Navigation and Exploration of Interconnected Pathways

Visualizing pathways, i. e. models of cellular functional networks, is a challenging task in computer assisted biomedicine. Pathways are represented as large collections of interwoven graphs, with complex structures present in both the individual graphs and their interconnections. This situation requires the development of novel visualization techniques to allow efficient visual exploration. We present the Caleydo framework, which incorporates a number of approaches to handle such pathways. Navigation in the network of pathways is facilitated by a hierarchical approach which dynamically selects a working set of individual pathways for closer inspection. These pathways are interactively rendered together with visual interconnections in a 2.5D view using graphics hardware acceleration. The layout of individual graphs is not computed automatically, but taken from the KEGG and BioCarta databases, which use layouts that life scientists are familiar with. Therefore they encode essential meta‐information. While the KEGG and BioCarta pathways use a pre‐defined layout, interactions such as linking+brushing, neighborhood search or detail on demand are still fully interactive in Caleydo. We have evaluated Caleydo with pathologists working on the determination of unknown gene functions. Informal experiences confirm that Caleydo is useful in both generating and validating such hypotheses. Even though the presented techniques are applied to medical pathways, the proposed way of interaction is not limited to cellular processes and therefore has the potential to open new possibilities in other fields of application.     

SetCoLa: High‐Level Constraints for Graph Layout

Constraints enable flexible graph layout by combining the ease of automatic layout with customizations for a particular domain. However, constraint‐based layout often requires many individual constraints defined over specific nodes and node pairs. In addition to the effort of writing and maintaining a large number of similar constraints, such constraints are specific to the particular graph and thus cannot generalize to other graphs in the same domain. To facilitate the specification of customized and generalizable constraint layouts, we contribute SetCoLa: a domain‐specific language for specifying high‐level constraints relative to properties of the backing data. Users identify node sets based on data or graph properties and apply high‐level constraints within each set. Applying constraints to node sets rather than individual nodes reduces specification effort and facilitates reapplication of customized layouts across distinct graphs. We demonstrate the conciseness, generalizability, and expressiveness of SetCoLa on a series of real‐world examples from ecological networks, biological systems, and social networks.     

Papilio: Visualizing Android Application Permissions

We introduce Papilio, a new visualization technique for visualizing permissions of real‐world Android applications. We explore the development of layouts that exploit the directed acyclic nature of Android application permission data to develop a new explicit layout technique that incorporates aspects of set membership, node‐link diagrams and matrix layouts. By grouping applications based on sets of requested permissions, a structure can be formed with partially ordered relations. The Papilio layout shows sets of applications centrally, the relations among applications on one side and application permissions, as the reason behind the existence of the partial order, on the other side. Using Papilio to explore a set of Android applications as a case study has led to new security findings regarding permission usage by Android applications.     

Pathfinder: Visual Analysis of Paths in Graphs

The analysis of paths in graphs is highly relevant in many domains. Typically, path‐related tasks are performed in node‐link layouts. Unfortunately, graph layouts often do not scale to the size of many real world networks. Also, many networks are multivariate, i.e., contain rich attribute sets associated with the nodes and edges. These attributes are often critical in judging paths, but directly visualizing attributes in a graph layout exacerbates the scalability problem. In this paper, we present visual analysis solutions dedicated to path‐related tasks in large and highly multivariate graphs. We show that by focusing on paths, we can address the scalability problem of multivariate graph visualization, equipping analysts with a powerful tool to explore large graphs. We introduce Pathfinder, a technique that provides visual methods to query paths, while considering various constraints. The resulting set of paths is visualized in both a ranked list and as a node‐link diagram. For the paths in the list, we display rich attribute data associated with nodes and edges, and the node‐link diagram provides topological context. The paths can be ranked based on topological properties, such as path length or average node degree, and scores derived from attribute data. Pathfinder is designed to scale to graphs with tens of thousands of nodes and edges by employing strategies such as incremental query results. We demonstrate Pathfinder's fitness for use in scenarios with data from a coauthor network and biological pathways.     

