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A Dynamic Algorithm for Network Propagation

Authors Barak Sternberg , Roded Sharan



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Author Details

Barak Sternberg
  • School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
Roded Sharan
  • School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

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Barak Sternberg and Roded Sharan. A Dynamic Algorithm for Network Propagation. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 7:1-7:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)
https://doi.org/10.4230/LIPIcs.WABI.2018.7

Abstract

Network propagation is a powerful transformation that amplifies signal-to-noise ratio in biological and other data. To date, most of its applications in the biological domain employed standard techniques for its computation that require O(m) time for a network with n vertices and m edges. When applied in a dynamic setting where the network is constantly modified, the cost of these computations becomes prohibitive. Here we study, for the first time in the biological context, the complexity of dynamic algorithms for network propagation. We develop a vertex decremental algorithm that is motivated by various biological applications and can maintain propagation scores over general weights at an amortized cost of O(m/(n^{1/4})) per update. In application to real networks, the dynamic algorithm achieves significant, 50- to 100-fold, speedups over conventional static methods for network propagation, demonstrating its great potential in practice.

Subject Classification

ACM Subject Classification
  • Theory of computation → Dynamic graph algorithms
Keywords
  • Network propagation
  • Dynamic graph algorithm
  • protein-protein interaction network

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