10,224 research outputs found

    Self-adaptive GA, quantitative semantic similarity measures and ontology-based text clustering

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    As the common clustering algorithms use vector space model (VSM) to represent document, the conceptual relationships between related terms which do not co-occur literally are ignored. A genetic algorithm-based clustering technique, named GA clustering, in conjunction with ontology is proposed in this article to overcome this problem. In general, the ontology measures can be partitioned into two categories: thesaurus-based methods and corpus-based methods. We take advantage of the hierarchical structure and the broad coverage taxonomy of Wordnet as the thesaurus-based ontology. However, the corpus-based method is rather complicated to handle in practical application. We propose a transformed latent semantic analysis (LSA) model as the corpus-based method in this paper. Moreover, two hybrid strategies, the combinations of the various similarity measures, are implemented in the clustering experiments. The results show that our GA clustering algorithm, in conjunction with the thesaurus-based and the LSA-based method, apparently outperforms that with other similarity measures. Moreover, the superiority of the GA clustering algorithm proposed over the commonly used k-means algorithm and the standard GA is demonstrated by the improvements of the clustering performance

    Measuring concept similarities in multimedia ontologies: analysis and evaluations

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    The recent development of large-scale multimedia concept ontologies has provided a new momentum for research in the semantic analysis of multimedia repositories. Different methods for generic concept detection have been extensively studied, but the question of how to exploit the structure of a multimedia ontology and existing inter-concept relations has not received similar attention. In this paper, we present a clustering-based method for modeling semantic concepts on low-level feature spaces and study the evaluation of the quality of such models with entropy-based methods. We cover a variety of methods for assessing the similarity of different concepts in a multimedia ontology. We study three ontologies and apply the proposed techniques in experiments involving the visual and semantic similarities, manual annotation of video, and concept detection. The results show that modeling inter-concept relations can provide a promising resource for many different application areas in semantic multimedia processing

    Semantics-based selection of everyday concepts in visual lifelogging

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    Concept-based indexing, based on identifying various semantic concepts appearing in multimedia, is an attractive option for multimedia retrieval and much research tries to bridge the semantic gap between the media’s low-level features and high-level semantics. Research into concept-based multimedia retrieval has generally focused on detecting concepts from high quality media such as broadcast TV or movies, but it is not well addressed in other domains like lifelogging where the original data is captured with poorer quality. We argue that in noisy domains such as lifelogging, the management of data needs to include semantic reasoning in order to deduce a set of concepts to represent lifelog content for applications like searching, browsing or summarisation. Using semantic concepts to manage lifelog data relies on the fusion of automatically-detected concepts to provide a better understanding of the lifelog data. In this paper, we investigate the selection of semantic concepts for lifelogging which includes reasoning on semantic networks using a density-based approach. In a series of experiments we compare different semantic reasoning approaches and the experimental evaluations we report on lifelog data show the efficacy of our approach

    A COMPARATIVE STUDY ON ONTOLOGY GENERATION AND TEXT CLUSTERING USING VSM, LSI, AND DOCUMENT ONTOLOGY MODELS

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    Although using ontologies to assist information retrieval and text document processing has recently attracted more and more attention, existing ontology-based approaches have not shown advantages over the traditional keywords-based Latent Semantic Indexing (LSI) method. This paper proposes an algorithm to extract a concept forest (CF) from a document with the assistance of a natural language ontology, the WordNet lexical database. Using concept forests to represent the semantics of text documents, the semantic similarities of these documents are then measured as the commonalities of their concept forests. Performance studies of text document clustering based on different document similarity measurement methods show that the CF-based similarity measurement is an effective alternative to the existing keywords-based methods. Especially, this CF-based approach has obvious advantages over the existing keywords-based methods, including LSI, in dealing with text abstract databases, such as MEDLINE, or in P2P environments where it is impractical to collect the entire document corpus for analysis

    Seeing the Forest for the Trees: Using the Gene Ontology to Restructure Hierarchical Clustering

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    Motivation: There is a growing interest in improving the cluster analysis of expression data by incorporating into it prior knowledge, such as the Gene Ontology (GO) annotations of genes, in order to improve the biological relevance of the clusters that are subjected to subsequent scrutiny. The structure of the GO is another source of background knowledge that can be exploited through the use of semantic similarity. Results: We propose here a novel algorithm that integrates semantic similarities (derived from the ontology structure) into the procedure of deriving clusters from the dendrogram constructed during expression-based hierarchical clustering. Our approach can handle the multiple annotations, from different levels of the GO hierarchy, which most genes have. Moreover, it treats annotated and unannotated genes in a uniform manner. Consequently, the clusters obtained by our algorithm are characterized by significantly enriched annotations. In both cross-validation tests and when using an external index such as protein–protein interactions, our algorithm performs better than previous approaches. When applied to human cancer expression data, our algorithm identifies, among others, clusters of genes related to immune response and glucose metabolism. These clusters are also supported by protein–protein interaction data. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.Lynne and William Frankel Center for Computer Science; Paul Ivanier center for robotics research and production; National Institutes of Health (R01 HG003367-01A1

    Inferring gene ontologies from pairwise similarity data.

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    MotivationWhile the manually curated Gene Ontology (GO) is widely used, inferring a GO directly from -omics data is a compelling new problem. Recognizing that ontologies are a directed acyclic graph (DAG) of terms and hierarchical relations, algorithms are needed that: analyze a full matrix of gene-gene pairwise similarities from -omics data; infer true hierarchical structure in these data rather than enforcing hierarchy as a computational artifact; and respect biological pleiotropy, by which a term in the hierarchy can relate to multiple higher level terms. Methods addressing these requirements are just beginning to emerge-none has been evaluated for GO inference.MethodsWe consider two algorithms [Clique Extracted Ontology (CliXO), LocalFitness] that uniquely satisfy these requirements, compared with methods including standard clustering. CliXO is a new approach that finds maximal cliques in a network induced by progressive thresholding of a similarity matrix. We evaluate each method's ability to reconstruct the GO biological process ontology from a similarity matrix based on (a) semantic similarities for GO itself or (b) three -omics datasets for yeast.ResultsFor task (a) using semantic similarity, CliXO accurately reconstructs GO (>99% precision, recall) and outperforms other approaches (<20% precision, <20% recall). For task (b) using -omics data, CliXO outperforms other methods using two -omics datasets and achieves ∼30% precision and recall using YeastNet v3, similar to an earlier approach (Network Extracted Ontology) and better than LocalFitness or standard clustering (20-25% precision, recall).ConclusionThis study provides algorithmic foundation for building gene ontologies by capturing hierarchical and pleiotropic structure embedded in biomolecular data

    An empirical study of inter-concept similarities in multimedia ontologies

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    Generic concept detection has been a widely studied topic in recent research on multimedia analysis and retrieval, but the issue of how to exploit the structure of a multimedia ontology as well as different inter-concept relations, has not received similar attention. In this paper, we present results from our empirical analysis of different types of similarity among semantic concepts in two multimedia ontologies, LSCOM-Lite and CDVP-206. The results show promise that the proposed methods may be helpful in providing insight into the existing inter-concept relations within an ontology and selecting the most facilitating set of concepts and hierarchical relations. Such an analysis as this can be utilized in various tasks such as building more reliable concept detectors and designing large-scale ontologies

    Discovering the Impact of Knowledge in Recommender Systems: A Comparative Study

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    Recommender systems engage user profiles and appropriate filtering techniques to assist users in finding more relevant information over the large volume of information. User profiles play an important role in the success of recommendation process since they model and represent the actual user needs. However, a comprehensive literature review of recommender systems has demonstrated no concrete study on the role and impact of knowledge in user profiling and filtering approache. In this paper, we review the most prominent recommender systems in the literature and examine the impression of knowledge extracted from different sources. We then come up with this finding that semantic information from the user context has substantial impact on the performance of knowledge based recommender systems. Finally, some new clues for improvement the knowledge-based profiles have been proposed.Comment: 14 pages, 3 tables; International Journal of Computer Science & Engineering Survey (IJCSES) Vol.2, No.3, August 201

    Integration of molecular network data reconstructs Gene Ontology.

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    Motivation: Recently, a shift was made from using Gene Ontology (GO) to evaluate molecular network data to using these data to construct and evaluate GO. Dutkowski et al. provide the first evidence that a large part of GO can be reconstructed solely from topologies of molecular networks. Motivated by this work, we develop a novel data integration framework that integrates multiple types of molecular network data to reconstruct and update GO. We ask how much of GO can be recovered by integrating various molecular interaction data. Results: We introduce a computational framework for integration of various biological networks using penalized non-negative matrix tri-factorization (PNMTF). It takes all network data in a matrix form and performs simultaneous clustering of genes and GO terms, inducing new relations between genes and GO terms (annotations) and between GO terms themselves. To improve the accuracy of our predicted relations, we extend the integration methodology to include additional topological information represented as the similarity in wiring around non-interacting genes. Surprisingly, by integrating topologies of bakers’ yeasts protein–protein interaction, genetic interaction (GI) and co-expression networks, our method reports as related 96% of GO terms that are directly related in GO. The inclusion of the wiring similarity of non-interacting genes contributes 6% to this large GO term association capture. Furthermore, we use our method to infer new relationships between GO terms solely from the topologies of these networks and validate 44% of our predictions in the literature. In addition, our integration method reproduces 48% of cellular component, 41% of molecular function and 41% of biological process GO terms, outperforming the previous method in the former two domains of GO. Finally, we predict new GO annotations of yeast genes and validate our predictions through GIs profiling. Availability and implementation: Supplementary Tables of new GO term associations and predicted gene annotations are available at http://bio-nets.doc.ic.ac.uk/GO-Reconstruction/. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online
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