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Browsing by Author "Bharadwaj, Aditya"

Now showing 1 - 3 of 3
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    Flud: A Hybrid Crowd–Algorithm Approach for Visualizing Biological Networks
    Bharadwaj, Aditya; Gwizdala, David; Kim, Yoonjin; Luther, Kurt; Murali, T. M. (2022-01)
    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.
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    Mixed-Initiative Methods for Following Design Guidelines in Creative Tasks
    Bharadwaj, Aditya (Virginia Tech, 2020-08-26)
    Practitioners in creative domains such as web design, data visualization, and software development face many challenges while trying to create novel solutions that satisfy the guidelines around practical constraints and quality considerations. My dissertation work addresses two of these challenges. First, guidelines may conflict with each other, creating a need for slow and time-consuming expert intervention. Second, guidelines may be hard to check programmatically, requiring experts to manually use multipage style guides that suffer from drawbacks related to searchability, navigation, conflict, and obsolescence. In my dissertation, I focus on exploring mixed-initiative methods as a solution to these challenges in two complex tasks: biological network visualization where guidelines may conflict, and web design where task requirements are hard to check programmatically. For biological network visualization, I explore the use of crowdsourcing to scale up time-consuming manual layout tasks. To support the network-based collaboration required for crowdsourcing, I first implemented a system called GraphSpace. It fosters online collaboration by allowing users to store, organize, explore, lay out, and share networks on a web platform. I then used GraphSpace as the infrastructure to support a novel mixed-initiative crowd-algorithm approach for creating high-quality, biological meaningful network visualizations. I also designed and implemented Flud, a system that gamifies the graph visualization task and uses flow theory concepts to make algorithmically generated suggestions more readily accessible to non-expert crowds. Then, I proposed DeepLayout, a novel learning-based approach as an alternative to the non-machine learning-based method used in Flud. It has the ability to learn how to balance complex conflicting guidelines from a layout process. Finally, in the domain of web design, I present a real-world iterative deployment of a system called Critter. Critter augments traditional quality assurance techniques used in structured domains, such as checklists and expert feedback, using mixed-initiative interactions. I hope this dissertation can serve to accelerate research on leveraging the complementary strengths of humans and computers in the context of creative processes that are generally considered out of bounds for automated methods.
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    XTALKDB: a database of signaling pathway crosstalk
    Sam, Sarah A.; Teel, Joelle; Tegge, Allison N.; Bharadwaj, Aditya; Murali, T. M. (2017-01-04)
    Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents crosstalk between specific pairs of signaling pathways. We have developed XTALKDB (http://www.xtalkdb.org) to fill this very important gap. XTALKDB contains curated information for 650 pairs of pathways from over 1600 publications. In addition, the database reports the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in which the crosstalk was observed. The XTALKDB website provides an easy-to- use interface for scientists to browse crosstalk information by querying one or more pathways or molecules of interest.