Novel scaling limits for critical inhomogeneous random graphs

We find scaling limits for the sizes of the largest components at criticality for rank-1 inhomogeneous random graphs with power-law degrees with power-law exponent \tau. We investigate the case where $\tau\in(3,4)$, so that the degrees have finite variance but infinite third moment. The sizes of the largest clusters, rescaled by $n^{-(\tau-2)/(\tau-1)}$, converge to hitting times of a "thinned" L\'{e}vy process, a special case of the general multiplicative coalescents studied by Aldous [Ann. Probab. 25 (1997) 812-854] and Aldous and Limic [Electron. J. Probab. 3 (1998) 1-59]. Our results should be contrasted to the case \tau>4, so that the third moment is finite. There, instead, the sizes of the components rescaled by $n^{-2/3}$ converge to the excursion lengths of an inhomogeneous Brownian motion, as proved in Aldous [Ann. Probab. 25 (1997) 812-854] for the Erd\H{o}s-R\'{e}nyi random graph and extended to the present setting in Bhamidi, van der Hofstad and van Leeuwaarden [Electron. J. Probab. 15 (2010) 1682-1703] and Turova [(2009) Preprint].Comment: Published in at http://dx.doi.org/10.1214/11-AOP680 the Annals of Probability (http://www.imstat.org/aop/) by the Institute of Mathematical Statistics (http://www.imstat.org

Universality for first passage percolation on sparse random graphs

We consider first passage percolation on the conguration model with n vertices, and general independent and identically distributed edge weights assumed to have a density. Assuming that the degree distribution satisfies a uniform X2 logX-condition, we analyze the asymptotic distribution for the minimal weight path between a pair of typical vertices, as well the number of edges on this path namely the hopcount. The hopcount satisfies a central limit theorem (CLT). Furthermore, writing Ln for the weight of this optimal path, then we shown that Ln(log n)= n converges to a limiting random variable, for some sequence n. This sequence n and the norming constants for the CLT are expressible in terms of the parameters of an associated continuous-time branching process that describes the growth of neighborhoods around a uniformly chosen vertex in the random graph. The limit of Ln(log n)= n equals the sum of the logarithm of the product of two independent martingale limits, and a Gumbel random variable. Till date, for sparse random graph models, such results have been shown only for the special case where the edge weights have an exponential distribution, wherein the Markov property of this distribution plays a crucial role in the technical analysis of the problem. The proofs in the paper rely on a refined coupling between shortest path trees and continuous- time branching processes, and on a Poisson point process limit for the potential closing edges of shortest-weight paths between the source and destination

Universality for first passage percolation on sparse uniform and rank-1 random graphs

In [3], we considered first passage percolation on the configuration model equipped with general independent and identically distributed edge weights, where the common distribution function admits a density. Assuming that the degree distribution satisfies a uniform X^2 log X - condition, we analyzed the asymptotic distribution for the minimal weight path between a pair of typical vertices, as well as the asymptotic distribution of the number of edges on this path. Given the interest in understanding such questions for various other random graph models, the aim of this paper is to show how these results extend to uniform random graphs with a given degree sequence and rank-one inhomogeneous random graphs

Degree distribution of shortest path trees and bias of network sampling algorithms

In this article, we explicitly derive the limiting distribution of the degree distribution of the shortest path tree from a single source on various random network models with edge weights. We determine the power-law exponent of the degree distribution of this tree and compare it to the degree distribution of the original graph. We perform this analysis for the complete graph with edge weights that are powers of exponential random variables (weak disorder in the stochastic mean-field model of distance) as well as on the configuration model with edge-weights drawn according to any continuous distribution. In the latter, the focus is on settings where the degrees obey a power law, and we show that the shortest path tree again obeys a power law with the same degree power-law exponent. We also consider random r-regular graphs for large r, and show that the degree distribution of the shortest path tree is closely related to the shortest path tree for the stochastic mean field model of distance. We use our results to explain an empirically observed bias in network sampling methods. This is part of a general program initiated in previous works by Bhamidi, van der Hofstad and Hooghiemstra [7, 8, 6] of analyzing the effect of attaching random edge lengths on the geometry of random network models

Probabilistic Analysis of Optimization Problems on Generalized Random Shortest Path Metrics

Simple heuristics often show a remarkable performance in practice for optimization problems. Worst-case analysis often falls short of explaining this performance. Because of this, "beyond worst-case analysis" of algorithms has recently gained a lot of attention, including probabilistic analysis of algorithms. The instances of many optimization problems are essentially a discrete metric space. Probabilistic analysis for such metric optimization problems has nevertheless mostly been conducted on instances drawn from Euclidean space, which provides a structure that is usually heavily exploited in the analysis. However, most instances from practice are not Euclidean. Little work has been done on metric instances drawn from other, more realistic, distributions. Some initial results have been obtained by Bringmann et al. (Algorithmica, 2013), who have used random shortest path metrics on complete graphs to analyze heuristics. The goal of this paper is to generalize these findings to non-complete graphs, especially Erd\H{o}s-R\'enyi random graphs. A random shortest path metric is constructed by drawing independent random edge weights for each edge in the graph and setting the distance between every pair of vertices to the length of a shortest path between them with respect to the drawn weights. For such instances, we prove that the greedy heuristic for the minimum distance maximum matching problem, the nearest neighbor and insertion heuristics for the traveling salesman problem, and a trivial heuristic for the $k$-median problem all achieve a constant expected approximation ratio. Additionally, we show a polynomial upper bound for the expected number of iterations of the 2-opt heuristic for the traveling salesman problem.Comment: An extended abstract appeared in the proceedings of WALCOM 201

Critical phenomena in exponential random graphs

The exponential family of random graphs is one of the most promising class of network models. Dependence between the random edges is defined through certain finite subgraphs, analogous to the use of potential energy to provide dependence between particle states in a grand canonical ensemble of statistical physics. By adjusting the specific values of these subgraph densities, one can analyze the influence of various local features on the global structure of the network. Loosely put, a phase transition occurs when a singularity arises in the limiting free energy density, as it is the generating function for the limiting expectations of all thermodynamic observables. We derive the full phase diagram for a large family of 3-parameter exponential random graph models with attraction and show that they all consist of a first order surface phase transition bordered by a second order critical curve.Comment: 14 pages, 8 figure

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

Ising models on power-law random graphs

We study a ferromagnetic Ising model on random graphs with a power-law degree distribution and compute the thermodynamic limit of the pressure when the mean degree is finite (degree exponent $\tau>2$), for which the random graph has a tree-like structure. For this, we adapt and simplify an analysis by Dembo and Montanari, which assumes finite variance degrees ($\tau>3$). We further identify the thermodynamic limits of various physical quantities, such as the magnetization and the internal energy

The C-Terminal Domain of the Arabinosyltransferase Mycobacterium tuberculosis EmbC Is a Lectin-Like Carbohydrate Binding Module

The D-arabinan-containing polymers arabinogalactan (AG) and lipoarabinomannan (LAM) are essential components of the unique cell envelope of the pathogen Mycobacterium tuberculosis. Biosynthesis of AG and LAM involves a series of membrane-embedded arabinofuranosyl (Araf) transferases whose structures are largely uncharacterised, despite the fact that several of them are pharmacological targets of ethambutol, a frontline drug in tuberculosis therapy. Herein, we present the crystal structure of the C-terminal hydrophilic domain of the ethambutol-sensitive Araf transferase M. tuberculosis EmbC, which is essential for LAM synthesis. The structure of the C-terminal domain of EmbC (EmbCCT) encompasses two sub-domains of different folds, of which subdomain II shows distinct similarity to lectin-like carbohydrate-binding modules (CBM). Co-crystallisation with a cell wall-derived di-arabinoside acceptor analogue and structural comparison with ligand-bound CBMs suggest that EmbCCT contains two separate carbohydrate binding sites, associated with subdomains I and II, respectively. Single-residue substitution of conserved tryptophan residues (Trp868, Trp985) at these respective sites inhibited EmbC-catalysed extension of LAM. The same substitutions differentially abrogated binding of di- and penta-arabinofuranoside acceptor analogues to EmbCCT, linking the loss of activity to compromised acceptor substrate binding, indicating the presence of two separate carbohydrate binding sites, and demonstrating that subdomain II indeed functions as a carbohydrate-binding module. This work provides the first step towards unravelling the structure and function of a GT-C-type glycosyltransferase that is essential in M. tuberculosis. Author Summary Top Tuberculosis (TB), an infectious disease caused by the bacillus Mycobacterium tuberculosis, burdens large swaths of the world population. Treatment of active TB typically requires administration of an antibiotic cocktail over several months that includes the drug ethambutol. This front line compound inhibits a set of arabinosyltransferase enzymes, called EmbA, EmbB and EmbC, which are critical for the synthesis of arabinan, a vital polysaccharide in the pathogen's unique cell envelope. How precisely ethambutol inhibits arabinosyltransferase activity is not clear, in part because structural information of its pharmacological targets has been elusive. Here, we report the high-resolution structure of the C-terminal domain of the ethambutol-target EmbC, a 390-amino acid fragment responsible for acceptor substrate recognition. Combining the X-ray crystallographic analysis with structural comparisons, site-directed mutagenesis, activity and ligand binding assays, we identified two regions in the C-terminal domain of EmbC that are capable of binding acceptor substrate mimics and are critical for activity of the full-length enzyme. Our results begin to define structure-function relationships in a family of structurally uncharacterised membrane-embedded glycosyltransferases, which are an important target for tuberculosis therapy