Browsing by Author "Gehlenborg, Nils"

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    PEAX: Interactive Visual Pattern Search in Sequential Data Using Unsupervised Deep Representation Learning
    (The Eurographics Association and John Wiley & Sons Ltd., 2020) Lekschas, Fritz; Peterson, Brant; Haehn, Daniel; Ma, Eric; Gehlenborg, Nils; Pfister, Hanspeter; Viola, Ivan and Gleicher, Michael and Landesberger von Antburg, Tatiana
    We present PEAX, a novel feature-based technique for interactive visual pattern search in sequential data, like time series or data mapped to a genome sequence. Visually searching for patterns by similarity is often challenging because of the large search space, the visual complexity of patterns, and the user's perception of similarity. For example, in genomics, researchers try to link patterns in multivariate sequential data to cellular or pathogenic processes, but a lack of ground truth and high variance makes automatic pattern detection unreliable. We have developed a convolutional autoencoder for unsupervised representation learning of regions in sequential data that can capture more visual details of complex patterns compared to existing similarity measures. Using this learned representation as features of the sequential data, our accompanying visual query system enables interactive feedback-driven adjustments of the pattern search to adapt to the users' perceived similarity. Using an active learning sampling strategy, PEAX collects user-generated binary relevance feedback. This feedback is used to train a model for binary classification, to ultimately find other regions that exhibit patterns similar to the search target. We demonstrate PEAX's features through a case study in genomics and report on a user study with eight domain experts to assess the usability and usefulness of PEAX. Moreover, we evaluate the effectiveness of the learned feature representation for visual similarity search in two additional user studies. We find that our models retrieve significantly more similar patterns than other commonly used techniques.
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    Tasks, Techniques, and Tools for Genomic Data Visualization
    (The Eurographics Association and John Wiley & Sons Ltd., 2019) Nusrat, Sabrina; Harbig, Theresa; Gehlenborg, Nils; Laramee, Robert S. and Oeltze, Steffen and Sedlmair, Michael
    Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this need has become crucial in genomics, as biomedical research is increasingly data-driven and many studies lack welldefined hypotheses. A key challenge in data-driven research is to discover unexpected patterns and to formulate hypotheses in an unbiased manner in vast amounts of genomic and other associated data. Over the past two decades, this has driven the development of numerous data visualization techniques and tools for visualizing genomic data. Based on a comprehensive literature survey, we propose taxonomies for data, visualization, and tasks involved in genomic data visualization. Furthermore, we provide a comprehensive review of published genomic visualization tools in the context of the proposed taxonomies.