Dynamic Influence Networks for Rule-based Models

We introduce the Dynamic Influence Network (DIN), a novel visual analytics technique for representing and analyzing rule-based models of protein-protein interaction networks. Rule-based modeling has proved instrumental in developing biological models that are concise, comprehensible, easily extensible, and that mitigate the combinatorial complexity of multi-state and multi-component biological molecules. Our technique visualizes the dynamics of these rules as they evolve over time. Using the data produced by KaSim, an open source stochastic simulator of rule-based models written in the Kappa language, DINs provide a node-link diagram that represents the influence that each rule has on the other rules. That is, rather than representing individual biological components or types, we instead represent the rules about them (as nodes) and the current influence of these rules (as links). Using our interactive DIN-Viz software tool, researchers are able to query this dynamic network to find meaningful patterns about biological processes, and to identify salient aspects of complex rule-based models. To evaluate the effectiveness of our approach, we investigate a simulation of a circadian clock model that illustrates the oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres

Fast filtering and animation of large dynamic networks

Detecting and visualizing what are the most relevant changes in an evolving network is an open challenge in several domains. We present a fast algorithm that filters subsets of the strongest nodes and edges representing an evolving weighted graph and visualize it by either creating a movie, or by streaming it to an interactive network visualization tool. The algorithm is an approximation of exponential sliding time-window that scales linearly with the number of interactions. We compare the algorithm against rectangular and exponential sliding time-window methods. Our network filtering algorithm: i) captures persistent trends in the structure of dynamic weighted networks, ii) smoothens transitions between the snapshots of dynamic network, and iii) uses limited memory and processor time. The algorithm is publicly available as open-source software.Comment: 6 figures, 2 table

A Fast and Scalable System to Visualize Contour Gradient from Spatio-temporal Data

Changes in geological processes that span over the years may often go unnoticed due to their inherent noise and variability. Natural phenomena such as riverbank erosion, and climate change in general, is invisible to humans unless appropriate measures are taken to analyze the underlying data. Visualization helps geological sciences to generate scientific insights into such long-term geological events. Commonly used approaches such as side-by-side contour plots and spaghetti plots do not provide a clear idea about the historical spatial trends. To overcome this challenge, we propose an image-gradient based approach called ContourDiff. ContourDiff overlays gradient vector over contour plots to analyze the trends of change across spatial regions and temporal domain. Our approach first aggregates for each location, its value differences from the neighboring points over the temporal domain, and then creates a vector field representing the prominent changes. Finally, it overlays the vectors (differential trends) along the contour paths, revealing the differential trends that the contour lines (isolines) experienced over time. We designed an interface, where users can interact with the generated visualization to reveal changes and trends in geospatial data. We evaluated our system using real-life datasets, consisting of millions of data points, where the visualizations were generated in less than a minute in a single-threaded execution. We show the potential of the system in detecting subtle changes from almost identical images, describe implementation challenges, speed-up techniques, and scope for improvements. Our experimental results reveal that ContourDiff can reliably visualize the differential trends, and provide a new way to explore the change pattern in spatiotemporal data. The expert evaluation of our system using real-life WRF (Weather Research and Forecasting) model output reveals the potential of our technique to generate useful insights on the spatio-temporal trends of geospatial variables

Robust Modeling of Epistemic Mental States

This work identifies and advances some research challenges in the analysis of facial features and their temporal dynamics with epistemic mental states in dyadic conversations. Epistemic states are: Agreement, Concentration, Thoughtful, Certain, and Interest. In this paper, we perform a number of statistical analyses and simulations to identify the relationship between facial features and epistemic states. Non-linear relations are found to be more prevalent, while temporal features derived from original facial features have demonstrated a strong correlation with intensity changes. Then, we propose a novel prediction framework that takes facial features and their nonlinear relation scores as input and predict different epistemic states in videos. The prediction of epistemic states is boosted when the classification of emotion changing regions such as rising, falling, or steady-state are incorporated with the temporal features. The proposed predictive models can predict the epistemic states with significantly improved accuracy: correlation coefficient (CoERR) for Agreement is 0.827, for Concentration 0.901, for Thoughtful 0.794, for Certain 0.854, and for Interest 0.913.Comment: Accepted for Publication in Multimedia Tools and Application, Special Issue: Socio-Affective Technologie

Dynamic Maps: Representations of Change in Geospatial Modeling and Visualization

By coining the descriptive phrase ―user-centric geographic cosmology, Goodchild (1998), challenges the geographically oriented to address GIS in the broadest imaginable context: as interlocutor between persons and geo-phenomena. This investigation responds both in a general way, and more specifically, to the representations of change in GIS modeling and visualization leading to dynamic mapping. The investigation, consisting of a report and a series of experiments, explores and demonstrates prototype workarounds that enhance GIS capabilities by drawing upon ideas, techniques, and components from agent-based modeling and visualization software, and suggests shifts at the conceptual, methodological, and technical levels. The workarounds and demonstrations presented here are four-dimensional visualizations, representing changes and behaviors of different types of entities such as living creatures, mobile assets, features, structures, and surfaces, using GIS, agent-based modeling and animation techniques. In a typical case, a creature begins as a point feature in GIS, becomes a mobile and interactive object in agent-based modeling, and is fleshed out to three dimensions in an animated representation. In contrast, a land surface remains much the same in all three stages. The experiments address change in location, orientation, shape, visual attributes, viewpoint, scale, and speed in applications representing predator-prey, search and destroy, sense and locate and urban sprawl. During the experiments, particular attention is paid to factors of modeling and visualization involved in engaging human sensing and cognitive abilities

Visual Support for the Modeling and Simulation of Cell Biological Processes

This dissertation aims at bringing information visualization closer to the demands of analytical problem solving for the specific domain of modeling and simulating cell biological systems. To this end, main segments of visual support in the domain are identified. For one of these segments, the visual analysis of simulation data, new concepts are developed. First, this includes the visualization of simulation data in the context of data generation. Second, new multiple view techniques for large and complex simulation data are introduced.Diese Arbeit verfolgt das Ziel, Informationsvisualisierung näher an die Anforderungen des Analyseprozesses heranzuführen, mit Blick auf die konkrete Anwendung der Modellierung und Simulation zellbiologischer Systeme. Dazu werden wesentliche Teilbereiche der visuellen Unterstützung identifiziert. Für den Teilbereich der visuellen Analyse von Simulationsdaten werden neue Konzepte entwickelt. Dies beinhaltet zum einen die Visualisierung von Simulationsdaten im Kontext der Datengenerierung. Zum anderen werden neue Multiple-View-Techniken für große und komplexe Simulationsdaten vorgestellt