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Open Access Research article

Inferring the physical connectivity of complex networks from their functional dynamics

Hung Xuan Ta1*, Chang No Yoon2, Liisa Holm1 and Seung Kee Han2*

Author Affiliations

1 Institute of Biotechnology, PO Box 56, 00014 University of Helsinki, Finland

2 Department of Physics & BK21 Physics Project, Chungbuk National University, Cheongju, Chungbuk 361-763, Republic of Korea

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BMC Systems Biology 2010, 4:70  doi:10.1186/1752-0509-4-70

Published: 26 May 2010



Biological networks, such as protein-protein interactions, metabolic, signalling, transcription-regulatory networks and neural synapses, are representations of large-scale dynamic systems. The relationship between the network structure and functions remains one of the central problems in current multidisciplinary research. Significant progress has been made toward understanding the implication of topological features for the network dynamics and functions, especially in biological networks. Given observations of a network system's behaviours or measurements of its functional dynamics, what can we conclude of the details of physical connectivity of the underlying structure?


We modelled the network system by employing a scale-free network of coupled phase oscillators. Pairwise phase coherence (PPC) was calculated for all the pairs of oscillators to present functional dynamics induced by the system. At the regime of global incoherence, we observed a Significant pairwise synchronization only between two nodes that are physically connected. Right after the onset of global synchronization, disconnected nodes begin to oscillate in a correlated fashion and the PPC of two nodes, either connected or disconnected, depends on their degrees.

Based on the observation of PPCs, we built a weighted network of synchronization (WNS), an all-to-all functionally connected network where each link is weighted by the PPC of two oscillators at the ends of the link. In the regime of strong coupling, we observed a Significant similarity in the organization of WNSs induced by systems sharing the same substrate network but different configurations of initial phases and intrinsic frequencies of oscillators.

We reconstruct physical network from the WNS by choosing the links whose weights are higher than a given threshold. We observed an optimal reconstruction just before the onset of global synchronization.

Finally, we correlated the topology of the background network to the observed change of the functional activities in the system.


The results presented in this study indicate a strong relationship between the structure and dynamics of complex network systems. As coupling strength increases, synchronization emerges among hub nodes and recruits small-degree nodes. The results show that the onset of global synchronization in the system hinders the reconstruction of an underlying complex structure. Our analysis helps to clarify how the synchronization is achieved in systems of different network topologies.