We consider the classic Moran process modeling the spread of genetic mutations, as extended to structured populations by (Nature, 2005). In this process, individuals are the vertices of a connected graph G. Initially, there is a single mutant vertex, chosen uniformly at random. In each step, a random vertex is selected for reproduction with a probability proportional to its fitness: mutants have fitness r > 1, while non-mutants have fitness 1. The vertex chosen to reproduce places a copy of itself to a uniformly random neighbor in G, replacing the individual that was there. The process ends when the mutation either reaches fixation (i.e., all vertices are mutants), or gets extinct. The principal quantity of interest is the probability with which each of the two outcomes occurs. A problem that has received significant attention recently concerns the existence of families of graphs, called strong amplifiers of selection, for which the fixation probability tends to 1 as the order n of the graph increases, and the existence of strong suppressors of selection, for which this probability tends to 0. For the case of directed graphs, it is known that both strong amplifiers and suppressors exist. For the case of undirected graphs, however, the problem has remained open, and the general belief has been that neither strong amplifiers nor suppressors exist. In this paper we disprove this belief, by providing the first examples of such graphs. The strong amplifier we present has fixation probability 1 − ˜ O(n^ −1 3), and the strong suppressor has fixation probability ˜O(n^−1 4). Both graph constructions are surprisingly simple. We also prove a general upper bound of 1 − ˜Ω(n^−1 3) on the fixation probability of any undirected graph. Hence, our strong amplifier is existentially optimal.
Several works have been devoted to the numerical computation of the fixation probability on specific classes of graphs, such as instances of bipartite graphs and Erd "os-R 'enyi random graphs @cite_3 @cite_18 @cite_34 @cite_4 .
@cite_18 @cite_34 @cite_4 @cite_3
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The problem of finding birth–death fixation probabilities for configurations of normal and mutants on an N -vertex graph is formulated in terms of a Markov process on the 2 N -dimensional state space of possible configurations. Upper and lower bounds on the fixation probability after any given number of iterations of the birth–death process are derived in terms of the transition matrix of this process. Consideration is then specialized to a family of graphs called circular flows, and we present a summation formula for the complete bipartite graph, giving the fixation probability for an arbitrary configuration of mutants in terms of a weighted sum of the single-vertex fixation probabilities. This also yields a closed-form solution for the fixation probability of bipartite graphs. Three entropy measures are introduced, providing information about graph structure. Finally, a number of examples are presented, illustrating cases of graphs that enhance or suppress fixation probability for fitness r >1 as well as graphs that enhance fixation probability for only a limited range of fitness. Results are compared with recent results reported in the literature, where a positive correlation is observed between vertex degree variance and fixation probability for undirected graphs. We show a similar correlation for directed graphs, with correlation not directly to fixation probability but to the difference between fixation probability for a given graph and a complete graph. Consider a collection of random variables attached to the vertices of a graph. The reconstruction problem requires to estimate one of them given far away' observations. Several theoretical results (and simple algorithms) are available when their joint probability distribution is Markov with respect to a tree. In this paper we consider the case of sequences of random graphs that converge locally to trees. In particular, we develop a sufficient condition for the tree and graph reconstruction problem to coincide. We apply such condition to colorings of random graphs. Further, we characterize the behavior of Ising models on such graphs, both with attractive and random interactions (respectively, ferromagnetic' and spin glass'). We study the existence of perfect matchings in suitably chosen induced subgraphs of random biregular bipartite graphs. We prove a result similar to a classical theorem of Erdos and Renyi about perfect matchings in random bipartite graphs. We also present an application to commutative graphs, a class of graphs that are featured in additive number theory. This work extends what is known so far for a basic model of evolutionary antagonism in undirected networks (graphs). More specifically, this work studies the generalized Moran process, as introduced by Lieberman, Hauert, and Nowak [Nature, 433:312-316, 