The BioDICE Taverna plugin for clustering and visualization of biological data: a workflow for molecular compounds exploration

Background: In many experimental pipelines, clustering of multidimensional biological datasets is used to detect hidden structures in unlabelled input data. Taverna is a popular workflow management system that is used to design and execute scientific workflows and aid in silico experimentation. The availability of fast unsupervised methods for clustering and visualization in the Taverna platform is important to support a data-driven scientific discovery in complex and explorative bioinformatics applications. Results: This work presents a Taverna plugin, the Biological Data Interactive Clustering Explorer (BioDICE), that performs clustering of high-dimensional biological data and provides a nonlinear, topology preserving projection for the visualization of the input data and their similarities. The core algorithm in the BioDICE plugin is Fast Learning Self Organizing Map (FLSOM), which is an improved variant of the Self Organizing Map (SOM) algorithm. The plugin generates an interactive 2D map that allows the visual exploration of multidimensional data and the identification of groups of similar objects. The effectiveness of the plugin is demonstrated on a case study related to chemical compounds. Conclusions: The number and variety of available tools and its extensibility have made Taverna a popular choice for the development of scientific data workflows. This work presents a novel plugin, BioDICE, which adds a data-driven knowledge discovery component to Taverna. BioDICE provides an effective and powerful clustering tool, which can be adopted for the explorative analysis of biological datasets.

Automatic visual dictionary generation through Optimum-Path Forest clustering

Image categorization by means of bag of visual words has received increasing attention by the image processing and vision communities in the last years. In these approaches, each image is represented by invariant points of interest which are mapped to a Hilbert Space representing a visual dictionary which aims at comprising the most discriminative features in a set of images. Notwithstanding, the main problem of such approaches is to find a compact and representative dictionary. Finding such representative dictionary automatically with no user intervention is an even more difficult task. In this paper, we propose a method to automatically find such dictionary by employing a recent developed graph-based clustering algorithm called Optimum-Path Forest, which does not make any assumption about the visual dictionary's size and is more efficient and effective than the state-of-the-art techniques used for dictionary generation. © 2012 IEEE.

Automatic visual dictionary generation through optimum-path forest clusteringautomatic visual dictionary generation through optimum-path forest clustering

Image categorization by means of bag of visual words has received increasing attention by the image processing and vision communities in the last years. In these approaches, each image is represented by invariant points of interest which are mapped to a Hilbert Space representing a visual dictionary which aims at comprising the most discriminative features in a set of images. Notwithstanding, the main problem of such approaches is to find a compact and representative dictionary. Finding such representative dictionary automatically with no user intervention is an even more difficult task. In this paper, we propose a method to automatically find such dictionary by employing a recent developed graph-based clustering algorithm called Optimum-Path Forest, which does not make any assumption about the visual dictionary's size and is more efficient and effective than the state-of-the-art techniques used for dictionary generation.

The Topology of Auditory and Visual Perception, Linguistic Communication, and Interactive Written Discourse

In this article, it is shown that IWD incorporates topological perceptual characteristics of both spoken and written language, and it is argued that these characteristics should not be ignored or given up when synchronous textual CMC is technologically developed and upgraded.

Monitoring visual attention on a neurorehabilitation environment based on interactive video

The use of new technologies in neurorehabilitation has led to higher intensity rehabilitation processes, extending therapies in an economically sustainable way. Interactive Video (IV) technology allows therapists to work with virtual environments that reproduce real situations. In this way, patients deal with Activities of the Daily Living (ADL) immersed within enhanced environments [1]. These rehabilitation exercises, which focus in re-learning lost functions, will try to modulate the neural plasticity processes [2]. This research presents a system where a neurorehabilitation IV-based environment has been integrated with an eye-tracker device in order to monitor and to interact using visual attention. While patients are interacting with the neurorehabilitation environment, their visual behavior is closely related with their cognitive state, which in turn mirrors the brain damage condition suffered by them [3] [4]. Patients’ gaze data can provide knowledge on their attention focus and their cognitive state, as well as on the validity of the rehabilitation tasks proposed [5].