Metro Transit‐Centric Visualization for City Tour Planning

In general, city trip planning consists of two main steps: knowing Points‐Of‐Interest (POIs), and then planning a tour route from the current point to next preferred POIs. We mainly consider the metro for traveling around touristic cities as the main means of transportation. In this context, existing tools lack a capability to effectively visualize POIs on the metro map for trip planning. To bridge this gap, we propose an interactive framework that holistically combines presentations of POIs and a metro network. Our idea is to identify popular POIs based on visual worth computation, and to introduce POI discovery for effectively identifying POIs within reach of a metro network for users. We use octilinear layouts to highlight the metro network, and show representative POI images in the layout space visualized within a user‐specified viewing window. We have implemented our working prototype showing touristic cities with a metro network. We have factored out various design guidelines that are basis for designing our method, and validated our approach with a user study surveying 70 individuals.     

Design of dual‐mode dual‐band rectangular waveguide filtering antenna

A dual‐mode dual‐band rectangular waveguide filtering antenna with fourth‐order Chebyshev response is presented. First, design equations and processes of filtering networks are presented. Then, filtering antenna is constructed through cross‐shaped slot for radiation instead of the output port of filtering networks. A pair of degenerated modes are exploited in waveguide resonator design to miniaturize the whole size and form two passbands. In addition, the bandwidth can be adjusted flexibly in proper range. A prototype at C‐band is fabricated and measured, showing two operation channels of 5 to 5.05 GHz and 5.1 to 5.15 GHz with high rejection between two bands. Good agreement is achieved between the simulations and measurements, showing excellent performance in terms of filtering, out‐of‐band rejection, and gain in bands.     

Tracing Field‐Coherent Quad Layouts

Given a cross field over a triangulated surface we present a practical and robust method to compute a field aligned coarse quad layout over the surface. The method works directly on a triangle mesh without requiring any parametrization and it is based on a new technique for tracing field‐coherent geodesic paths directly on a triangle mesh, and on a new relaxed formulation of a binary LP problem, which allows us to extract both conforming quad layouts and coarser layouts containing t‐junctions. Our method is easy to implement, very robust, and, being directly based on the input cross field, it is able to generate better aligned layouts, even with complicated fields containing many singularities. We show results on a number of datasets and comparisons with state‐of‐the‐art methods.     

LinkLPA: A Link‐Based Label Propagation Algorithm for Overlapping Community Detection in Networks

Community detection is an important methodology for understanding the intrinsic structure and function of complex networks. Because overlapping community is one of the characteristics of real‐world networks and should be considered for community detection, in this article, we propose an algorithm, called link‐based label propagation algorithm (LinkLPA), to detect overlapping communities. Because the link partition is conceptually natural for the problem of overlapping community detection, LinkLPA first transforms node partition problem into link partition problem and employs a new label propagation algorithm with preference on links instead of nodes to detect communities due to the simplicity and efficiency of label propagation algorithm. Then the proposed LinkLPA performs a postprocessing to refine the detected overlapping communities by avoiding over‐overlapping and incorrect partition of weak ties. Experimental results on a large number of real‐world and synthetic networks show that the proposed method achieves high accuracy on detecting overlapping communities in networks.     

TimeArcs: Visualizing Fluctuations in Dynamic Networks

In this paper we introduce TimeArcs, a novel visualization technique for representing dynamic relationships between entities in a network. Force‐directed layouts provide a way to highlight related entities by positioning them near to each other Entities are brought closer to each other (forming clusters) by forces applied on nodes and connections between nodes. In many application domains, relationships between entities are not temporally stable, which means that cluster structures and cluster memberships also may vary across time. Our approach merges multiple force‐directed layouts at different time points into a single comprehensive visualization that provides a big picture overview of the most significant clusters within a user‐defined period of time. TimeArcs also supports a range of interactive features, such as allowing users to drill‐down in order to see details about a particular cluster. To highlight the benefits of this technique, we demonstrate its application to various datasets, including the IMDB co‐star network, a dataset showing conflicting evidences within biomedical literature of protein interactions, and collocated popular phrases obtained from political blogs.     

Layout optimization of looped networks by constrained ant colony optimisation algorithm

A constrained version of ant colony optimisation algorithm (ACOA) is proposed in this paper for layout optimization of looped water distribution networks. A novel formulation is used to represent the layout optimization problem of pipe networks in the proper form required for the application of the ant algorithm. The proposed formulation is based on the engineering concept of reliability in which the number of independent paths from the source node to each of the network nodes is considered as a measure of reliability. In the proposed formulation, the ants are constrained to choose from the options provided by a constraining procedure so that only looped layouts are constructed by the ant leading to huge reduction of search space size compared to the original search space. Three different constraining procedures are used leading to three different algorithms. The proposed methods are used to find the optimal layout of three benchmark examples from the literature and the results are presented and compared to the results of the conventional ant colony optimization algorithm. The results show the efficiency and effectiveness of the proposed method for optimal layout determination of looped networks.     

