Context-aware visual exploration of molecular databases

Facilitating the visual exploration of scientific data has received increasing attention in the past decade or so. Especially in life science related application areas the amount of available data has grown at a breath taking pace. In this paper we describe an approach that allows for visual inspection of large collections of molecular compounds. In contrast to classical visualizations of such spaces we incorporate a specific focus of analysis, for example the outcome of a biological experiment such as high throughout screening results. The presented method uses this experimental data to select molecular fragments of the underlying molecules that have interesting properties and uses the resulting space to generate a two dimensional map based on a singular value decomposition algorithm and a self organizing map. Experiments on real datasets show that the resulting visual landscape groups molecules of similar chemical properties in densely connected regions

OpenLearn and knowledge maps for language learning

This chapter presents new methodologies designed to facilitate language acquisition in open learning communities via open educational resources and knowledge mapping. It specifically focuses on the OpenLearn project developed by the Open University. This offers a virtual learning environment based on Moodle platform with free educational materials and knowledge media tools such as the instant messaging MSG, the video webconference FlashMeeting and the knowledge mapping software tool Compendium. In this work, these technologies and mapping techniques are introduced in order to promote open language learning. Ways in which teachers and students can make use of these OpenLearn tools and resources are discussed and some benefits fully described

From Keyword Search to Exploration: How Result Visualization Aids Discovery on the Web

A key to the Web's success is the power of search. The elegant way in which search results are returned is usually remarkably effective. However, for exploratory search in which users need to learn, discover, and understand novel or complex topics, there is substantial room for improvement. Human computer interaction researchers and web browser designers have developed novel strategies to improve Web search by enabling users to conveniently visualize, manipulate, and organize their Web search results. This monograph offers fresh ways to think about search-related cognitive processes and describes innovative design approaches to browsers and related tools. For instance, while key word search presents users with results for specific information (e.g., what is the capitol of Peru), other methods may let users see and explore the contexts of their requests for information (related or previous work, conflicting information), or the properties that associate groups of information assets (group legal decisions by lead attorney). We also consider the both traditional and novel ways in which these strategies have been evaluated. From our review of cognitive processes, browser design, and evaluations, we reflect on the future opportunities and new paradigms for exploring and interacting with Web search results

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones", ie sub-communities that create an interface around specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and Technology (2012) 10.1002/asi.2264

Information visualization for DNA microarray data analysis: A critical review

Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work

Curbing domestic violence: instantiating C-K theory with formal concept analysis and emergent self organizing maps.

In this paper we propose a human-centered process for knowledge discovery from unstructured text that makes use of Formal Concept Analysis and Emergent Self Organizing Maps. The knowledge discovery process is conceptualized and interpreted as successive iterations through the Concept-Knowledge (C-K) theory design square. To illustrate its effectiveness, we report on a real-life case study of using the process at the Amsterdam-Amstelland police in the Netherlands aimed at distilling concepts to identify domestic violence from the unstructured text in actual police reports. The case study allows us to show how the process was not only able to uncover the nature of a phenomenon such as domestic violence, but also enabled analysts to identify many types of anomalies in the practice of policing. We will illustrate how the insights obtained from this exercise resulted in major improvements in the management of domestic violence cases.Formal concept analysis; Emergent self organizing map; C-K theory; Text mining; Actionable knowledge discovery; Domestic violence;