Exploring coordinated relationships is an important task in data analytics. For example, an intelligence analyst may want to find three suspicious people who all visited the same four cities. However, existing techniques that display individual relationships, such as between lists of entities, require repetitious manual selection and significant mental aggregation in cluttered visualizations to find coordinated relationships. This work presents a visual analytics approach that applies biclusters to support coordinated relationships exploration. Each computed bicluster aggregates individual relationships into coordinated sets. Thus, coordinated relationships can be formalized as biclusters. However, how to incorporate biclusters into a visual analytics tool to support sensemaking tasks is challenging. To address this, this work features three key contributions: 1) a five-level design framework for bicluster visualizations, 2) BiSet, highlighting bicluster-based edge bundling, seriation-based multiple lists ordering, and interactions for dynamic information foraging and management, and 3) an evaluation of BiSet. / Ph. D.

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Biological network data is plentiful with practically every experimental methodology giving 'network views' into cellular function and behavior. Bioinformatic screens that yield network data include, for example, genome-wide deletion screens, protein-protein interaction assays, RNA interference experiments, and methods to probe metabolic pathways. Efficient and comprehensive computational approaches are required to model these screens and gain insight into the nature of biological networks. This thesis presents three new algorithms to model and mine network datasets. First, we present an algorithm that models genome-wide perturbation screens by deriving relations between phenotypes and subsequently using these relations in a local manner to derive genephenotype relationships. We show how this algorithm outperforms all previously described algorithms for gene-phenotype modeling. We also present theoretical insight into the convergence and accuracy properties of this approach. Second, we define a new data mining problem–constrained minimal separator mining—and propose algorithms as well as applications to modeling gene perturbation screens by viewing the perturbed genes as a graph separator. Both of these data mining applications are evaluated on network datasets from S. cerevisiae and C. elegans. Finally, we present an approach to model the relationship between metabolic pathways and operon structure in prokaryotic genomes. In this approach, we present a new pattern class—biclusters over domains with supplied partial orders—and present algorithms for systematically detecting such biclusters. Together, our data mining algorithms provide a comprehensive arsenal of techniques for modeling gene perturbation screens and metabolic pathways. / Ph. D.

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