List of publications as of November 2009

regurlaly updated

Visual analytics: A novel Approach in corpus linguistics and the Nuevo Diccionario Histórico del Español

ROBERTO THERÓN, LAURA FONTANILLO FONTANILLO, ANDRÉS ESTEBAN MARCOS, CARLOS SEGUÍN HERRERO

III CONGRESO INTERNACIONAL DE LINGÜÍSTICA DE CORPUS

Abstract
The aim of this article is to introduce visual analysis in corpus linguistics. This is a novel approach that is based on the integration of automated processes and the unique humans' abilities, within a common effort to gain insight into complex problems that have to deal with vast amounts of data. Concretely, we intend to advance in the application of information visualization techniques to the diachronic linguistics field. The proposal of novel, highly interactive, visual solutions is approached by means of the Computational Information Design methodology, an integral process that brings together fields such as information visualization, computational linguistics, data mining and graphic design, for the realization of tools that truly support knowledge discovery and other general tasks of linguists. We discuss here the choices made for the design and development of interactive visual tools triggered by the creation of the New Spanish Historical Dictionary (Nuevo Diccionario Histórico del Español, NDHE).

CorpusExplorer : Supporting a Deeper Understanding of Linguistic Corpora

Andrés Esteban, Roberto Therón (2011)  CorpusExplorer : Supporting a Deeper Understanding of Linguistic Corpora  In:Smart Graphics - 11th International Symposium, SG 2011, Bremen, Germany, July 18-20, 2011. Proceedings, vol. 6815 126-129 Lecture Notes in Computer Science, Springer 

Word trees are a common way of representing frequency in-
formation obtained by analyzing natural language data. This article ex-plores their usage and possibilities, and addresses the development of an application to visualize the relative frequencies of 2-grams and 3-grams in Google's "English One Million" corpus using a two-sided word tree and sparklines to show usage trends through time. It also discusses how
the raw data was processed and trimmed to speed up access to it.

Usability Evaluation of a Visual Modelling Tool for OWL Ontologies

Juan Garcí­a, Francisco J Garcí­a-Peñalvo, Roberto Therón, Patricia Ordoñez de Pablos (2011) Usability Evaluation of a Visual Modelling Tool for OWL Ontologies Journal of Universal Computer Science 17: 9. 1299-1313 may

The literature in educational research has established that monitoring student learning is a crucial component of high quality education. When instructors and students are not in a face-to-face traditional environment, new forms of student monitoring must be explored. The effective use of CMS requires that instructors have been provided with appropriate means of diagnosing problems so that they can take immediate actions to prevent or overcome those situations. The aim of this paper is to present an analysis of an Object Oriented Programming course supported by a Moodle platform. Therefore, we have carried out the mining of an eLearning database and represented the more relevant results by depicting them a visualization based on the tag cloud visual representation.

Visual Analysis of a Moodle-based Object Oriented Programming Course

F J G-Penalvo, Miguel A Conde, Sergio Bravo, Diego A Gomez and Roberto Theron. Visual Analysis of a Moodle-based Object Oriented Programming Course. IJCA Proceedings on Design and Evaluation of Digital Content for Education (DEDCE) (1):8–14, 2011. Published by Foundation of Computer Science

The literature in educational research has established that monitoring student learning is a crucial component of high quality education. When instructors and students are not in a face-to-face traditional environment, new forms of student monitoring must be explored. The effective use of CMS requires that instructors have been provided with appropriate means of diagnosing problems so that they can take immediate actions to prevent or overcome those situations. The aim of this paper is to present an analysis of an Object Oriented Programming course supported by a Moodle platform. Therefore, we have carried out the mining of an eLearning database and represented the more relevant results by depicting them a visualization based on the tag cloud visual representation.

Data Mining (Chapter 4 in Mastering The Information Age – Solving Problems with Visual Analytics)

Authors: Kai Puolamäki, Alessio Bertone, Roberto Theron, Otto Huisman, Jimmy Johansson, Silvia Miksch, Panagiotis Papapetrou, Salvo Rinzivillo

This book is the result of a community effort of the partners of the VisMaster Coordinated Action funded by the European Union. The overarching aim of VisMaster was to create a research roadmap that outlines the current state of visual analytics across many disciplines, and to describe the next steps that have to be taken to foster a strong visual analytics community, thus enabling the development of advanced visual analytic applications.

