Supported algorithms

Overview

Algorithm	Motif size range	Directed / Undirected	Multi-threading	Prob. Counting	Key publication	More information
mfinder	\(3 \le s \le 8\)	Both	No	Yes	Network Motifs: Simple Building Blocks of Complex Networks [3]	Website
fanmod	\(3 \le s\) [1]	Both	No	Yes	FANMOD: a tool for fast network motif detection [4]	Website [2]
NetMODE	\(3 \le k \le 6\)	Both	Yes	No	NetMODE: Network Motif Detection without Nauty [5]	Website
PGD	\(2 \le k \le 4\)	Undirected	Yes	No	Efficient Graphlet Counting for Large Networks [6]	Website

Notes

• mfinder reports a motif class even if it has zero samples enumerated

  • NetMODE reports only those that were enumerated.

• pgd reports a motif distribution for undirected motifs of size \(2,3,4\) simultaneously, as a result of the same “run”.

  • Because of the way pgd reports its results, the motif_id is given in the format (motif_id, N_NODES).

  • Both of these numbers can be used with the :ref:motif_id_to_adj_mat() to reconstruct the adjacency matrix without ambiguity.

[1]

fanmod itself does not enforce a strict limit to the size of motifs it can enumerate but the underlying nauty library will complain for motif sizes greater than 8.

[2]

Please note that the original fanmod `website is no longer accessible. An Internet Archive snapshot of it can be found here. The original fanmod was operated only via a wxwidgets Graphical User Interface (GUI). Subsequent work (by Sebastian Bücker) produced fanmod_cmd and that version was used as the basis for the code-base that produces the binary used in this project.

[3]

Milo R., Shen-Orr S., Itzkovitz S., Kashtan N., Chklovskii D., and Alon U., ‘Network Motifs: Simple Building Blocks of Complex Networks’, Science, vol. 298, no. 5594, pp. 824–827, Oct. 2002, doi: 10.1126/science.298.5594.824.

[4]

S. Wernicke and F. Rasche, ‘FANMOD: a tool for fast network motif detection’, Bioinformatics, vol. 22, no. 9, pp. 1152–1153, May 2006, doi: 10.1093/bioinformatics/btl038.

[5]

X. Li, R. J. Stones, H. Wang, H. Deng, X. Liu, and G. Wang, ‘NetMODE: Network Motif Detection without Nauty’, PLOS ONE, vol. 7, no. 12, p. e50093, Dec. 2012, doi: 10.1371/journal.pone.0050093.

[6]

N. K. Ahmed, J. Neville, R. A. Rossi, and N. Duffield, ‘Efficient Graphlet Counting for Large Networks’, in 2015 IEEE International Conference on Data Mining, Nov. 2015, pp. 1–10. doi: 10.1109/ICDM.2015.141.