Identifying basic building blocks/motifs of networks

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The optimal subgraph decomposition of an electronic circuit.

There are many verbal descriptions for network motifs: characteristic connectivity patterns, over represented subgraphs, recurrent circuits, basic building-blocks of networks just to name a few. However, as with most concepts in network science network motifs are maybe best explained in terms of empirical observations. For instance the most basic example of a network motif is the motif consisting of tree mutually connected nodes that is: a triangle. Many real world networks ranging from the internet to social networks to biological networks contain many more triangles than one would expect if they were wired randomly. In certain cases there exist good explanations for the large number of triangles found in the network. For instance, the presence of many triangles in friendship networks simply tell us that we are more likely to be friends with the friends of our friends. In biological networks triangles and other motifs are believed to contribute to the overall function of the network by performing modular tasks such as information processing and therefore are believed to be favoured by natural selection.

The predominant definition of network motifs is due to Milo et al. [1]  and defines network motifs on the basis of how surprising their frequency in the network is when compared to randomized version of the network. The randomized version of the network is usually taken to be the configuration model i.e. the ensemble of all networks that have the same degree distribution as the original network. Following this definition motifs are identified by comparing their counts in the original network with a large sample of this null model. The approach of Milo et al. formalizes the concept of network motifs as over represented connectivity patterns. However, the results of the method are highly dependent on the choice of null model.

In my talk I presented an alternative approach to motif analysis [2] that seeks to formalize the network motifs from the perspective of simple building blocks. The approach is based on finding an optimal decomposition of the network into subgraphs. Here, subgraph decompositions are defined as subgraph covers which are sets of subgraphs such that every edge of the network is contained in at least one of the subgraphs in the cover. It follows from this definition that a subgraph cover is a representation of the network in the sense that given a subgraph cover the network can be recovered fully by simply taking the union of the edge sets of the subgraphs in the cover. In fact many network representations including edge lists, adjacency lists, bipartite representations and power-graphs fall into the category of subgraph covers. For instance, the edge list representation is equivalent to the cover consisting of all single edge subgraphs of the network and bipartite representations are simply covers which consist of cliques of various sizes.

Given that there are many competing ways of representing a network as a subgraph cover the question of how one picks one of the covers over the other arises. In order to address this problem we consider the total information of subgraph covers as a measure of optimality. The total information is a information measure introduced by Gell-Mann and Hartle [3] which given a model for a certain entity e is defined to be sum of the entropy and effective complexity of M. While the entropy measures the information required to describe e given M and the effective complexity measures the amount of information required to specify M which is given by its algorithmic information content. The total information also provides a framework for model selection:  given two or more models for the same entity one picks the one that has lowest total information and if two models have the same total information one picks the one that has lower effective complexity i.e. the simpler one. This essentially tells us how to trade off goodness of fit and model complexity.

In the context of subgraph covers the entropy of a cover corresponds to the information required to give the positions of the subgraphs in the cover given the different motifs that occur in C and their respective frequencies in C. On the other hand the effective complexity of C corresponds to the information required to describe the set of motifs occurring in the cover together with their respective frequencies. While the entropy of subgraph covers can be calculated analytically their effective complexity is not computable due to the halting problem. However, in practice one can use approximations in the form of upper bounds.

Following the total information approach we now define an optimal subgraph cover of network G to be a subgraph cover that minimizes the total information and the network motifs of G to be the motifs/connectivity patterns that occur in such an optimal cover.
The problem of finding an optimal cover turns out to be computationally rather challenging. Besides the usual difficulties associated to counting subgraphs  (subgraph isomorphism problem-NP complete) and classifying subgraphs (graph isomorphism problem-complexity unknown) the problem is a non-linear set covering problem and therefore NP-hard. Consequently, we construct a greedy heuristic for the problem.

When applied to real world networks the method finds very similar motifs in networks representing similar systems. Moreover, the counts of the motifs in networks of the same type scale approximately with network size. Consequently, the method can also be used to classify networks according to their subgraph structure.

 

References:

[1] R. Milo, S. Shen-Orr, S. Itzkovitz, N. Kashtan, D. Chklovskii, and U. Alon, Network Motifs: Simple Building Blocks of Complex Networks, Science 298, 824 (2002)

[2] Wegner, A. E. Subgraph covers: An information-theoretic approach to motif analysis in
networks. Phys. Rev. X, 4:041026, Nov 2014

[3] M. Gell-Mann and S. Lloyd, Information Measures, Effective Complexity, and Total Information, Complexity 2, 44 (1996).