Datamining for Web-Enabled Electronic Business Applications

Web-Enabled Electronic Business is generating massive amount of data on customer purchases, browsing patterns, usage times and preferences at an increasing rate. Data mining techniques can be applied to all the data being collected for obtaining useful information. This chapter attempts to present issues associated with data mining for web-enabled electronic-business

Data Mining for Web-Enabled Electronic Business Applications

Web-enabled electronic business is generating massive amounts of data on customer purchases, browsing patterns, usage times, and preferences at an increasing rate. Data mining techniques can be applied to all the data being collected for obtaining useful information. This chapter attempts to present issues associated with data mining for Web-enabled electronicbusiness. Copyright Idea Group Inc

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

An essential prerequisite for any systems-level understanding of cellular functions is to correctly uncover and annotate all functional interactions among proteins in the cell. Toward this goal, remarkable progress has been made in recent years, both in terms of experimental measurements and computational prediction techniques. However, public efforts to collect and present protein interaction information have struggled to keep up with the pace of interaction discovery, partly because protein–protein interaction information can be error-prone and require considerable effort to annotate. Here, we present an update on the online database resource Search Tool for the Retrieval of Interacting Genes (STRING); it provides uniquely comprehensive coverage and ease of access to both experimental as well as predicted interaction information. Interactions in STRING are provided with a confidence score, and accessory information such as protein domains and 3D structures is made available, all within a stable and consistent identifier space. New features in STRING include an interactive network viewer that can cluster networks on demand, updated on-screen previews of structural information including homology models, extensive data updates and strongly improved connectivity and integration with third-party resources. Version 9.0 of STRING covers more than 1100 completely sequenced organisms; the resource can be reached at http://string-db.org

Challenges and opportunities of context-aware information access

Ubiquitous computing environments embedding a wide range of pervasive computing technologies provide a challenging and exciting new domain for information access. Individuals working in these environments are increasingly permanently connected to rich information resources. An appealing opportunity of these environments is the potential to deliver useful information to individuals either from their previous information experiences or external sources. This information should enrich their life experiences or make them more effective in their endeavours. Information access in ubiquitous computing environments can be made "context-aware" by exploiting the wide range context data available describing the environment, the searcher and the information itself. Realizing such a vision of reliable, timely and appropriate identification and delivery of information in this way poses numerous challenges. A central theme in achieving context-aware information access is the combination of information retrieval with multiple dimensions of available context data. Potential context data sources, include the user's current task, inputs from environmental and biometric sensors, associated with the user's current context, previous contexts, and document context, which can be exploited using a variety of technologies to create new and exciting possibilities for information access

Magpie: towards a semantic web browser

Web browsing involves two tasks: finding the right web page and then making sense of its content. So far, research has focused on supporting the task of finding web resources through ‘standard’ information retrieval mechanisms, or semantics-enhanced search. Much less attention has been paid to the second problem. In this paper we describe Magpie, a tool which supports the interpretation of web pages. Magpie offers complementary knowledge sources, which a reader can call upon to quickly gain access to any background knowledge relevant to a web resource. Magpie automatically associates an ontologybased semantic layer to web resources, allowing relevant services to be invoked within a standard web browser. Hence, Magpie may be seen as a step towards a semantic web browser. The functionality of Magpie is illustrated using examples of how it has been integrated with our lab’s web resources

Large-scale interactive exploratory visual search

Large scale visual search has been one of the challenging issues in the era of big data. It demands techniques that are not only highly effective and efficient but also allow users conveniently express their information needs and refine their intents. In this thesis, we focus on developing an exploratory framework for large scale visual search. We also develop a number of enabling techniques in this thesis, including compact visual content representation for scalable search, near duplicate video shot detection, and action based event detection. We propose a novel scheme for extremely low bit rate visual search, which sends compressed visual words consisting of vocabulary tree histogram and descriptor orientations rather than descriptors. Compact representation of video data is achieved through identifying keyframes of a video which can also help users comprehend visual content efficiently. We propose a novel Bag-of-Importance model for static video summarization. Near duplicate detection is one of the key issues for large scale visual search, since there exist a large number nearly identical images and videos. We propose an improved near-duplicate video shot detection approach for more effective shot representation. Event detection has been one of the solutions for bridging the semantic gap in visual search. We particular focus on human action centred event detection. We propose an enhanced sparse coding scheme to model human actions. Our proposed approach is able to significantly reduce computational cost while achieving recognition accuracy highly comparable to the state-of-the-art methods. At last, we propose an integrated solution for addressing the prime challenges raised from large-scale interactive visual search. The proposed system is also one of the first attempts for exploratory visual search. It provides users more robust results to satisfy their exploring experiences

Massive NGS data analysis reveals hundreds of potential novel gene fusions in human cell lines

Background: Gene fusions derive from chromosomal rearrangements and the resulting chimeric transcripts are often endowed with oncogenic potential. Furthermore, they serve as diagnostic tools for the clinical classification of cancer subgroups with different prognosis and, in some cases, they can provide specific drug targets. So far, many efforts have been carried out to study gene fusion events occurring in tumor samples. In recent years, the availability of a comprehensive Next Generation Sequencing dataset for all the existing human tumor cell lines has provided the opportunity to further investigate these data in order to identify novel and still uncharacterized gene fusion events. Results: In our work, we have extensively reanalyzed 935 paired-end RNA-seq experiments downloaded from "The Cancer Cell Line Encyclopedia" repository, aiming at addressing novel putative cell-line specific gene fusion events in human malignancies. The bioinformatics analysis has been performed by the execution of four different gene fusion detection algorithms. The results have been further prioritized by running a bayesian classifier which makes an in silico validation. The collection of fusion events supported by all of the predictive softwares results in a robust set of ∼ 1,700 in-silico predicted novel candidates suitable for downstream analyses. Given the huge amount of data and information produced, computational results have been systematized in a database named LiGeA. The database can be browsed through a dynamical and interactive web portal, further integrated with validated data from other well known repositories. Taking advantage of the intuitive query forms, the users can easily access, navigate, filter and select the putative gene fusions for further validations and studies. They can also find suitable experimental models for a given fusion of interest. Conclusions: We believe that the LiGeA resource can represent not only the first compendium of both known and putative novel gene fusion events in the catalog of all of the human malignant cell lines, but it can also become a handy starting point for wet-lab biologists who wish to investigate novel cancer biomarkers and specific drug targets