Improving the use of visual interactive simulation as a knowledge elicitation tool

Knowledge elicitation is a well-known bottleneck in the production of knowledge-based systems (KBS). Past research has shown that visual interactive simulation (VIS) could effectively be used to elicit episodic knowledge that is appropriate for machine learning purposes, with a view to building a KBS. Nonetheless, the VIS-based elicitation process still has much room for improvement. Based in the Ford Dagenham Engine Assembly Plant, a research project is being undertaken to investigate the individual/joint effects of visual display level and mode of problem case generation on the elicitation process. This paper looks at the methodology employed and some issues that have been encountered to date. Copyright © 2007 Inderscience Enterprises Ltd.

A visual interactive modelling system as a learning tool

This paper presents a case study of the use of a visual interactive modelling system to investigate issues involved in the management of a hospital ward. Visual Interactive Modelling systems are seen to offer the learner the opportunity to explore operational management issues from a varied perspective and to provide an interactive system in which the learner receives feedback on the consequences of their actions. However to maximise the potential learning experience for a student requires the recognition that they require task structure which helps them to understand the concepts involved. These factors can be incorporated into the visual interactive model by providing an interface customised to guide the student through the experimentation. Recent developments of VIM systems in terms of their connectivity with the programming language Visual Basic facilitates this customisation.

Does the Swedish Interactive Threshold Algorithm (SITA) accurately map visual field loss attributed to vigabatrin?

Background: Vigabatrin (VGB) is an anti-epileptic medication which has been linked to peripheral constriction of the visual field. Documenting the natural history associated with continued VGB exposure is important when making decisions about the risk and benefits associated with the treatment. Due to its speed the Swedish Interactive Threshold Algorithm (SITA) has become the algorithm of choice when carrying out Full Threshold automated static perimetry. SITA uses prior distributions of normal and glaucomatous visual field behaviour to estimate threshold sensitivity. As the abnormal model is based on glaucomatous behaviour this algorithm has not been validated for VGB recipients. We aim to assess the clinical utility of the SITA algorithm for accurately mapping VGB attributed field loss. Methods: The sample comprised one randomly selected eye of 16 patients diagnosed with epilepsy, exposed to VGB therapy. A clinical diagnosis of VGB attributed visual field loss was documented in 44% of the group. The mean age was 39.3 years∈±∈14.5 years and the mean deviation was -4.76 dB ±4.34 dB. Each patient was examined with the Full Threshold, SITA Standard and SITA Fast algorithm. Results: SITA Standard was on average approximately twice as fast (7.6 minutes) and SITA Fast approximately 3 times as fast (4.7 minutes) as examinations completed using the Full Threshold algorithm (15.8 minutes). In the clinical environment, the visual field outcome with both SITA algorithms was equivalent to visual field examination using the Full Threshold algorithm in terms of visual inspection of the grey scale plots, defect area and defect severity. Conclusions: Our research shows that both SITA algorithms are able to accurately map visual field loss attributed to VGB. As patients diagnosed with epilepsy are often vulnerable to fatigue, the time saving offered by SITA Fast means that this algorithm has a significant advantage for use with VGB recipients.

Full threshold vs. Swedish interactive threshold algorithm (SITA) em pacientes glaucomatosos submetidos à perimetria computadorizada pela primeira vez

PURPOSE: To compare the Full Threshold (FT) and SITA Standard (SS) strategies in glaucomatous patients undergoing automated perimetry for the first time. METHODS: Thirty-one glaucomatous patients who had never undergone perimetry underwent automated perimetry (Humphrey, program 30-2) with both FT and SS on the same day, with an interval of at least 15 minutes. The order of the examination was randomized, and only one eye per patient was analyzed. Three analyses were performed: a) all the examinations, regardless of the order of application; b) only the first examinations; c) only the second examinations. In order to calculate the sensitivity of both strategies, the following criteria were used to define abnormality: glaucoma hemifield test (GHT) outside normal limits, pattern standard deviation (PSD) <5%, or a cluster of 3 adjacent points with p<5% at the pattern deviation probability plot. RESULTS: When the results of all examinations were analyzed regardless of the order in which they were performed, the number of depressed points with p<0.5% in the pattern deviation probability map was significantly greater with SS (p=0.037), and the sensitivities were 87.1% for SS and 77.4% for FT (p=0.506). When only the first examinations were compared, there were no statistically significant differences regarding the number of depressed points, but the sensitivity of SS (100%) was significantly greater than that obtained with FT (70.6%) (p=0.048). When only the second examinations were compared, there were no statistically significant differences regarding the number of depressed points, and the sensitivities of SS (76.5%) and FT (85.7%) (p=0.664). CONCLUSION: SS may have a higher sensitivity than FT in glaucomatous patients undergoing automated perimetry for the first time. However, this difference tends to disappear in subsequent examinations.

