Modern experiments in many disciplines generate large quantities of network (graph) data. Researchers require aesthetic layouts of these networks that clearly convey the domain knowledge and meaning. However, the problem remains challenging due to multiple conflicting aesthetic criteria and complex domain-specific constraints. In this article, we present a strategy for generating visualizations that can help network biologists understand the protein interactions that underlie processes that take place in the cell. Specifically, we have developed Flud, a crowd-powered system that allows humans with no expertise to design biologically meaningful graph layouts with the help of algorithmically generated suggestions. Furthermore, we propose a novel hybrid approach for graph layout wherein crowd workers and a simulated annealing algorithm build on each other’s progress. A study of about 2,000 crowd workers on Amazon Mechanical Turk showed that the hybrid crowd–algorithm approach outperforms the crowd-only approach and state-of-the-art techniques when workers were asked to lay out complex networks that represent signaling pathways. Another study of seven participants with biological training showed that Flud layouts are more effective compared to those created by state-of-the-art techniques. We also found that the algorithmically generated suggestions guided the workers when they are stuck and helped them improve their score. Finally, we discuss broader implications for mixed-initiative interactions in layout design tasks beyond biology.

Checklists and guidelines have played an increasingly important role in complex tasks ranging from the cockpit to the operating theater. Their role in creative tasks like design is less explored. In a needfinding study with expert web designers, we identified designers' challenges in adhering to a checklist of design guidelines. We built Critter, which addressed these challenges with three components: Dynamic Checklists that progressively disclose guideline complexity with a self-pruning hierarchical view, AutoQA to automate common quality assurance checks, and guideline-specific feedback provided by a reviewer to highlight mistakes as they appear. In an observational study, we found that the more engaged a designer was with Critter, the fewer mistakes they made in following design guidelines. Designers rated the AutoQA and contextual feedback experience highly, and provided feedback on the tradeoffs of the hierarchical Dynamic Checklists. We additionally found that a majority of designers rated the AutoQA experience as excellent and felt that it increased the quality of their work. Finally, we discuss broader implications for supporting complex creative tasks.

Given a network, can we visualize it for any given task, highlighting the important characteristics? Networks are widespread, and hence summarizing and visualizing them is of primary interest for many applications such as viral marketing, extracting communities and immunization. Summaries can help in solving new problems in visualization, sense-making, and in many other goals. However, most prior work focuses on generic structural summarization techniques or on developing specific algorithms for specific tasks. This is both tedious and challenging. As a result, for several popular tasks, there do not exist readymade summarization methods. In this paper, we explore a promising alternative approach instead. We propose NetGist, a framework which automatically learns how to generate a summary for a given task on a given network. In addition to generating the required summary, this also allows us to reuse the learned process on other similar networks. We formulate a novel task-based graph summarization problem and leverage reinforcement learning to design a flexible framework for our solution. Via extensive experiments, we show that NetGist robustly and effectively learns meaningful summaries, and helps solve challenging problems, and aids in complex task-based sense-making of networks.

Modern networks are very large in size and also evolve with time. As their sizes grow, the complexity of performing network analysis grows as well. Getting a smaller representation of a temporal network with similar properties will help in various data mining tasks. In this paper, we study the novel problem of getting a smaller diffusion-equivalent representation of a set of time-evolving networks. We first formulate a well-founded and general temporal-network condensation problem based on the so-called systemmatrix of the network. We then propose NETCONDENSE, a scalable and effective algorithm which solves this problem using careful transformations in sub-quadratic running time, and linear space complexities. Our extensive experiments show that we can reduce the size of large real temporal networks (from multiple domains such as social, co-authorship, and email) significantly without much loss of information. We also show the wide-applicability of NETCONDENSE by leveraging it for several tasks: for example, we use it to understand, explore, and visualize the original datasets and to also speed-up algorithms for the influence-maximization and event detection problems on temporal networks.

Modern networks are very large in size and also evolve with time. As their size grows, the complexity of performing network analysis grows as well. Getting a smaller representation of a temporal network with similar properties will help in various data mining tasks. In this paper, we study the novel problem of getting a smaller diffusion-equivalent representation of a set of time-evolving networks. We first formulate a well-founded and general temporal-network condensation problem based on the so-called system-matrix of the network. We then propose NetCon-dense, a scalable and effective algorithm which solves this problem using careful transformations in sub-quadratic running time, and linear space complexities. Our extensive experiments show that we can reduce the size of large real temporal networks (from multiple domains such as social, co-authorship and email) significantly without much loss of information. We also show the wide-applicability of Net-Condense by leveraging it for several tasks: for example, we use it to understand, explore and visualize the original datasets and to also speed-up algorithms for the influence-maximization problem on temporal networks.

SUMMARY: Networks have become ubiquitous in systems biology. Visualization is a crucial component in their analysis. However, collaborations within research teams in network biology are hampered by software systems that are either specific to a computational algorithm, create visualizations that are not biologically meaningful, or have limited features for sharing networks and visualizations. We present GraphSpace, a web-based platform that fosters team science by allowing collaborating research groups to easily store, interact with, layout and share networks. AVAILABILITY AND IMPLEMENTATION: Anyone can upload and share networks at http://graphspace.org. In addition, the GraphSpace code is available at http://github.com/Murali-group/graphspace if a user wants to run his or her own server. CONTACT: [email protected]. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.