, by different people, between the paragraphs of each of a number of full-text documents. Our results show little similary between the sets of links identified by different people; this finding is comparable with those of studies of inter-indexer consistency, where it has been found that there is generally only a low level of agreement between the sets of idenx terms assigned to a document by different indexers

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Abstract

Purpose - The purpose of this paper is to suggest an alternative to the widely used Times Cited criterion for analysing citation networks. The approach involves taking account of the natures of the papers that cite a given paper, so as to differentiate between papers that attract the same number of citations. Design/methodology/approach - ArticleRank is an algorithm that has been derived from Google's PageRank algorithm to measure the influence of journal articles. ArticleRank is applied to two datasets - a citation network based on an early paper on webometrics, and a self-citation network based on the 19 most cited papers in the Journal of Documentation - using citation data taken from the Web of Knowledge database. Findings - ArticleRank values provide a different ranking of a set of papers from that provided by the corresponding Times Cited values, and overcomes the inability of the latter to differentiate between papers with the same numbers of citations. The difference in rankings between Times Cited and ArticleRank is greatest for the most heavily cited articles in a dataset. Originality/value - This is a novel application of the PageRank algorithm.

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Abstract

Purpose Open-access mega-journals (OAMJs) represent an increasingly important part of the scholarly communication landscape. OAMJs, such as PLOS ONE, are large scale, broad scope journals that operate an open access business model (normally based on article-processing charges), and which employ a novel form of peer review, focussing on scientific "soundness" and eschewing judgement of novelty or importance. The purpose of this paper is to examine the discourses relating to OAMJs, and their place within scholarly publishing, and considers attitudes towards mega-journals within the academic community. Design/methodology/approach This paper presents a review of the literature of OAMJs structured around four defining characteristics: scale, disciplinary scope, peer review policy, and economic model. The existing scholarly literature was augmented by searches of more informal outputs, such as blogs and e-mail discussion lists, to capture the debate in its entirety. Findings While the academic literature relating specifically to OAMJs is relatively sparse, discussion in other fora is detailed and animated, with debates ranging from the sustainability and ethics of the mega-journal model, to the impact of soundness-only peer review on article quality and discoverability, and the potential for OAMJs to represent a paradigm-shifting development in scholarly publishing. Originality/value This paper represents the first comprehensive review of the mega-journal phenomenon, drawing not only on the published academic literature, but also grey, professional and informal sources. The paper advances a number of ways in which the role of OAMJs in the scholarly communication environment can be conceptualised.

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Abstract

Purpose The purpose of this paper is to provide insights into publication practices from the perspective of academics working within four disciplinary communities: biosciences, astronomy/physics, education and history. The paper explores the ways in which these multiple overlapping communities intersect with the journal landscape and the implications for the adoption and use of new players in the scholarly communication system, particularly open-access mega-journals (OAMJs). OAMJs (e.g. PLOS ONE and Scientific Reports) are large, broad scope, open-access journals that base editorial decisions solely on the technical/scientific soundness of the article. Design/methodology/approach Focus groups with active researchers in these fields were held in five UK Higher Education Institutions across Great Britain, and were complemented by interviews with pro-vice-chancellors for research at each institution. Findings A strong finding to emerge from the data is the notion of researchers belonging to multiple overlapping communities, with some inherent tensions in meeting the requirements for these different audiences. Researcher perceptions of evaluation mechanisms were found to play a major role in attitudes towards OAMJs, and interviews with the pro-vice-chancellors for research indicate that there is a difference between researchers' perceptions and the values embedded in institutional frameworks. Originality/value This is the first purely qualitative study relating to researcher perspectives on OAMJs. The findings of the paper will be of interest to publishers, policy-makers, research managers and academics.

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Abstract

An important stage in the process of retrieval of objects from a hypertext database is the creation of a set of internodal links that are intended to represent the relationships existing between objetcs; an operation that is usually undertaken manually such as the allocation of subject index terms to documents. Reports results of a study in which several different sets of hypertext links were inserted, each by a different person, between the paragraphs of each of a number of full text documents. The similarity between the members of each pair of link sets was then evaluated. Results indicated that little similarity existed among the link sets, a finding comparable with those of studies of inter indexer consistency, which suggests that there is generally only a low level of agreemenet between the sets of index terms assigned to a document by indexers. Concludes with that part of the study designed to test the validity of making these kinds of assumptions in the context of hypertext link sets

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Abstract

Reviews the basic techniques involving genetic algorithms and their application to 2 problems in information retrieval: the generation of equifrequent groups of index terms; and the identification of optimal query and term weights. The algorithm developed for the generation of equifrequent groupings proved to be effective in operation, achieving results comparable with those obtained using a good deterministic algorithm. The algorithm developed for the identification of optimal query and term weighting involves fitness function that is based on full relevance information

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Abstract

Describes the development of a genetic algorithm (GA) for the assignment of weights to query terms in a ranked output document retrieval system. The GA involves a fitness function that is based on full relevance information, and the rankings resulting from the use of these weights are compared with the Robertson-Sparck Jones F4 retrospective relevance weight

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Abstract

An important stage in the process or retrieval of objects from a hypertext database is the creation of a set of internodal links that are intended to represent the relationships existing between objects; this operation is often undertaken manually, just as index terms are often manually assigned to documents in a conventional retrieval system. In an earlier article (1994), the results were published of a study in which several different sets of links were inserted, each by a different person, between the paragraphs of each of a number of full-text documents. These results showed little similarity between the link-sets, a finding that was comparable with those of studies of inter-indexer consistency, which suggest that there is generally only a low level of agreement between the sets of index terms assigned to a document by different indexers. In this article, a description is provided of an investigation into the nature of the relationship existing between (i) the levels of inter-linker consistency obtaining among the group of hypertext databases used in our earlier experiments, and (ii) the levels of effectiveness of a number of searches carried out in those databases. An account is given of the implementation of the searches and of the methods used in the calculation of numerical values expressing their effectiveness. Analysis of the results of a comparison between recorded levels of consistency and those of effectiveness does not allow us to draw conclusions about the consistency - effectiveness relationship that are equivalent to those drawn in comparable studies of inter-indexer consistency

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Abstract

Studies of document retrieval systems have suggested that the degree of consistency in the terms assigned to documents by indexers is positively associated with retrieval effectiveness. The study investigated the consistency of assignment of links in separate hypertext versions of the same full text database assuming that a measure of agreement may be related to the subsequent utility of the resulting hypertext document. Describes the calculations involved in measuring the degree of similarity between pairs of structured objetcs of a certain type (Those that may be represented in graph theoretic form). Initial results show little similarity between the sets of links identified by different people and this finding is comparable with those of studies of inter indexer consistency, where it has been found that there is generally only alow level of agreement between the sets of indexing terms assigned to a document of different indexers

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Abstract

Provides an introduction to the computational techniques that underlie best match searching retrieval systems. Discusses: problems of traditional Boolean systems; characteristics of best-match searching; automatic indexing; term conflation; matching of documents and queries (dealing with similarity measures, initial weights, relevance weights, and the matching algorithm); and describes operational best-match systems