Coordination of passive systems under quantized measurements

In this paper we investigate a passivity approach to collective coordination and synchronization problems in the presence of quantized measurements and show that coordination tasks can be achieved in a practical sense for a large class of passive systems.Comment: 40 pages, 1 figure, submitted to journal, second round of revie

Computational methods in cancer gene networking

In the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques such as “next generation” genome sequencing, chip-on-chip, microarray and so on can be used to measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are more comprehensive and unbiased, but ‘real signals’ or biological insights, molecular mechanisms and biological principles are buried in the flood of data. In current biological studies, the bottleneck is no longer a lack of data, but the lack of ingenuity and computational means to extract biological insights and principles by integrating knowledge and high-throughput data. 

Here I am reviewing the concepts and principles of network biology and the computational methods which can be applied to cancer research. Furthermore, I am providing a practical guide for computational analysis of cancer gene networks

A new design principle of robust onion-like networks self-organized in growth

Today's economy, production activity, and our life are sustained by social and technological network infrastructures, while new threats of network attacks by destructing loops have been found recently in network science. We inversely take into account the weakness, and propose a new design principle for incrementally growing robust networks. The networks are self-organized by enhancing interwoven long loops. In particular, we consider the range-limited approximation of linking by intermediations in a few hops, and show the strong robustness in the growth without degrading efficiency of paths. Moreover, we demonstrate that the tolerance of connectivity is reformable even from extremely vulnerable real networks according to our proposed growing process with some investment. These results may indicate a prospective direction to the future growth of our network infrastructures.Comment: 21 pages, 10 figures, 1 tabl

Cayley digraphs of finite abelian groups and monomial ideals

In the study of double-loop computer networks, the diagrams known as L-shapes arise as a graphical representation of an optimal routing for every graph’s node. The description of these diagrams provides an efficient method for computing the diameter and the average minimum distance of the corresponding graphs. We extend these diagrams to multiloop computer networks. For each Cayley digraph with a finite abelian group as vertex set, we define a monomial ideal and consider its representations via its minimal system of generators or its irredundant irreducible decomposition. From this last piece of information, we can compute the graph’s diameter and average minimum distance. That monomial ideal is the initial ideal of a certain lattice with respect to a graded monomial ordering. This result permits the use of Gr¨obner bases for computing the ideal and finding an optimal routing. Finally, we present a family of Cayley digraphs parametrized by their diameter d, all of them associated to irreducible monomial ideals

Observer Placement for Source Localization: The Effect of Budgets and Transmission Variance

When an epidemic spreads in a network, a key question is where was its source, i.e., the node that started the epidemic. If we know the time at which various nodes were infected, we can attempt to use this information in order to identify the source. However, maintaining observer nodes that can provide their infection time may be costly, and we may have a budget $k$ on the number of observer nodes we can maintain. Moreover, some nodes are more informative than others due to their location in the network. Hence, a pertinent question arises: Which nodes should we select as observers in order to maximize the probability that we can accurately identify the source? Inspired by the simple setting in which the node-to-node delays in the transmission of the epidemic are deterministic, we develop a principled approach for addressing the problem even when transmission delays are random. We show that the optimal observer-placement differs depending on the variance of the transmission delays and propose approaches in both low- and high-variance settings. We validate our methods by comparing them against state-of-the-art observer-placements and show that, in both settings, our approach identifies the source with higher accuracy.Comment: Accepted for presentation at the 54th Annual Allerton Conference on Communication, Control, and Computin

Stability of shortest paths in complex networks with random edge weights

We study shortest paths and spanning trees of complex networks with random edge weights. Edges which do not belong to the spanning tree are inactive in a transport process within the network. The introduction of quenched disorder modifies the spanning tree such that some edges are activated and the network diameter is increased. With analytic random-walk mappings and numerical analysis, we find that the spanning tree is unstable to the introduction of disorder and displays a phase-transition-like behavior at zero disorder strength $\epsilon=0$. In the infinite network-size limit ($N\to \infty$), we obtain a continuous transition with the density of activated edges $\Phi$ growing like $\Phi \sim \epsilon^1$ and with the diameter-expansion coefficient $\Upsilon$ growing like $\Upsilon\sim \epsilon^2$ in the regular network, and first-order transitions with discontinuous jumps in $\Phi$ and $\Upsilon$ at $\epsilon=0$ for the small-world (SW) network and the Barab\'asi-Albert scale-free (SF) network. The asymptotic scaling behavior sets in when $N\gg N_c$, where the crossover size scales as $N_c\sim \epsilon^{-2}$ for the regular network, $N_c \sim \exp[\alpha \epsilon^{-2}]$ for the SW network, and $N_c \sim \exp[\alpha |\ln \epsilon| \epsilon^{-2}]$ for the SF network. In a transient regime with $N\ll N_c$, there is an infinite-order transition with $\Phi\sim \Upsilon \sim \exp[-\alpha / (\epsilon^2 \ln N)]$ for the SW network and $\sim \exp[ -\alpha / (\epsilon^2 \ln N/\ln\ln N)]$ for the SF network. It shows that the transport pattern is practically most stable in the SF network.Comment: 9 pages, 7 figur