Fuse: Multiple Network Alignment via Data Fusion

Vladimir Gligorijevic, Noel Malod-Dognin and Natasa Przulj

Corresponding author: Prof. Natasa Przulj, e-mail: natasa [AT] cs.ucl.ac.uk

Fuse is a novel global multiple network aligner. First, it computes novel similarity scores between proteins by fusing sequence similarities and network wiring patterns over all proteins in all PPI networks being aligned, using non-negative matrix tri-factorization (NMTF). Second, it construct a one-to-one global multiple network alignment by using an approximate maximum weight k-partite matching solver.


How to run Fuse

Data-fusion step

To fuse PPI networks, you need:

Example of command line (in MATLAB console):

run_nmtf({'./Nets/CElegans.edgelist', './Nets/DMelanogaster.edgelist', './Nets/HSapiens.edgelist', './Nets/MMusculus.edgelist', './Nets/SCerevisiae.edgelist'}, 'sequence_scores.lst', [80, 90, 80, 70, 50], 1000, 0.01, 'nmft_scores.lst")

Data-fusion step produces an output file "nmft_scores.lst", which is an input file for the alignment step.

Alignment step

To align PPI networks with Fuse, you need:
Example of command line: ``./FUSE.exe -n network_list.txt -s sequence_scores.lst -t nmft_scores.lst -o an_output_file''
You can alternatively run ``./FUSE.exe -h'' to get the complete list of parameters.

Table of predicted clusters

Other multiple network alignment algorithms

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