HELIN Data Analytics Task Force Final Report

The main task undertaken by the HELIN Data Analytics Task Force was to conduct a proof-of-concept usability test of HELIN OneSearch, which is the Consortium’s brand name for the Encore Duet discovery service. After the initial meeting in November 2014, the Task Force met 6 times in 2015 to plan and execute a prototype test. Staff members from EBSCO Information Services’ User Research group acted as usability test advisers and coordinators and attended all meetings, either onsite or via WebEx. Task Force members collaborated to come up with specific scenarios and personas which would best emphasize patron likes, dislikes and general understanding of OneSearch. Using a small sample of volunteer student test subjects from 3 different HELIN institutions, testing took place in mid-April. The results were analyzed by EBSCO and presented at the final meeting of the Task Force on April 28. Based on this limited testing, general findings were as follows: Students who don’t receive prior information instruction are generally not aware of OneSearch. Students who do know about OneSearch do not necessarily understand the difference between OneSearch and the HELIN Catalog. Most students still continue to do their research by searching database lists, LibGuides, the Journal A to Z list, and the HELIN catalog (although not necessarily in that order). When features and operation of OneSearch are explained to students, they recognize its usefulness (especially facets, which many referred to as “filters”). Lack of clarity on how to get directly to full text items causes frustration. A larger and more comprehensive usability test would be needed to draw out more specific conclusions. Secondary tasks undertaken by the Task Force included trials and reviews of 5 data analysis tools, as well as a review of EBSCO User Research, which is quantitative data on the use of OneSearch available directly from EBSCO. The remainder of this document is a detailed account of the proceedings of the HELIN Data Analytics Task Force

An ontology enhanced parallel SVM for scalable spam filter training

This is the post-print version of the final paper published in Neurocomputing. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2013 Elsevier B.V.Spam, under a variety of shapes and forms, continues to inflict increased damage. Varying approaches including Support Vector Machine (SVM) techniques have been proposed for spam filter training and classification. However, SVM training is a computationally intensive process. This paper presents a MapReduce based parallel SVM algorithm for scalable spam filter training. By distributing, processing and optimizing the subsets of the training data across multiple participating computer nodes, the parallel SVM reduces the training time significantly. Ontology semantics are employed to minimize the impact of accuracy degradation when distributing the training data among a number of SVM classifiers. Experimental results show that ontology based augmentation improves the accuracy level of the parallel SVM beyond the original sequential counterpart

The Artificial Intelligence Workbench: a retrospective review

Last decade, biomedical and bioinformatics researchers have been demanding advanced and user-friendly applications for real use in practice. In this context, the Artificial Intelligence Workbench, an open-source Java desktop application framework for scientific software development, emerged with the goal of provid-ing support to both fundamental and applied research in the domain of transla-tional biomedicine and bioinformatics. AIBench automatically provides function-alities that are common to scientific applications, such as user parameter defini-tion, logging facilities, multi-threading execution, experiment repeatability, work-flow management, and fast user interface development, among others. Moreover, AIBench promotes a reusable component based architecture, which also allows assembling new applications by the reuse of libraries from existing projects or third-party software. Ten years have passed since the first release of AIBench, so it is time to look back and check if it has fulfilled the purposes for which it was conceived to and how it evolved over time

A very simple and fast way to access and validate algorithms in reproducible research

The reproducibility of research in bioinformatics refers to the notion that new methodologies/ algorithms and scientific claims have to be published together with their data and source code, in a way that other researchers may verify the findings to further build more knowledge upon them. The replication and corroboration of research results are key to the scientific process and many journals are discussing the matter nowadays, taking concrete steps in this direction. In this journal itself, a very recent opinion note has appeared highlighting the increasing importance of this topic in bioinformatics and computational biology, inviting the community to further discuss the matter. In agreement with that article, we would like to propose here another step into that direction with a tool that allows the automatic generation of a web interface, named web-demo, directly from source code in a very simple and straightforward way. We believe this contribution can help make research not only reproducible but also more easily accessible. A web-demo associated to a published paper can accelerate an algorithm validation with real data, wide-spreading its use with just a few clicks.Fil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Pividori, Milton Damián. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; Argentin