A miniature coupled‐line‐based 3‐dB directional coupler using GaAs PHEMT process

A novel complementary‐conducting‐strip (CCS) coupled‐line (CL) design is proposed to achieve compact size by applying two‐dimensional layout and standard gallium‐arsenide (GaAs) thin‐film technology. To obtain high coupling and satisfy the design rules of GaAs process, mixed‐couple mechanism with edge and broadside coupling are also used. A CCS CL‐based Ka‐band 3‐dB directional coupler is fabricated using WIN 0.15‐μm GaAs pseudomorphic high electron mobility transistor technology. Experimental results show that the proposed directional coupler can cover the entire Ka‐band (26–40 GHz) with through and coupling of approximately 3.7 ± 0.25 dB, and isolation of better than 13 dB. In addition, the phase difference between the two output ports is approximately 90° ± 5°. The occupied area of the prototype (without I/O networks) is only 220 × 220 μm². © 2015 Wiley Periodicals, Inc. Int J RF and Microwave CAE 26:21–26, 2016.     

MIQP‐based Layout Design for Building Interiors

We propose a hierarchical framework for the generation of building interiors. Our solution is based on a mixed integer quadratic programming (MIQP) formulation. We parametrize a layout by polygons that are further decomposed into small rectangles. We identify important high‐level constraints, such as room size, room position, room adjacency, and the outline of the building, and formulate them in a way that is compatible with MIQP and the problem parametrization. We also propose a hierarchical framework to improve the scalability of the approach. We demonstrate that our algorithm can be used for residential building layouts and can be scaled up to large layouts such as office buildings, shopping malls, and supermarkets. We show that our method is faster by multiple orders of magnitude than previous methods.     

Performance evaluation of multi‐primary color‐matrix layouts for mobile displays

Abstract— Different subpixel layouts for multi‐primary displays will be presented and their spatial performance analyzed. The layouts studied include red, green, blue, yellow, and cyan subpixels, arranged in 5/5, 5/4, and 5/3 configurations. In the 5/5 configuration, five primaries are arranged on five subpixels forming a square pixel. In the 5/4 configuration, five primaries are arranged on two square units, each of which have four subpixels so that the cyan and yellow subpixels are missing in alternate pixels. In the 5/3 layout, the multi‐primary color matrix is placed on top of a standard RGB TFT backplane with a subpixel aspect ratio of 1:3, resulting in an increased period of the full color sequence. Different data‐rendering methods for the modified color sequences were studied and their implication on the spatial performance were analyzed, given in terms of reproduction accuracy, i.e., the average S‐CIELAB error between data reproduced on a reference display and that reproduced on the examined layout. The reproduction error as a function of the angular substance of a pixel is reported for different layouts and rendering methods and are compared to that of an RGB display. It will be shown that the modified multi‐primary layouts reduce power consumption and provide good image quality for mobile applications.     

LPX: Overlapping community detection based on X‐means and label propagation algorithm in attributed networks

Traditional community detection methods in attributed networks (eg, social network) usually disregard abundant node attribute information and only focus on structural information of a graph. Existing community detection methods in attributed networks are mostly applied in the detection of nonoverlapping communities and cannot be directly used to detect the overlapping structures. This article proposes an overlapping community detection algorithm in attributed networks. First, we employ the modified X‐means algorithm to cluster attributes to form different themes. Second, we employ the label propagation algorithm (LPA), which is based on neighborhood network conductance for priority and the rule of theme weight, to detect communities in each theme. Finally, we perform redundant processing to form the final community division. The proposed algorithm improves the X‐means algorithm to avoid the effects of outliers. Problems of LPA such as instability of division and adjacent communities being easily merged can be corrected by prioritizing the node neighborhood network conductance. As the community is detected in the attribute subspace, the algorithm can find overlapping communities. Experimental results on real‐attributed and synthetic‐attributed networks show that the performance of the proposed algorithm is excellent with multiple evaluation metrics.     

