title: Multiple graph regularized protein domain ranking.
abstract: BACKGROUND
  Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.
  
  
  RESULTS
  To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.
  
  
  CONCLUSIONS
  The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications.
authors.affiliation: Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia. xin.gao@kaust.edu.sa
authors.forename: Jim Jing-Yan
authors.initials: JJ
authors.lastname: Wang
authors.forename: Halima
authors.initials: H
authors.lastname: Bensmail
authors.forename: Xin
authors.initials: X
authors.lastname: Gao
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods*; D012984:Software