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In the network querying problem, one is given a protein complex or pathway of species A and a protein-protein interaction network of species B; the goal is to identify subnetworks of B that are similar to the query in terms of sequence, topology, or both. Existing approaches mostly depend on knowledge of the interaction topology of the query in the network(More)
TORQUE is a tool for cross-species querying of protein-protein interaction networks. It aims to answer the following question: given a set of proteins constituting a known complex or a pathway in one species, can a similar complex or pathway be found in the protein network of another species? To this end, Torque seeks a matching set of proteins that are(More)
We present a general visual analytics architecture that is constructed and implemented to effectively analyze un-structured social media data on a large scale. Pipelined based on a high-performance cluster configuration, MPI processing, and interactive visual analytics interfaces, our architecture, I-SI, closely integrates data-driven analytical methods and(More)
The NP-hard Colorful Components problem is, given a vertex-colored graph, to delete a minimum number of edges such that no connected component contains two vertices of the same color. It has applications in multiple sequence alignment and in multiple network alignment where the colors correspond to species. We initiate a systematic complexity-theoretic(More)
Complex modular networks appear frequently, notably in the biological or social sciences. We focus on two current challenges regarding network modularity: the ability to identify (i) the modules of a given network, and (ii) the hub states as nodes with highest importance in terms of the communication between modules. Our approach towards these goals uses(More)
The core–periphery model for protein interaction (PPI) networks assumes that protein complexes in these networks consist of a dense core and a possibly sparse periphery that is adjacent to vertices in the core of the complex. In this work, we aim at uncovering a global core–periphery structure for a given PPI network. We propose two exact graph-theoretic(More)
The NP-hard Colorful Components problem is a graph partitioning problem on vertex-colored graphs. We identify a new application of Colorful Components in the correction of Wikipedia interlanguage links, and describe and compare three exact and two heuris-tic approaches. In particular, we devise two ILP formulations, one based on Hitting Set and one based on(More)
Visualizing correlations, i.e., the tendency of uncertain data values at different spatial positions to change contrarily or according to each other, allows inferring on the possible variations of structures in the data. Visualizing global correlation structures, however, is extremely challenging since it is not clear how the visualization of complicated(More)
Most network clustering methods share the assumption that the network can be completely decomposed into modules, that is, every node belongs to (usually exactly one) module. Forcing this constraint can lead to misidentification of modules where none exist, while the true modules are drowned out in the noise, as has been observed e. g. for protein(More)
Multidimensional multivariate data can be visualized using many different well-known charts, such as bar charts, stacked bar charts, grouped bar charts, scatterplots, or pivot tables, or also using more advanced high-dimensional techniques such as scatterplot matrices (SPLOMs) or parallel coordinate plots (PCPs). These many techniques have different(More)