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SANA

Network alignment using simulated annealing

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SANA

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SANA performs network alignment using simulated annealing. SANA can optimize the S3[1] and WEC network alignment measures, the DS3[2] and DWEC[2] dynamic network alignment measures, and node conservation (i.e. the assignment problem), as well as convex combinations of any of these measures.

SANA.jl is a partial implementation of this paper [3]. SANA.jl is similar to the paper in that it uses the same swapping mechanism to find neighbors of an alignment, and it optimizes some of the same network alignment measures. It is different from the paper in that it calculates initial temperature (k) and temperature decay rate (lambda) using different heuristics, since the heuristics used in the paper weren't published. Simulated annealing is highly dependent on the k and lambda parameters; so this will not have similar results to that of the paper.

[1] MAGNA++: Maximizing Accuracy in Global Network Alignment via both node and edge conservation, V. Vijayan, V. Saraph, and T. Milenkovic, Bioinformatics, Volume 31, Issue 14, 15 July 2015, Pages 2409-2411. [2] Alignment of dynamic networks, V. Vijayan, D. Critchlow, and T. Milenkovic, Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages i180-i189. [3] SANA: simulated annealing far outperforms many other search algorithms for biological network alignment" Nil Mamano Wayne B. Hayes Bioinformatics, Volume 33, Issue 14, 15 July 2017, Pages 2156-2164

Example usage

using SANA, LightGraphs

g1 = erdos_renyi(200,0.1)
g2 = g1
G1 = adjacency_matrix(g1)
G2 = adjacency_matrix(g2)

res = sanas3(G1,G2,maxtime=600,tempschedule=TempAdaptive())
f = res.f
mean(1:length(f) .== f[1:length(f)])

res = sanas3(G1,G2,maxtime=600,tempschedule=TempDecay())
f = res.f
mean(1:length(f) .== f[1:length(f)])

SANA can be installed as follows.

Pkg.clone("https://github.com/vvjn/SANA.jl")

Documentation

Available here.

First Commit

02/04/2018

Last Touched

almost 2 years ago

Commits

3 commits

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