goCluster integrates statistical analysis and functional interpretation of microarray expression data

Motivation: Several tools that facilitate the interpretation of transcriptional profiles using gene annotation data are available but most of them combine a particular statistical analysis strategy with functional information. goCluster extends this concept by providing a modular framework that facilitates integration of statistical and functional microarray data analysis with data interpretation. Results: goCluster enables scientists to employ annotation information, clustering algorithms and visualization tools in their array data analysis and interpretation strategy. The package provides four clustering algorithms and GeneOntology terms as prototype annotation data. The functional analysis is based on the hypergeometric distribution whereby the Bonferroni correction or the false discovery rate can be used to correct for multiple testing. The approach implemented in goCluster was successfully applied to interpret the results of complex mammalian and yeast expression data obtained with high density oligonucleotide microarrays (GeneChips). Availability: goCluster is available via the BioConductor portal at www.bioconductor.org. The software package, detailed documentation, user- and developer guides as well as other background information are also accessible via a web portal at http://www.bioz.unibas.ch/gocluster. Contact: [email protected]

Concept-based Interactive Query Expansion Support Tool (CIQUEST)

This report describes a three-year project (2000-03) undertaken in the Information Studies Department at The University of Sheffield and funded by Resource, The Council for Museums, Archives and Libraries. The overall aim of the research was to provide user support for query formulation and reformulation in searching large-scale textual resources including those of the World Wide Web. More specifically the objectives were: to investigate and evaluate methods for the automatic generation and organisation of concepts derived from retrieved document sets, based on statistical methods for term weighting; and to conduct user-based evaluations on the understanding, presentation and retrieval effectiveness of concept structures in selecting candidate terms for interactive query expansion. The TREC test collection formed the basis for the seven evaluative experiments conducted in the course of the project. These formed four distinct phases in the project plan. In the first phase, a series of experiments was conducted to investigate further techniques for concept derivation and hierarchical organisation and structure. The second phase was concerned with user-based validation of the concept structures. Results of phases 1 and 2 informed on the design of the test system and the user interface was developed in phase 3. The final phase entailed a user-based summative evaluation of the CiQuest system. The main findings demonstrate that concept hierarchies can effectively be generated from sets of retrieved documents and displayed to searchers in a meaningful way. The approach provides the searcher with an overview of the contents of the retrieved documents, which in turn facilitates the viewing of documents and selection of the most relevant ones. Concept hierarchies are a good source of terms for query expansion and can improve precision. The extraction of descriptive phrases as an alternative source of terms was also effective. With respect to presentation, cascading menus were easy to browse for selecting terms and for viewing documents. In conclusion the project dissemination programme and future work are outlined

Advances in Teaching & Learning Day Abstracts 2005

Proceedings of the Advances in Teaching & Learning Day Regional Conference held at The University of Texas Health Science Center at Houston in 2005

Statistical Semantic Classification of Crisis Information

The rise of social media as an information channel during crisis has become key to community response. However, existing crisis awareness applications, often struggle to identify relevant information among the high volume of data that is generated over social platforms. A wide range of statistical features and machine learning methods have been researched in recent years to automatically classify this information. In this paper we aim to complement previous studies by exploring the use of semantics as additional features to identify relevant crisis in- formation. Our assumption is that entities and concepts tend to have a more consistent correlation with relevant and irrelevant information, and therefore can enhance the discrimination power of classifiers. Our results, so far, show that some classification improvements can be obtained when using semantic features, reaching +2.51% when the classifier is applied to a new crisis event (i.e., not in training set)

BCAS: A Web-enabled and GIS-based Decision Support System for the Diagnosis and Treatment of Breast Cancer

For decades, geographical variations in cancer rates have been observed but the precise determinants of such geographic differences in breast cancer development are unclear. Various statistical models have been proposed. Applications of these models, however, require that the data be assembled from a variety of sources, converted into the statistical models’ parameters and delivered effectively to researchers and policy makers. A web-enabled and GIS-based system can be developed to provide the needed functionality. This article overviews the conceptual web-enabled and GIS-based system (BCAS), illustrates the system’s use in diagnosing and treating breast cancer and examines the potential benefits and implications for breast cancer research and practice

Effective pattern discovery for text mining

Many data mining techniques have been proposed for mining useful patterns in text documents. However, how to effectively use and update discovered patterns is still an open research issue, especially in the domain of text mining. Since most existing text mining methods adopted term-based approaches, they all suffer from the problems of polysemy and synonymy. Over the years, people have often held the hypothesis that pattern (or phrase) based approaches should perform better than the term-based ones, but many experiments did not support this hypothesis. This paper presents an innovative technique, effective pattern discovery which includes the processes of pattern deploying and pattern evolving, to improve the effectiveness of using and updating discovered patterns for finding relevant and interesting information. Substantial experiments on RCV1 data collection and TREC topics demonstrate that the proposed solution achieves encouraging performance