Risk Factors for Visual Field Progression in Treated Glaucoma

Objective: To determine intraocular pressure (IOP)-dependent and IOP-independent variables associated with visual field (VF) progression in treated glaucoma. Design: Retrospective cohort of the Glaucoma Progression Study. Methods: Consecutive, treated glaucoma patients with repeatable VF loss who had 8 or more VF examinations of either eye, using the Swedish Interactive Threshold Algorithm (24-2 SITA-Standard, Humphrey Field Analyzer II; Carl Zeiss Meditec, Inc, Dublin, California), during the period between January 1999 and September 2009 were included. Visual field progression was evaluated using automated pointwise linear regression. Evaluated data included age, sex, race, central corneal thickness, baseline VF mean deviation, mean follow-up IOP, peak IOP, IOP fluctuation, a detected disc hemorrhage, and presence of beta-zone parapapillary atrophy. Results: We selected 587 eyes of 587 patients (mean [SD] age, 64.9 [13.0] years). The mean (SD) number of VFs was 11.1 (3.0), spanning a mean (SD) of 6.4 (1.7) years. In the univariable model, older age (odds ratio [OR], 1.19 per decade; P = .01), baseline diagnosis of exfoliation syndrome (OR, 1.79; P = .01), decreased central corneal thickness (OR, 1.38 per 40 mu m thinner; P < .01), a detected disc hemorrhage (OR, 2.31; P < .01), presence of beta-zone parapapillary atrophy (OR, 2.17; P < .01), and all IOP parameters (mean follow-up, peak, and fluctuation; P < .01) were associated with increased risk of VF progression. In the multivariable model, peak IOP (OR, 1.13; P < .01), thinner central corneal thickness (OR, 1.45 per 40 mu m thinner; P < .01), a detected disc hemorrhage (OR, 2.59; P < .01), and presence of beta-zone parapapillary atrophy (OR, 2.38; P < .01) were associated with VF progression. Conclusions: IOP-dependent and IOP-independent risk factors affect disease progression in treated glaucoma. Peak IOP is a better predictor of progression than is IOP mean or fluctuation.

Using visual spatial search interface for WWW applications

Most Internet search engines are keyword-based. They are not efficient for the queries where geographical location is important, such as finding hotels within an area or close to a place of interest. A natural interface for spatial searching is a map, which can be used not only to display locations of search results but also to assist forming search conditions. A map-based search engine requires a well-designed visual interface that is intuitive to use yet flexible and expressive enough to support various types of spatial queries as well as aspatial queries. Similar to hyperlinks for text and images in an HTML page, spatial objects in a map should support hyperlinks. Such an interface needs to be scalable with the size of the geographical regions and the number of websites it covers. In spite of handling typically a very large amount of spatial data, a map-based search interface should meet the expectation of fast response time for interactive applications. In this paper we discuss general requirements and the design for a new map-based web search interface, focusing on integration with the WWW and visual spatial query interface. A number of current and future research issues are discussed, and a prototype for the University of Queensland is presented. (C) 2001 Published by Elsevier Science Ltd.

Combining Formal Methods and Functional Strategies Regarding the Reverse Engineering of Interactive Applications

Abstract. Graphical user interfaces (GUIs) make software easy to use by providing the user with visual controls. Therefore, correctness of GUI’s code is essential to the correct execution of the overall software. Models can help in the evaluation of interactive applications by allowing designers to concentrate on its more important aspects. This paper describes our approach to reverse engineer an abstract model of a user interface directly from the GUI’s legacy code. We also present results from a case study. These results are encouraging and give evidence that the goal of reverse engineering user interfaces can be met with more work on this technique.

Gestão da identidade visual corporativa nos meios digitais: o caso RTP

Relatório de estágio apresentado à Escola Superior de Comunicação Social como parte dos requisitos para obtenção de grau de mestre em Gestão Estratégica das Relações Públicas.

Algorithms for information extraction and signal annotation on long-term biosignals using clustering techniques

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica