Approximation Algorithms and Hardness Results for Shortest Path Based Graph Orientations

The graph orientation problem calls for orienting the edges of an undirected graph so as to maximize the number of pre-specified source-target vertex pairs that admit a directed path from the source to the target. Most algorithmic approaches to this problem share a common preprocessing step, in which the input graph is reduced to a tree by repeatedly contracting its cycles. While this reduction is valid from an algorithmic perspective, the assignment of directions to the edges of the contracted cycles becomes arbitrary, and the connecting source-target paths may be arbitrarily long. In the context of biological networks, the connection of vertex pairs via shortest paths is highly motivated, leading to the following variant: Given an undirected graph and a collection of source-target vertex pairs, assign directions to the edges so as to maximize the number of pairs that are connected by a shortest (in the original graph) directed path. Here we study this variant, provide strong inapproximability results for it and propose an approximation algorithm for the problem, as well as for relaxations of it where the connecting paths need only be approximately shortest.

[1]  Anupam Gupta,et al.  Discovering pathways by orienting edges in protein interaction networks , 2010, Nucleic acids research.

[2]  Noga Alon,et al.  A Graph-Theoretic Game and Its Application to the k-Server Problem , 1995, SIAM J. Comput..

[3]  J. Håstad Clique is hard to approximate withinn1−ε , 1999 .

[4]  Tommi S. Jaakkola,et al.  Physical Network Models , 2004, J. Comput. Biol..

[5]  Roded Sharan,et al.  Optimally Orienting Physical Networks , 2011, RECOMB.

[6]  Ittai Abraham,et al.  Nearly Tight Low Stretch Spanning Trees , 2008, 2008 49th Annual IEEE Symposium on Foundations of Computer Science.

[7]  Roded Sharan,et al.  Approximation Algorithms for Orienting Mixed Graphs , 2011, CPM.

[8]  Beverly Sackler,et al.  An Algorithm for Orienting Graphs Based on Cause-Eect Pairs and Its Applications to Orienting Protein Networks , 2008 .

[9]  Shang-Hua Teng,et al.  Lower-stretch spanning trees , 2004, STOC '05.

[10]  S. Fields High‐throughput two‐hybrid analysis , 2005, The FEBS journal.

[11]  A. Vinayagam,et al.  A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction , 2011, Science Signaling.

[12]  Roded Sharan,et al.  An Algorithm for Orienting Graphs Based on Cause-Effect Pairs and Its Applications to Orienting Protein Networks , 2008, WABI.

[13]  Rita Casadio,et al.  Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings , 2005, WABI.

[14]  Johan Håstad,et al.  Clique is hard to approximate within n1-epsilon , 1996, Electron. Colloquium Comput. Complex..

[15]  P. Bork,et al.  Functional organization of the yeast proteome by systematic analysis of protein complexes , 2002, Nature.

[16]  D. Whelan,et al.  THE PROMISE ( AND PERIL ) , 2017 .

[17]  Roded Sharan,et al.  Improved Orientations of Physical Networks , 2010, WABI.