Spectral Analysis of Protein-Protein Interactions in Drosophila melanogaster

Within a case study on the protein-protein interaction network (PIN) of Drosophila melanogaster we investigate the relation between the network's spectral properties and its structural features such as the prevalence of specific subgraphs or duplicate nodes as a result of its evolutionary history. The discrete part of the spectral density shows fingerprints of the PIN's topological features including a preference for loop structures. Duplicate nodes are another prominent feature of PINs and we discuss their representation in the PIN's spectrum as well as their biological implications.Comment: 9 pages RevTeX including 8 figure

On the push&pull protocol for rumour spreading

The asynchronous push&pull protocol, a randomized distributed algorithm for spreading a rumour in a graph $G$, works as follows. Independent Poisson clocks of rate 1 are associated with the vertices of $G$. Initially, one vertex of $G$ knows the rumour. Whenever the clock of a vertex $x$ rings, it calls a random neighbour $y$: if $x$ knows the rumour and $y$ does not, then $x$ tells $y$ the rumour (a push operation), and if $x$ does not know the rumour and $y$ knows it, $y$ tells $x$ the rumour (a pull operation). The average spread time of $G$ is the expected time it takes for all vertices to know the rumour, and the guaranteed spread time of $G$ is the smallest time $t$ such that with probability at least $1-1/n$, after time $t$ all vertices know the rumour. The synchronous variant of this protocol, in which each clock rings precisely at times $1,2,\dots$, has been studied extensively. We prove the following results for any $n$-vertex graph: In either version, the average spread time is at most linear even if only the pull operation is used, and the guaranteed spread time is within a logarithmic factor of the average spread time, so it is $O(n\log n)$. In the asynchronous version, both the average and guaranteed spread times are $\Omega(\log n)$. We give examples of graphs illustrating that these bounds are best possible up to constant factors. We also prove theoretical relationships between the guaranteed spread times in the two versions. Firstly, in all graphs the guaranteed spread time in the asynchronous version is within an $O(\log n)$ factor of that in the synchronous version, and this is tight. Next, we find examples of graphs whose asynchronous spread times are logarithmic, but the synchronous versions are polynomially large. Finally, we show for any graph that the ratio of the synchronous spread time to the asynchronous spread time is $O(n^{2/3})$.Comment: 25 page

Achlioptas processes are not always self-averaging

We consider a class of percolation models, called Achlioptas processes, discussed in [Science 323, 1453 (2009)] and [Science 333, 322 (2011)]. For these the evolution of the order parameter (the rescaled size of the largest connected component) has been the main focus of research in recent years. We show that, in striking contrast to `classical' models, self-averaging is not a universal feature of these new percolation models: there are natural Achlioptas processes whose order parameter has random fluctuations that do not disappear in the thermodynamic limit.Comment: 4 pages, 3 figures. Revised and expanded. Title change

Random graph model with power-law distributed triangle subgraphs

Clustering is well-known to play a prominent role in the description and understanding of complex networks, and a large spectrum of tools and ideas have been introduced to this end. In particular, it has been recognized that the abundance of small subgraphs is important. Here, we study the arrangement of triangles in a model for scale-free random graphs and determine the asymptotic behavior of the clustering coefficient, the average number of triangles, as well as the number of triangles attached to the vertex of maximum degree. We prove that triangles are power-law distributed among vertices and characterized by both vertex and edge coagulation when the degree exponent satisfies $2<\beta<2.5$; furthermore, a finite density of triangles appears as $\beta=2+1/3$.Comment: 4 pages, 2 figure; v2: major conceptual change

A preferential attachment model with random initial degrees

In this paper, a random graph process ${G(t)}_{t\geq 1}$ is studied and its degree sequence is analyzed. Let $(W_t)_{t\geq 1}$ be an i.i.d. sequence. The graph process is defined so that, at each integer time $t$, a new vertex, with $W_t$ edges attached to it, is added to the graph. The new edges added at time t are then preferentially connected to older vertices, i.e., conditionally on $G(t-1)$, the probability that a given edge is connected to vertex i is proportional to $d_i(t-1)+\delta$, where $d_i(t-1)$ is the degree of vertex $i$ at time $t-1$, independently of the other edges. The main result is that the asymptotical degree sequence for this process is a power law with exponent $\tau=\min\{\tau_{W}, \tau_{P}\}$, where $\tau_{W}$ is the power-law exponent of the initial degrees $(W_t)_{t\geq 1}$ and $\tau_{P}$ the exponent predicted by pure preferential attachment. This result extends previous work by Cooper and Frieze, which is surveyed.Comment: In the published form of the paper, the proof of Proposition 2.1 is incomplete. This version contains the complete proo

Laplacian spectra of complex networks and random walks on them: Are scale-free architectures really important?

We study the Laplacian operator of an uncorrelated random network and, as an application, consider hopping processes (diffusion, random walks, signal propagation, etc.) on networks. We develop a strict approach to these problems. We derive an exact closed set of integral equations, which provide the averages of the Laplacian operator's resolvent. This enables us to describe the propagation of a signal and random walks on the network. We show that the determining parameter in this problem is the minimum degree $q_m$ of vertices in the network and that the high-degree part of the degree distribution is not that essential. The position of the lower edge of the Laplacian spectrum $\lambda_c$ appears to be the same as in the regular Bethe lattice with the coordination number $q_m$. Namely, $\lambda_c>0$ if $q_m>2$, and $\lambda_c=0$ if $q_m\leq2$. In both these cases the density of eigenvalues $\rho(\lambda)\to0$ as $\lambda\to\lambda_c+0$, but the limiting behaviors near $\lambda_c$ are very different. In terms of a distance from a starting vertex, the hopping propagator is a steady moving Gaussian, broadening with time. This picture qualitatively coincides with that for a regular Bethe lattice. Our analytical results include the spectral density $\rho(\lambda)$ near $\lambda_c$ and the long-time asymptotics of the autocorrelator and the propagator.Comment: 25 pages, 4 figure

Models and Algorithms for Graph Watermarking

We introduce models and algorithmic foundations for graph watermarking. Our frameworks include security definitions and proofs, as well as characterizations when graph watermarking is algorithmically feasible, in spite of the fact that the general problem is NP-complete by simple reductions from the subgraph isomorphism or graph edit distance problems. In the digital watermarking of many types of files, an implicit step in the recovery of a watermark is the mapping of individual pieces of data, such as image pixels or movie frames, from one object to another. In graphs, this step corresponds to approximately matching vertices of one graph to another based on graph invariants such as vertex degree. Our approach is based on characterizing the feasibility of graph watermarking in terms of keygen, marking, and identification functions defined over graph families with known distributions. We demonstrate the strength of this approach with exemplary watermarking schemes for two random graph models, the classic Erd\H{o}s-R\'{e}nyi model and a random power-law graph model, both of which are used to model real-world networks

Clustering in Complex Directed Networks

Many empirical networks display an inherent tendency to cluster, i.e. to form circles of connected nodes. This feature is typically measured by the clustering coefficient (CC). The CC, originally introduced for binary, undirected graphs, has been recently generalized to weighted, undirected networks. Here we extend the CC to the case of (binary and weighted) directed networks and we compute its expected value for random graphs. We distinguish between CCs that count all directed triangles in the graph (independently of the direction of their edges) and CCs that only consider particular types of directed triangles (e.g., cycles). The main concepts are illustrated by employing empirical data on world-trade flows

Slow relaxation in the Ising model on a small-world network with strong long-range interactions

We consider the Ising model on a small-world network, where the long-range interaction strength $J_2$ is in general different from the local interaction strength $J_1$, and examine its relaxation behaviors as well as phase transitions. As $J_2/J_1$ is raised from zero, the critical temperature also increases, manifesting contributions of long-range interactions to ordering. However, it becomes saturated eventually at large values of $J_2/J_1$ and the system is found to display very slow relaxation, revealing that ordering dynamics is inhibited rather than facilitated by strong long-range interactions. To circumvent this problem, we propose a modified updating algorithm in Monte Carlo simulations, assisting the system to reach equilibrium quickly.Comment: 5 pages, 5 figure

Properties of contact matrices induced by pairwise interactions in proteins

The total conformational energy is assumed to consist of pairwise interaction energies between atoms or residues, each of which is expressed as a product of a conformation-dependent function (an element of a contact matrix, C-matrix) and a sequence-dependent energy parameter (an element of a contact energy matrix, E-matrix). Such pairwise interactions in proteins force native C-matrices to be in a relationship as if the interactions are a Go-like potential [N. Go, Annu. Rev. Biophys. Bioeng. 12. 183 (1983)] for the native C-matrix, because the lowest bound of the total energy function is equal to the total energy of the native conformation interacting in a Go-like pairwise potential. This relationship between C- and E-matrices corresponds to (a) a parallel relationship between the eigenvectors of the C- and E-matrices and a linear relationship between their eigenvalues, and (b) a parallel relationship between a contact number vector and the principal eigenvectors of the C- and E-matrices; the E-matrix is expanded in a series of eigenspaces with an additional constant term, which corresponds to a threshold of contact energy that approximately separates native contacts from non-native ones. These relationships are confirmed in 182 representatives from each family of the SCOP database by examining inner products between the principal eigenvector of the C-matrix, that of the E-matrix evaluated with a statistical contact potential, and a contact number vector. In addition, the spectral representation of C- and E-matrices reveals that pairwise residue-residue interactions, which depends only on the types of interacting amino acids but not on other residues in a protein, are insufficient and other interactions including residue connectivities and steric hindrance are needed to make native structures the unique lowest energy conformations.Comment: Errata in DOI:10.1103/PhysRevE.77.051910 has been corrected in the present versio