Jonathan Qiang Jiang

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We propose here a multi-label semi-supervised learning algorithm , PfunBG, to predict protein functions, employing a bi-relational graph (BG) of proteins and function annotations. Different from most, if not all, existing methods that only consider the partially labeled protein-protein interaction (PPI) network, the BG comprises three components, a PPI(More)
Assigning biological functions to uncharacterized proteins is a fundamental problem in the postgenomic era. The increasing availability of large amounts of data on protein-protein interactions (PPIs) has led to the emergence of a considerable number of computational methods for determining protein function in the context of a network. These algorithms,(More)
Proteins that interact in vivo tend to reside within the same or "adjacent" subcellular compartments. This observation provides opportunities to reveal protein subcellular localization in the context of the protein-protein interaction (PPI) network. However, so far, only a few efforts based on heuristic rules have been made in this regard. We systematically(More)
We show here that the problem of maximizing a family of quantitative functions, encompassing both the modularity (Q-measure) and modularity density (D-measure), for community detection can be uniformly understood as a combinatoric optimization involving the trace of a matrix called modularity Laplacian. Instead of using traditional spectral relaxation, we(More)
We propose a generalized stochastic block model to explore the mesoscopic structures in signed networks by grouping vertices that exhibit similar positive and negative connection profiles into the same cluster. In this model, the group memberships are viewed as hidden or unobserved quantities, and the connection patterns between groups are explicitly(More)
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