Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs

@inproceedings{Saha2010DenseSW,
  title={Dense Subgraphs with Restrictions and Applications to Gene Annotation Graphs},
  author={Barna Saha and Allison Hoch and Samir Khuller and Louiqa Raschid and Xiao-Ning Zhang},
  booktitle={RECOMB},
  year={2010}
}
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… CONTINUE READING
BETA

Similar Papers

Figures and Topics from this paper.

Citations

Publications citing this paper.
SHOWING 1-10 OF 57 CITATIONS, ESTIMATED 79% COVERAGE

Mining Dual Networks: Models, Algorithms, and Applications

  • TKDD
  • 2016
VIEW 4 EXCERPTS
CITES BACKGROUND & METHODS
HIGHLY INFLUENCED

Algorithms and Models for the Web Graph

  • Lecture Notes in Computer Science
  • 2014
VIEW 5 EXCERPTS
CITES BACKGROUND
HIGHLY INFLUENCED

Finding Cross Genome Patterns in Annotation Graphs

VIEW 7 EXCERPTS
CITES METHODS & BACKGROUND
HIGHLY INFLUENCED

2 All Densest Subgraphs and Almost Dense Subgraphs

VIEW 6 EXCERPTS
CITES METHODS
HIGHLY INFLUENCED

Exploiting Efficient Densest Subgraph Discovering Methods for Big Data

  • IEEE Transactions on Big Data
  • 2017
VIEW 4 EXCERPTS
CITES BACKGROUND
HIGHLY INFLUENCED

Efficient and Effective Local Algorithms for Analyzing Massive Graphs

VIEW 10 EXCERPTS
CITES BACKGROUND & METHODS
HIGHLY INFLUENCED

POST-SILICON TEST OPTIMIZATION USING METHODS FROM BIOINFORMATICS

VIEW 3 EXCERPTS
CITES METHODS
HIGHLY INFLUENCED

Mining Patterns from Clinical Trial Annotated Datasets by Exploiting the NCI Thesaurus

  • International Semantic Web Conference
  • 2012
VIEW 8 EXCERPTS
CITES BACKGROUND & METHODS
HIGHLY INFLUENCED

FILTER CITATIONS BY YEAR

2009
2019

CITATION STATISTICS

  • 11 Highly Influenced Citations

  • Averaged 5 Citations per year over the last 3 years

References

Publications referenced by this paper.
SHOWING 1-10 OF 25 REFERENCES

Dense subgraph with restrictions and applications to gene annotation

B. Saha, A. Hoch, S. Khuller, L. Raschid, X. Zhang
  • graphs. http://www.cs.umd.edu/∼samir/grant/recomb-full.pdf,
  • 2010
VIEW 4 EXCERPTS
HIGHLY INFLUENTIAL

Discovering protein complexes in dense reliable neighborhoods of protein interaction networks.

  • Computational systems bioinformatics. Computational Systems Bioinformatics Conference
  • 2007
VIEW 2 EXCERPTS

Modularity and community structure in networks.

  • Proceedings of the National Academy of Sciences of the United States of America
  • 2006
VIEW 1 EXCERPT