A survey on subgraph counting: concepts, algorithms, and applications to network motifs and graphlets

P Ribeiro, P Paredes, MEP Silva, D Aparicio… - ACM computing surveys …, 2021 - dl.acm.org
Computing subgraph frequencies is a fundamental task that lies at the core of several
network analysis methodologies, such as network motifs and graphlet-based metrics, which …

Network analysis of particles and grains

L Papadopoulos, MA Porter, KE Daniels… - Journal of Complex …, 2018 - academic.oup.com
The arrangements of particles and forces in granular materials have a complex organization
on multiple spatial scales that range from local structures to mesoscale and system-wide …

Tempme: Towards the explainability of temporal graph neural networks via motif discovery

J Chen, R Ying - Advances in Neural Information …, 2023 - proceedings.neurips.cc
Temporal graphs are widely used to model dynamic systems with time-varying interactions.
In real-world scenarios, the underlying mechanisms of generating future interactions in …

A subgraph isomorphism algorithm and its application to biochemical data

V Bonnici, R Giugno, A Pulvirenti, D Shasha, A Ferro - BMC bioinformatics, 2013 - Springer
Background Graphs can represent biological networks at the molecular, protein, or species
level. An important query is to find all matches of a pattern graph to a target graph …

Homomorphisms are a good basis for counting small subgraphs

R Curticapean, H Dell, D Marx - Proceedings of the 49th Annual ACM …, 2017 - dl.acm.org
We introduce graph motif parameters, a class of graph parameters that depend only on the
frequencies of constant-size induced subgraphs. Classical works by Lovász show that many …

Higher-order networks representation and learning: A survey

H Tian, R Zafarani - ACM SIGKDD Explorations Newsletter, 2024 - dl.acm.org
Network data has become widespread, larger, and more complex over the years. Traditional
network data is dyadic, capturing the relations among pairs of entities. With the need to …

Biological network motif detection: principles and practice

E Wong, B Baur, S Quader… - Briefings in bioinformatics, 2012 - academic.oup.com
Network motifs are statistically overrepresented sub-structures (sub-graphs) in a network,
and have been recognized as 'the simple building blocks of complex networks'. Study of …

A survey of current software for network analysis in molecular biology

S Thomas, D Bonchev - Human genomics, 2010 - Springer
Software for network motifs and modules is briefly reviewed, along with programs for
network comparison. The three major software packages for network analysis …

A survey of pattern mining in dynamic graphs

P Fournier‐Viger, G He, C Cheng, J Li… - … : Data Mining and …, 2020 - Wiley Online Library
Graph data is found in numerous domains such as for the analysis of social networks,
sensor networks, bioinformatics, industrial systems, and chemistry. Analyzing graphs to …

MODA: an efficient algorithm for network motif discovery in biological networks

S Omidi, F Schreiber, A Masoudi-Nejad - Genes & genetic systems, 2009 - jstage.jst.go.jp
In recent years, interest has been growing in the study of complex networks. Since Erdös
and Rényi (1960) proposed their random graph model about 50 years ago, many …