Large scale network analysis with interactive visualisation

This paper proposes a new interactive visualisation for analysing large hierarchical structures and networks. The technique combines of different graph layout methods with a layout refinement process, an interactive navigation mechanism and clustering algorithms. The integration of these components makes it flexible in dealing with a variety of graph and hierarchical structures. Interactive exploration is enabled with chaincontext view. We aim to provide user with an effective mechanism for understanding of the nature of various networks. This could lead to the discovering and revealing of the hidden structures and relationships among elements as well as relationships associated with the elements. © 2009 IEEE

Towards Interactive Multidimensional Visualisations for Corpus Linguistics

We propose the novel application of dynamic and interactive visualisation techniques to support the iterative and exploratory investigations typical of the corpus linguistics methodology. Very large scale text analysis is already carried out in corpus-based language analysis by employing methods such as frequency profiling, keywords, concordancing, collocations and n-grams. However, at present only basic visualisation methods are utilised. In this paper, we describe case studies of multiple types of key word clouds, explorer tools for collocation networks, and compare network and language distance visualisations for online social networks. These are shown to fit better with the iterative data-driven corpus methodology, and permit some level of scalability to cope with ever increasing corpus size and complexity. In addition, they will allow corpus linguistic methods to be used more widely in the digital humanities and social sciences since the learning curve with visualisations is shallower for non-expert

Engineering simulations for cancer systems biology

Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions

Using treemaps for variable selection in spatio-temporal visualisation

We demonstrate and reflect upon the use of enhanced treemaps that incorporate spatial and temporal ordering for exploring a large multivariate spatio-temporal data set. The resulting data-dense views summarise and simultaneously present hundreds of space-, time-, and variable-constrained subsets of a large multivariate data set in a structure that facilitates their meaningful comparison and supports visual analysis. Interactive techniques allow localised patterns to be explored and subsets of interest selected and compared with the spatial aggregate. Spatial variation is considered through interactive raster maps and high-resolution local road maps. The techniques are developed in the context of 42.2 million records of vehicular activity in a 98 km(2) area of central London and informally evaluated through a design used in the exploratory visualisation of this data set. The main advantages of our technique are the means to simultaneously display hundreds of summaries of the data and to interactively browse hundreds of variable combinations with ordering and symbolism that are consistent and appropriate for space- and time- based variables. These capabilities are difficult to achieve in the case of spatio-temporal data with categorical attributes using existing geovisualisation methods. We acknowledge limitations in the treemap representation but enhance the cognitive plausibility of this popular layout through our two-dimensional ordering algorithm and interactions. Patterns that are expected (e.g. more traffic in central London), interesting (e.g. the spatial and temporal distribution of particular vehicle types) and anomalous (e.g. low speeds on particular road sections) are detected at various scales and locations using the approach. In many cases, anomalies identify biases that may have implications for future use of the data set for analyses and applications. Ordered treemaps appear to have potential as interactive interfaces for variable selection in spatio-temporal visualisation. Information Visualization (2008) 7, 210-224. doi: 10.1057/palgrave.ivs.950018

Simulation modelling and visualisation: toolkits for building artificial worlds

Simulations users at all levels make heavy use of compute resources to drive computational simulations for greatly varying applications areas of research using different simulation paradigms. Simulations are implemented in many software forms, ranging from highly standardised and general models that run in proprietary software packages to ad hoc hand-crafted simulations codes for very specific applications. Visualisation of the workings or results of a simulation is another highly valuable capability for simulation developers and practitioners. There are many different software libraries and methods available for creating a visualisation layer for simulations, and it is often a difficult and time-consuming process to assemble a toolkit of these libraries and other resources that best suits a particular simulation model. We present here a break-down of the main simulation paradigms, and discuss differing toolkits and approaches that different researchers have taken to tackle coupled simulation and visualisation in each paradigm

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool

Interactive Visual Analysis of Networked Systems: Workflows for Two Industrial Domains

We report on a first study of interactive visual analysis of networked systems. Working with ABB Corporate Research and Ericsson Research, we have created workflows which demonstrate the potential of visualization in the domains of industrial automation and telecommunications. By a workflow in this context, we mean a sequence of visualizations and the actions for generating them. Visualizations can be any images that represent properties of the data sets analyzed, and actions typically either change the selection of data visualized or change the visualization by choice of technique or change of parameters

Enhancing urban sustainability using 3D visualisation

This paper presents the results of an initial application of a prototype simulation and visualisation tool (S-City VT) thatwas developed to enable all stakeholders, regardless of background or experience, to understand, interact with and influence decisions made on the sustainability of urban design. The tool takes the unique approach of combining three-dimensional (3D) interactive and immersive technologies with computer modelling to present stakeholders with an interactive virtual development. Use of outputs from the model and a 3D visualisation of the development can help decision-makers judge the relative sustainability of different aspects of a development. The tool employs a number of different methods to present sustainability results to stakeholders. Initial tests on the effectiveness of the different visualisation methods are described and discussed. The paper then presents some conclusions on further development and application of the tool to model and visualise possible results of decisions made at different stages of the project