This chapter considers data mining, which is seen as fundamental to the automated analysis components of visual analytics. Since today’s datasets are often extremely large and complex, the combination of human and automatic analysis is key to solving many information gathering tasks. Some case studies are presented which illustrate the use of knowledge discovery and data mining (KDD) in bioinformatics and climate change. The authors then pose the question of whether industry is ready for visual analytics, citing examples of the pharmaceutical, software and marketing industries. The state of the art section gives a comprehensive review of data mining/analysis tools such as statistical and mathematical tools, visual data mining tools, Web tools and packages. Some current data mining/visual analytics approaches are then described with examples from the bioinformatics and graph visualisation fields. Technical challenges specific to data mining are described such as achieving data cleaning, integration, data fusion etc. in real-time and providing the necessary infrastructure to support data mining. The challenge of integrating the human into the data process to go towards a visual analytics approach is discussed together with issues regarding its evaluation. Several opportunities are then identified, such as the need for generic tools and methods, visualisation of models and collaboration between the KDD and visualisation communities.

Special Issue of International Journal of Creative Interfaces and Computer Graphics Vol. 1, Issue 2, 2010

Co-edited with Marc Christie

In this special issue, we have gathered five contributions that offer a typical overview of research topics at the core of the Smartgraphics event, ranging from viewpoint computation, data visualization, intelligent user interfaces, to augmented reality for graphical augmentation of instruments.

TagClusters: Enhancing Semantic Understanding of Collaborative Tags

Ya-Xi Chen (Media Informatics, University of Munich, Germany); Rodrigo Santamaría (Department of Informatics and Automatics, University of Salamanca, Spain); Andreas Butz (Media Informatics, University of Munich, Germany); Roberto Therón (Department of Informatics and Automatics, University of Salamanca, Spain)

Many online communities use TagClouds, an aesthetic and easy to understand visualization, to represent popular tags collaboratively generated by their users. However, due to the free nature of tagging, such collaborative tags have linguistic problems and limitations, such as high semantic density. Moreover, the alphabetical order of TagClouds poorly supports a hierarchical exploration among tags. This paper presents an exploration to support semantic understanding of collaborative tags beyond TagClouds. Based on the results of the authors’ survey of practical usages of collaborative tags, they developed a visualization named TagClusters, in which tags are clustered into different groups, with font size representing tag popularity and the spatial distance indicating the semantic similarity between tags. The subgroups in each group and the overlap between groups are highlighted, illustrating the underlying hierarchical structure and semantic relations between groups. The authors conducted a comparative evaluation with TagClouds and TagClusters based on the same tag set. The results confirmed the advantage of TagClusters in facilitating browsing, comparing and comprehending semantic relations between tags.

Visual Analysis of Time-Motion in Basketball Games

Roberto Therón and Laura Casares. 2010.  Smart Graphics Lecture Notes in Computer Science, 2010, Volume 6133/2010, 196-207, DOI: 10.1007/978-3-642-13544-6_19

This work aims to facilitate the task of basketball coaches, by means of the visualization and analysis of the players’ movements in the court. This is possible thanks to the use of Global Positioning System (GPS) devices that generate data of the position of the player, almost in real time. The main objective of our proposal consists on the tracking, both statistics and kinematics, of a basketball player due to the physical activity developed during a match. The comparison of the data from several players or between two teams also will improve the performance and tactical capacity of players and trainers.
On one hand, the study of time-motion in sports is largely covered in the literature. On the other hand, the use of personal GPS devices for training purposes is a common practice. However, the design of interactive visualization tools that exploit the data stored in GPS devices during a match, thus enabling to perform its visual analysis, is still an open area. The work presented in this paper identifies the relevant aspects of the basketball game that are valuable for a coach in terms of team and individual performance analysis, and discusses the design and implementation of a tool that exploits the methods and techniques of a visual analytics approach.

Treevolution: visual analysis of phylogenetic trees

Co-authored with Rodrigo Santamaría. 2009 Bioinformatics  Volume25, Issue15  Pp. 1970-1971

Summary: Treevolution is a tool for the representation and exploration of phylogenetic trees that facilitates visual analysis. There are several useful tools to visualize phylogenetic trees, but their level of interaction is usually low, especially in the case of radial representations. Highly interactive visualizations can improve the exploration and understanding of phylogenetic trees. Treevolution implements strategies to interact with phylogenetic trees in order to allow a more thorough analysis by users.

Availability: Treevolution is available at http://vis.usal.es/treevolution

Supplementary material: Additional figures, a user's guide, a video demo and some examples are available at http://vis.usal.es/treevolution

NAPROC-13: a database for the dereplication of natural product mixtures in bioassay-guided protocols

Bioinformatics  23 (23): 3256-3257  2007  José Luis López-Pérez, Roberto Therón, Esther del Olmo, and David Díaz

Motivation: Although natural products represent a reservoir of molecular diversity, the process of isolating and identifying active compounds is a bottleneck in drug discovery programs. The rapid isolation and identification of the bioactive component(s) of natural product mixtures during the bioassay-guided fractionation have become crucial factors in the competition with chemical compound libraries and combinatorial synthetic efforts. In this respect, the use of spectral databases in identification processes is indispensable.

Results: We have developed a database containing 13C spectral information of over 6000 natural compounds, which allows for fast identifications of known compounds present in the crude extracts and provides insight into the structural elucidation of unknown compounds.

Availability: http://c13.usal.es

Visualization of intersecting groups based on hypergraphs

Rodrigo SANTAMARÍA and Roberto THERÓN. 2010. IEICE TRANSACTIONS on Information and Systems  Vol.E93-D  No.7  pp.1957-1964

Hypergraphs drawn in the subset standard are useful to represent group relationships using topographic characteristics such as intersection, exclusion and enclosing. However, they present cluttering when dealing with a moderately high number of nodes (more than 20) and large hyperedges (connecting more than 10 nodes, with three or more overlapping nodes).
At this complexity level, a study of the visual encoding of hypergraphs is required in order to reduce cluttering and increase the understanding of larger sets. Here we present a graph model and a visual design that help in the visualization of group relationships represented by hypergraphs. This is done by the use of superimposed visualization layers with different abstraction levels
and the help of interaction and navigation through the display.
key words: information visualization, graph drawing, intersecting groups, hypergraphs

Semantic Spiral Timelines Used as Support for e- Learning

Diego A Gómez-Aguilar, R Therón, Francisco J García-Peñalvo  (2009)  Semantic spiral timeline as a support for e-learning  Journal of universal Computer Science  15:  7.  1526-1545

This article presents Semantic Spiral Timelines (SST) as an interactive visual tool aimed at the exploration and analysis of additional academic information stored in current elearning platforms. Despite the development of contents specifically for these platforms, and in
spite of the various features they provide, knowledge of the actual use made by individual participants is emerging as an unavoidable necessity, so as to ensure proper operation and effective use of e-learning platforms. SST supports the discovery of temporal patterns by incorporating an innovative highly interactive visual representation, which can be explored at various levels. This tool makes it possible to assess, at first glance, the use of the e-learning platform during the development of courses; one can also perceive how it is used by class
participants. Then, through different interaction mechanisms, it is possible for students and professors to uncover specific details about courses, which would otherwise remain hidden.

A visual analytics approach for understanding biclustering results from microarray data

  BMC Bioinformatics  9:  247. 2008

Background Microarray analysis is an important area of bioinformatics. In the last few years, biclustering has become one of the most popular methods for classifying data from microarrays. Although biclustering can be used in any kind of classification problem, nowadays it is mostly used for microarray data classification. A large number of biclustering algorithms have been developed over the years, however little effort has been devoted to the representation of the results. Results We present an interactive framework that helps to infer differences or similarities between biclustering results, to unravel trends and to highlight robust groupings of genes and conditions. These linked representations of biclusters can complement biological analysis and reduce the time spent by specialists on interpreting the results. Within the framework, besides other standard representations, a visualization technique is presented which is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions. This microarray analysis framework (BicOverlapper), is available at http://vis.usal.es/bicoverlapper Conclusions The main visualization technique, tested with different biclustering results on a real dataset, allows researchers to extract interesting features of the biclustering results, especially the highlighting of overlapping zones that usually represent robust groups of genes and/or conditions. The visual analytics methodology will permit biology experts to study biclustering results without inspecting an overwhelming number of biclusters individually.

BicOverlapper: a tool for bicluster visualization

Bioinformatics  24:  9.  1212-1213  May, 2008

BicOverlapper is a tool to visualize biclusters from gene-expression matrices in a way that helps to compare biclustering methods, to unravel trends and to highlight relevant genes and conditions. A visual approach can complement biological and statistical analysis and reduce the time spent by specialists interpreting the results of biclustering algorithms. The technique is based on a force-directed graph where biclusters are represented as flexible overlapped groups of genes and conditions. AVAILABILITY: The BicOverlapper software and supplementary material are available at http://vis.usal.es/bicoverlapper

Hierarchical-Temporal Data Visualization Using a Tree-Ring Metaphor

6th International Symposium, SG 2006, Vancouver, Canada, July 23-25, 2006. http://www.springerlink.com/content/w513gu1683h8/#section=538134&page=1&locus=0

This paper describes a novel and efficient visualization technique intended for hierarchical-temporal data using a tree-ring like layout.
Temporal hierarchies appear in numerous fields such as genealogy, evolution taxonomies or time lines. In many cases, state-of-the-art static diagrams are produced in these fields. By using several information visualization strategies, such as focus + context, the tree-ring approach
has the ability to visualize and navigate these, potentially complex, hierarchies trough time. Thus, a deeper insight into the problem at hand can be gained

Visual Analytics of Paleoceanographic Conditions

Roberto Therón  (2006)  Visual Analytics of Paleoceanographic Conditions  In: Visual Analytics Science And Technology, 2006 IEEE Symposium On  19-26  IEEE PRESS

Decade scale oceanic phenomena like El Ni˜no are correlated with weather anomalies all over the globe. Only by understanding the events that produced the climatic conditions in the past will it be possible to forecast abrupt climate changes and prevent disastrous consequences for human beings and their environment. Paleoceanography research is a collaborative effort that requires the analysis of paleo time-series, which are obtained from a number of independent techniques and instruments and produced by a variety of different researchers and/or laboratories. The complexity of these fenomena that consist of massive, dynamic and often conflicting data can only be faced bymeans of analytical reasoning supported by a highly interactive visual interface. This paper presents an interactive visual analysis environment for paleoceanography that permits to gain insight into the paleodata and allow the control and steering of the analitycal methods involved in the reconstruction of the climatic conditions of the past.

Visual Sensitivity Analysis for Artificial Neural Networks

Roberto Therón, Juan Francisco de Paz: Visual Sensitivity Analysis for Artificial Neural Networks. IDEAL 2006: 191-198

A challenge in ANN research is how to reduce the number of
inputs to the model in high dimensional problems, so it can be efficiently applied. The ANNs black-box operation makes not possible to explain the relationships between features and inputs. Some numerical methods, such as sensitivity analysis, try to fight this problem. In this paper, we combine a sensitivity analysis with a linked multi-dimensional visualization that
takes advantage of user interaction, providing and efficient way to analyze and asses both the dimension reduction results and the ANN behavior.

Combined visualization of structural and metric information for software evolution analysis

Gonzalez, Antonio; Theron, Roberto; Telea, Alexandru; Garcia, Francisco J. (2009)

This paper discusses a proposal for the visualization of software
evolution, with a focus on combining insight on changes that affect software metrics at project and class level, the project structure, the class hierarchy and the viewing of source code correlated to indirect class coupling. The proposed visualization supports several tasks: the comparison of structural information, including class hierarchies, across several revisions; uncovering collaboration patterns between developers; and determining which classes have been added or deleted to the project during the creation of a given revision.
We propose and discuss several design elements supporting
these tasks, including interaction patterns and linked views.

Overlapper: movie analyzer

Tagclusters: Semantic aggregation of collaborative tags beyond tagclouds

A Mathematical Formalism for the Evaluation of C-Space for Redundant Robots

Roberto Therón, Vidal Moreno, Bel´en Curto, and Francisco J. Blanco

EUROCAST 2005

This paper presents a new general method for obstacle representation in the configuration space (C-space) for redundant robots.
The method is based on the analytical deconstruction of the C-space, i.e., the separated evaluation of the C-space portion contributed by the collisions of each link in the kinematic chain. The systematic application of a simple convolution of two functions describing each link and the workspace, respectively, is applied. In order to do that, the transformation of the workspace among reference systems located at one point of
each link is needed; in this step a well-known and sound method is used.

The Use of Information Visualization to Support Software Configuration Management

Overlapping Clustered Graphs: Co-authorship Networks Visualization

Co-authored by: Rodrigo Santamaría and Roberto Therón
Lecture Notes in Computer Science. Smart Graphics 2008. Vol. 5166

The analysis of scientific articles produced by different groups of authors helps to identify and characterize research groups and collaborations among them. Although this is a quite studied area, some issues, such as quick understanding of groups and visualization of large social networks still pose some interesting
challenges. In order to contribute to this study, we present a solution based in Overlapper, a tool for the visualization of overlapping groups that makes use of an enhanced variation of force-directed graphs. For a real case study, the tool has
been applied to articles in the DBLP database

A Framework to Analyze Biclustering Results on Microarray Experiments

Visualising semantic coupling among entities in an OWL ontology

Methods to Bicluster Validation and Comparison In Microarray Data

biclust: Bicluster algorithms

Rapid reconstruction of paleoenvironmental features using a new multiplatform program

Defining Coupling Metrics among Classes in an OWL Ontology

Proceedings of the 10th International Symposium on Smart Graphics

Visual Interactive Analysis: Insights into Software Comprehension

Understanding Educational Relationships in Moodle with ViMoodle

Design of New Chemoinformatic Tools for the Analysis of Virtual Screening Studies: Application to Tubulin Inhibitors

A visual analytics tool for software project structure and relationships among classes

Application of Chemoinformatics to the Structural Elucidation of Natural Compounds

Visualization of Large Software Projects by using Advanced Techniques