Improved Orientations of Physical Networks

@inproceedings{Gamzu2010ImprovedOO,
  title={Improved Orientations of Physical Networks},
  author={Iftah Gamzu and Danny Segev and Roded Sharan},
  booktitle={WABI},
  year={2010}
}
The orientation of physical networks is a prime task in deciphering the signaling-regulatory circuitry of the cell. One manifestation of this computational task is as a maximum graph orientation problem, where given an undirected graph on n vertices and a collection of vertex pairs, the goal is to orient the edges of the graph so that a maximum number of pairs are connected by a directed path. We develop a novel approximation algorithm for this problem with a performance guarantee of O(log n… 
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References

SHOWING 1-10 OF 23 REFERENCES
An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks
TLDR
This work considers a graph orientation problem arising in the study of biological networks, and provides an O(logn) approximation algorithm for the general case that achieves very tight approximation ratios in practice and is able to infer edge directions with high accuracy on both simulated and real network data.
Orienting Graphs to Optimize Reachability
Robust subgraphs for trees and paths
TLDR
This article considers the problems of finding heavy paths and heavy trees of k edges and shows that in every complete weighted graph on n vertices there exists a subgraph with approximately α/1−α2n edges that contains an α-approximate solution for every k = 1,…, n − 1.
A Sublogarithmic Approximation for Highway and Tollbooth Pricing
TLDR
The main result is a deterministic algorithm for the tollbooth problem on trees whose approximation ratio is O(log m/log logm), where m denotes the number of edges in the underlying graph.
Covering Graphs Using Trees and Stars
TLDR
This paper provides constant factor approximation algorithms for finding tree and star covers of graphs, in the rooted and un-rooted versions.
The SONET edge-partition problem
Motivated by a problem arising in the design of telecommunications networks using the SONET standard, we consider the problem of covering all edges of a graph using subgraphs that contain at most k
Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings
TLDR
A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem and Semi-definite Programming to Enhance Supertree Resolvability are presented.
The Probabilistic Method
TLDR
A particular set of problems - all dealing with “good” colorings of an underlying set of points relative to a given family of sets - is explored.
A note on orientations of mixed graphs
Improved Rounding Techniques for the MAX 2-SAT and MAX DI-CUT Problems
TLDR
Improved approximation algorithms for the MAX 2-SAT and MAX DI-CUT problems are obtained, which are essentially the best performance ratios that can be achieved using any combination of prerounding rotations and skewed distributions of hyperplanes, and even using more general families of rounding procedures.
...
...