Proper evaluation of alignment-free network comparison methods

Bioinformatics
Ömer Nebil YaveroğluNatasa Przulj

Abstract

Network comparison is a computationally intractable problem with important applications in systems biology and other domains. A key challenge is to properly quantify similarity between wiring patterns of two networks in an alignment-free fashion. Also, alignment-based methods exist that aim to identify an actual node mapping between networks and as such serve a different purpose. Various alignment-free methods that use different global network properties (e.g. degree distribution) have been proposed. Methods based on small local subgraphs called graphlets perform the best in the alignment-free network comparison task, due to high level of topological detail that graphlets can capture. Among different graphlet-based methods, Graphlet Correlation Distance (GCD) was shown to be the most accurate for comparing networks. Recently, a new graphlet-based method called NetDis was proposed, which was claimed to be superior. We argue against this, as the performance of NetDis was not properly evaluated to position it correctly among the other alignment-free methods. We evaluate the performance of available alignment-free network comparison methods, including GCD and NetDis. We do this by measuring accuracy of each method (in a systematic ...Continue Reading

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Oct 4, 2016·PloS One·Alberto J M MartinTomas Perez-Acle
Oct 14, 2016·Scientific Reports·Anida SarajlićNataša Pržulj
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Aug 23, 2018·Scientific Reports·Shawn GuTijana Milenković
Nov 28, 2019·Scientific Reports·Mattia TantardiniCarlo Piccardi

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Software Mentioned

RGFD
BioGRID
STICKY
NetDis
NETAL
GHOST
GCD
GRAAL
MI

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