7,030 research outputs found
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
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
Doctor of Philosophy
dissertationA broad range of applications capture dynamic data at an unprecedented scale. Independent of the application area, finding intuitive ways to understand the dynamic aspects of these increasingly large data sets remains an interesting and, to some extent, unsolved research problem. Generically, dynamic data sets can be described by some, often hierarchical, notion of feature of interest that exists at each moment in time, and those features evolve across time. Consequently, exploring the evolution of these features is considered to be one natural way of studying these data sets. Usually, this process entails the ability to: 1) define and extract features from each time step in the data set; 2) find their correspondences over time; and 3) analyze their evolution across time. However, due to the large data sizes, visualizing the evolution of features in a comprehensible manner and performing interactive changes are challenging. Furthermore, feature evolution details are often unmanageably large and complex, making it difficult to identify the temporal trends in the underlying data. Additionally, many existing approaches develop these components in a specialized and standalone manner, thus failing to address the general task of understanding feature evolution across time. This dissertation demonstrates that interactive exploration of feature evolution can be achieved in a non-domain-specific manner so that it can be applied across a wide variety of application domains. In particular, a novel generic visualization and analysis environment that couples a multiresolution unified spatiotemporal representation of features with progressive layout and visualization strategies for studying the feature evolution across time is introduced. This flexible framework enables on-the-fly changes to feature definitions, their correspondences, and other arbitrary attributes while providing an interactive view of the resulting feature evolution details. Furthermore, to reduce the visual complexity within the feature evolution details, several subselection-based and localized, per-feature parameter value-based strategies are also enabled. The utility and generality of this framework is demonstrated by using several large-scale dynamic data sets
GraphMaps: Browsing Large Graphs as Interactive Maps
Algorithms for laying out large graphs have seen significant progress in the
past decade. However, browsing large graphs remains a challenge. Rendering
thousands of graphical elements at once often results in a cluttered image, and
navigating these elements naively can cause disorientation. To address this
challenge we propose a method called GraphMaps, mimicking the browsing
experience of online geographic maps.
GraphMaps creates a sequence of layers, where each layer refines the previous
one. During graph browsing, GraphMaps chooses the layer corresponding to the
zoom level, and renders only those entities of the layer that intersect the
current viewport. The result is that, regardless of the graph size, the number
of entities rendered at each view does not exceed a predefined threshold, yet
all graph elements can be explored by the standard zoom and pan operations.
GraphMaps preprocesses a graph in such a way that during browsing, the
geometry of the entities is stable, and the viewer is responsive. Our case
studies indicate that GraphMaps is useful in gaining an overview of a large
graph, and also in exploring a graph on a finer level of detail.Comment: submitted to GD 201
Embedding Spatial Software Visualization in the IDE: an Exploratory Study
Software visualization can be of great use for understanding and exploring a
software system in an intuitive manner. Spatial representation of software is a
promising approach of increasing interest. However, little is known about how
developers interact with spatial visualizations that are embedded in the IDE.
In this paper, we present a pilot study that explores the use of Software
Cartography for program comprehension of an unknown system. We investigated
whether developers establish a spatial memory of the system, whether clustering
by topic offers a sound base layout, and how developers interact with maps. We
report our results in the form of observations, hypotheses, and implications.
Key findings are a) that developers made good use of the map to inspect search
results and call graphs, and b) that developers found the base layout
surprising and often confusing. We conclude with concrete advice for the design
of embedded software maps.Comment: To appear in proceedings of SOFTVIS 2010 conferenc
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