Search beyond traditional probabilistic information retrieval

"This thesis focuses on search beyond probabilistic information retrieval. Three ap- proached are proposed beyond the traditional probabilistic modelling. First, term associ- ation is deeply examined. Term association considers the term dependency using a factor analysis based model, instead of treating each term independently. Latent factors, con- sidered the same as the hidden variables of ""eliteness"" introduced by Robertson et al. to gain understanding of the relation among term occurrences and relevance, are measured by the dependencies and occurrences of term sequences and subsequences. Second, an entity-based ranking approach is proposed in an entity system named ""EntityCube"" which has been released by Microsoft for public use. A summarization page is given to summarize the entity information over multiple documents such that the truly relevant entities can be highly possibly searched from multiple documents through integrating the local relevance contributed by proximity and the global enhancer by topic model. Third, multi-source fusion sets up a meta-search engine to combine the ""knowledge"" from different sources. Meta-features, distilled as high-level categories, are deployed to diversify the baselines. Three modified fusion methods are employed, which are re- ciprocal, CombMNZ and CombSUM with three expanded versions. Through extensive experiments on the standard large-scale TREC Genomics data sets, the TREC HARD data sets and the Microsoft EntityCube Web collections, the proposed extended models beyond probabilistic information retrieval show their effectiveness and superiority.

Factors affecting the effectiveness of biomedical document indexing and retrieval based on terminologies

International audienceThe aim of this work is to evaluate a set of indexing and retrieval strategies based on the integration of several biomedical terminologies on the available TREC Genomics collections for an ad hoc information retrieval (IR) task.Materials and methodsWe propose a multi-terminology based concept extraction approach to selecting best concepts from free text by means of voting techniques. We instantiate this general approach on four terminologies (MeSH, SNOMED, ICD-10 and GO). We particularly focus on the effect of integrating terminologies into a biomedical IR process, and the utility of using voting techniques for combining the extracted concepts from each document in order to provide a list of unique concepts.ResultsExperimental studies conducted on the TREC Genomics collections show that our multi-terminology IR approach based on voting techniques are statistically significant compared to the baseline. For example, tested on the 2005 TREC Genomics collection, our multi-terminology based IR approach provides an improvement rate of +6.98% in terms of MAP (mean average precision) (p < 0.05) compared to the baseline. In addition, our experimental results show that document expansion using preferred terms in combination with query expansion using terms from top ranked expanded documents improve the biomedical IR effectiveness.ConclusionWe have evaluated several voting models for combining concepts issued from multiple terminologies. Through this study, we presented many factors affecting the effectiveness of biomedical IR system including term weighting, query expansion, and document expansion models. The appropriate combination of those factors could be useful to improve the IR performance

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Data visualization is an essential component of genomic data analysis. However, the size and diversity of the data sets produced by today's sequencing and array-based profiling methods present major challenges to visualization tools. The Integrative Genomics Viewer (IGV) is a high-performance viewer that efficiently handles large heterogeneous data sets, while providing a smooth and intuitive user experience at all levels of genome resolution. A key characteristic of IGV is its focus on the integrative nature of genomic studies, with support for both array-based and next-generation sequencing data, and the integration of clinical and phenotypic data. Although IGV is often used to view genomic data from public sources, its primary emphasis is to support researchers who wish to visualize and explore their own data sets or those from colleagues. To that end, IGV supports flexible loading of local and remote data sets, and is optimized to provide high-performance data visualization and exploration on standard desktop systems. IGV is freely available for download from http://www.broadinstitute.org/igv, under a GNU LGPL open-source license