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.
Interesting recent approaches to visualizing dynamic data include Archambault and Purchase's work on dynamic attribute cascades @cite_21 , 's @cite_31 , and 's @cite_19 and @cite_35 techniques. However, since a main goal of our visualization was to emphasize the relationship of rules to other rules, we elected to use a visual representation that made it easier to apply visual encodings to the links between nodes (see DIN_Section ). Techniques by @cite_24 @cite_60 , @cite_65 , and @cite_6 present multiple synchronized representations of a dynamic brain network to provide additional insight into the community dynamics within the network. Our tool also presents auxiliary representations to support the analysis of dynamic data, providing detail on demand for selected nodes.
@cite_35 @cite_60 @cite_21 @cite_65 @cite_6 @cite_24 @cite_19 @cite_31
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The dynamic network visualization has been a challenging topic due to the complexity introduced by the extra time dimension. Existing solutions to this problem are usually good for the overview and presentation, but not for the interactive analysis. We propose in this paper a new approach which only considers the dynamic network central to a focus node (aka dynamic ego network). The navigation of the entire network is achieved by switching the focus node with user interactions. With this approach, the complexity of the compressed dynamic network is greatly reduced without sacrificing the network and time affinity central to the focus node. As a result, we are able to present each dynamic ego network in a single static view, well supporting user analysis on temporal network patterns. We describe our general framework including the network data pre-processing, 1.5D network and trend visualization design, layout algorithms, as well as several customized interactions. In addition, we show that our approach can also be extended to visualize the event-based and multimodal dynamic networks. Finally, we demonstrate, through two practical case studies, the effectiveness of our solution in support of visual evidence and pattern discovery. We introduce the concept of dynamic image , a novel compact representation of videos useful for video analysis, particularly in combination with convolutional neural networks (CNNs). A dynamic image encodes temporal data such as RGB or optical flow videos by using the concept of ‘rank pooling’. The idea is to learn a ranking machine that captures the temporal evolution of the data and to use the parameters of the latter as a representation. We call the resulting representation dynamic image because it summarizes the video dynamics in addition to appearance. This powerful idea allows to convert any video to an image so that existing CNN models pre-trained with still images can be immediately extended to videos. We also present an efficient approximate rank pooling operator that runs two orders of magnitude faster than the standard ones with any loss in ranking performance and can be formulated as a CNN layer. To demonstrate the power of the representation, we introduce a novel four stream CNN architecture which can learn from RGB and optical flow frames as well as from their dynamic image representations. We show that the proposed network achieves state-of-the-art performance, 95.5 and 72.5 percent accuracy, in the UCF101 and HMDB51, respectively. The visualization and analysis of dynamic networks have become increasingly important in several fields, for instance sociology or economics. The dynamic and multi-relational nature of this data poses the challenge of understanding both its topological structure and how it changes over time. In this paper we propose a visual analytics approach for analyzing dynamic networks that integrates: a dynamic layout with user-controlled trade-off between stability and consistency; three temporal views based on different combinations of node-link diagrams (layer superimposition, layer juxtaposition, and two-and-a-half-dimensional view); the visualization of social network analysis metrics; and specific interaction techniques for tracking node trajectories and node connectivity over time. This integration of visual, interactive, and automatic methods supports the multi-faceted analysis of dynamically changing networks. Dynamic graph visualization focuses on the challenge of representing the evolution of relationships between entities in readable, scalable and effective diagrams. This work surveys the growing number of approaches in this discipline. We derive a hierarchical taxonomy of techniques by systematically categorizing and tagging publications. While static graph visualizations are often divided into node-link and matrix representations, we identify the representation of time as the major distinguishing feature for dynamic graph visualizations: either graphs are represented as animated diagrams or as static charts based on a timeline. Evaluations of animated approaches focus on dynamic stability for preserving the viewer's mental map or, in general, compare animated diagrams to timeline-based ones. A bibliographic analysis provides insights into the organization and development of the field and its community. Finally, we identify and discuss challenges for future research. We also provide feedback from experts, collected with a questionnaire, which gives a broad perspective of these challenges and the current state of the field.