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Journal of the ACM (JACM)
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Finding a Maximum Density Subgraph
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Dense subgraphs with restrictions and applications to gene annotation graphs
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Dense subgraphs with restrictions and applications to gene annotation graphs
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IPEC'12 Proceedings of the 7th international conference on Parameterized and Exact Computation
Towards realistic team formation in social networks based on densest subgraphs
Proceedings of the 22nd international conference on World Wide Web
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In this paper, we focus on finding complex annotation patterns representing novel and interesting hypotheses from gene annotation data We define a generalization of the densest subgraph problem by adding an additional distance restriction (defined by a separate metric) to the nodes of the subgraph We show that while this generalization makes the problem NP-hard for arbitrary metrics, when the metric comes from the distance metric of a tree, or an interval graph, the problem can be solved optimally in polynomial time We also show that the densest subgraph problem with a specified subset of vertices that have to be included in the solution can be solved optimally in polynomial time In addition, we consider other extensions when not just one solution needs to be found, but we wish to list all subgraphs of almost maximum density as well We apply this method to a dataset of genes and their annotations obtained from The Arabidopsis Information Resource (TAIR) A user evaluation confirms that the patterns found in the distance restricted densest subgraph for a dataset of photomorphogenesis genes are indeed validated in the literature; a control dataset validates that these are not random patterns Interestingly, the complex annotation patterns potentially lead to new and as yet unknown hypotheses We perform experiments to determine the properties of the dense subgraphs, as we vary parameters, including the number of genes and the distance.