Visualizing Waypoints‐Constrained Origin‐Destination Patterns for Massive Transportation Data

Origin‐destination (OD) pattern is a highly useful means for transportation research since it summarizes urban dynamics and human mobility. However, existing visual analytics are insufficient for certain OD analytical tasks needed in transport research. For example, transport researchers are interested in path‐related movements across congested roads, besides global patterns over the entire domain. Driven by this need, we propose waypoints‐constrained OD visual analytics, a new approach for exploring path‐related OD patterns in an urban transportation network. First, we use hashing‐based query to support interactive filtering of trajectories through user‐specified waypoints. Second, we elaborate a set of design principles and rules, and derive a novel unified visual representation called the waypoints‐constrained OD view by carefully considering the OD flow presentation, the temporal variation, spatial layout and user interaction. Finally, we demonstrate the effectiveness of our interface with two case studies and expert interviews with five transportation experts.     

Substrate integrated waveguide based cavity‐backed self‐triplexing slot antenna for X‐Ku band applications

A planar substrate integrated waveguide (SIW) based cavity‐backed self‐triplexing slot antenna is proposed for X‐Ku band applications. The antenna comprises of the SIW cavity, radiating slots, and feeding networks. The radiating slots; that are etched on the upper metallic plane of the SIW, are backed up by the three radiated quarter cavities (QCs). The radiating slots in the respective QCs are of different lengths, excited by three separated orthogonal feed lines to resonate at three different frequencies as 11.01, 12.15, and 13.1 GHz. By fine‐tuning the antenna parameters, an intrinsic input port isolation of better than 26 dB is realized which helps in achieving the self‐triplexing property. The behaviors of individual cavity modes at three resonant frequencies are explained with the help of Z‐parameter. The proposed antenna layout is easy to integrate with the planar circuit. The proposed antenna is fabricated and measured results display a close concern with the simulated results. Moreover, a unidirectional radiation pattern and gain of 5.1, 5.54, and 6.12 dBi at resonant frequencies are realized.     

Analysis and testing of black‐box component‐based systems by inferring partial models

From experience in component‐based software engineering, it is known that the integration of high‐quality components may not yield high‐quality software systems. It is difficult to evaluate all possible interactions between the components in the system to uncover inter‐component misfunctions. The problem is even harder when the components are used without source code, specifications or formal models. Such components are called black boxes in literature. This paper presents an iterative approach of combining model learning and testing techniques for the formal analysis of a system of black‐box components. In the approach, individual components in the system are learned as finite state machines that (partially) model the behavioural structure of the components. The learned models are then used to derive tests for refining the partial models and/or finding integration faults in the system. The approach has been applied on case studies that have produced encouraging results. Copyright © 2013 John Wiley & Sons, Ltd.     

Graph Layouts by t‐SNE

We propose a new graph layout method based on a modification of the t‐distributed Stochastic Neighbor Embedding (t‐SNE) dimensionality reduction technique. Although t‐SNE is one of the best techniques for visualizing high‐dimensional data as 2D scatterplots, t‐SNE has not been used in the context of classical graph layout. We propose a new graph layout method, tsNET, based on representing a graph with a distance matrix, which together with a modified t‐SNE cost function results in desirable layouts. We evaluate our method by a formal comparison with state‐of‐the‐art methods, both visually and via established quality metrics on a comprehensive benchmark, containing real‐world and synthetic graphs. As evidenced by the quality metrics and visual inspection, tsNET produces excellent layouts.     

A Community Structure‐Based Approach for Network Immunization

We propose a community structure‐based approach that does not require community labels of nodes, for network immunization. Social networks have been widely used as daily communication infrastructures these days. However, fast spreading of information over networks may have downsides such as computer viruses or epidemics of diseases. Because contamination is propagated among subgraphs (communities) along links in a network, use of community structure of the network would be effective for network immunization. However, despite various research efforts, it is still difficult to identify ground‐truth community labels of nodes in a network. Because communities are often interwoven through intermediate nodes, we propose to identify such nodes based on the community structure of a network without requiring community labels. By regarding the community structure in terms of nodes, we construct a vector representation of nodes based on a quality measure of communities. The distribution of the constructed vectors is used for immunizing intermediate nodes among communities, through the hybrid use of the norm and the relation in the vector representation. Experiments are conducted over both synthetic and real‐world networks, and our approach is compared with other network centrality‐based approaches. The results are encouraging and indicate that it is worth pursuing this path.