Exploring self-similarity of complex cellular networks: The edge-covering method with simulated annealing and log-periodic sampling

TL;DR

This paper introduces a new edge-covering box-counting method with simulated annealing and log-periodic sampling to better analyze the self-similarity and fractal properties of cellular networks, addressing biases in previous methods.

Contribution

The authors develop a novel edge-covering approach combined with simulated annealing and log-periodic sampling, improving fractal dimension estimation in cellular networks.

Findings

Edge-covering method outperforms node-covering in self-similar networks

Fractal dimension of cellular networks estimated as D_E=2.67±0.15

Evidence of log-periodic oscillations indicating discrete scale hierarchy

Abstract

Song, Havlin and Makse (2005) have recently used a version of the box-counting method, called the node-covering method, to quantify the self-similar properties of 43 cellular networks: the minimal number $N_V$ of boxes of size $\ell$ needed to cover all the nodes of a cellular network was found to scale as the power law $N_V \sim (\ell+1)^{-D_V}$ with a fractal dimension $D_V=3.53\pm0.26$. We propose a new box-counting method based on edge-covering, which outperforms the node-covering approach when applied to strictly self-similar model networks, such as the Sierpinski network. The minimal number $N_E$ of boxes of size $\ell$ in the edge-covering method is obtained with the simulated annealing algorithm. We take into account the possible discrete scale symmetry of networks (artifactual and/or real), which is visualized in terms of log-periodic oscillations in the dependence of the logarithm of $N_E$ as a function of the logarithm of $\ell$. In this way, we are able to remove the bias of the estimator of the fractal dimension, existing for finite networks. With this new methodology, we find that $N_E$ scales with respect to $\ell$ as a power law $N_E \sim \ell^{-D_E}$ with $D_E=2.67\pm0.15$ for the 43 cellular networks previously analyzed by Song, Havlin and Makse (2005). Bootstrap tests suggest that the analyzed cellular networks may have a significant log-periodicity qualifying a discrete hierarchy with a scaling ratio close to 2. In sum, we propose that our method of edge-covering with simulated annealing and log-periodic sampling minimizes the significant bias in the determination of fractal dimensions in log-log regressions.