2005], where the individuals of a population reside on the vertices of an undirected connected graph. The initial population has a single mutant of a fitness value r (typically r>1), residing at some vertex v of the graph, while every other vertex is initially occupied by an individual of fitness 1. At every step of this process, an individual (i.e. vertex) is randomly chosen for reproduction with probability proportional to its fitness, and then it places a copy of itself on a random neighbor, thus replacing the individual that was residing there. The main quantity of interest is the fixation probability, i.e. the probability that eventually the whole graph is occupied by descendants of the mutant. In this work we concentrate on the fixation probability when the mutant is initially on a specific vertex v, thus refining the older notion of which studied the fixation probability when the initial mutant is placed at a random vertex. We then aim at finding graphs that have many "strong starts" (or many "weak starts") for the mutant. Thus we introduce a parameterized notion of selective amplifiers (resp. selective suppressors) of evolution. We prove the existence of strong selective amplifiers (i.e. for h(n)=Θ(n) vertices v the fixation probability of v is at least @math for a function c(r) that depends only on r), and the existence of quite strong selective suppressors. Regarding the traditional notion of fixation probability from a random start, we provide strong upper and lower bounds: first we demonstrate the non-existence of "strong universal" amplifiers, and second we prove the Thermal Theorem which states that for any undirected graph, when the mutant starts at vertex v, the fixation probability at least @math . This theorem (which extends the "Isothermal Theorem" of for regular graphs) implies an almost tight lower bound for the usual notion of fixation probability. Our proof techniques are original and are based on new domination arguments which may be of general interest in Markov Processes that are of the general birth-death type. We consider the classic Moran process modeling the spread of genetic mutations, as extended to structured populations by (Nature, 2005). In this process, individuals are the vertices of a connected graph G. Initially, there is a single mutant vertex, chosen uniformly at random. In each step, a random vertex is selected for reproduction with a probability proportional to its fitness: mutants have fitness r > 1, while non-mutants have fitness 1. The vertex chosen to reproduce places a copy of itself to a uniformly random neighbor in G, replacing the individual that was there. The process ends when the mutation either reaches fixation (i.e., all vertices are mutants), or gets extinct. The principal quantity of interest is the probability with which each of the two outcomes occurs. A problem that has received significant attention recently concerns the existence of families of graphs, called strong amplifiers of selection, for which the fixation probability tends to 1 as the order n of the graph increases, and the existence of strong suppressors of selection, for which this probability tends to 0. For the case of directed graphs, it is known that both strong amplifiers and suppressors exist. For the case of undirected graphs, however, the problem has remained open, and the general belief has been that neither strong amplifiers nor suppressors exist. In this paper we disprove this belief, by providing the first examples of such graphs. The strong amplifier we present has fixation probability 1 − ˜ O(n^ −1 3), and the strong suppressor has fixation probability ˜O(n^−1 4). Both graph constructions are surprisingly simple. We also prove a general upper bound of 1 − ˜Ω(n^−1 3) on the fixation probability of any undirected graph. Hence, our strong amplifier is existentially optimal. Consider the random graph on n vertices 1,...,n. Each vertex i is assigned a type x(i) with x(1),...,x(n) being independent identically distributed as a nonnegative random variable X. We assume that EX3 < infinity. Given types of all vertices, an edge exists between vertices i and j independent of anything else and with probability min 1, x(i)x(j) n (1 + a n(1 3)) . We study the critical phase, which is known to take place when EX2 = 1. We prove that normalized by n(-2 3) the asymptotic joint distributions of component sizes of the graph equals the joint distribution of the excursions of a reflecting Brownian motion with diffusion coefficient root EXEX3 and drift a - EX3 EX s. In particular, we conclude that the size of the largest connected component is of order n(2 3). (c) 2013 Wiley Periodicals, Inc. Random Struct. Alg., 43, 486-539, 2013 (Less) The following question is due to Chatterjee and Varadhan 2011. Fix 0<p<r<1 and take G Gn,p, the Erdi¾?s-Renyi random graph with edge density p, conditioned to have at least as many triangles as the typical Gn,r. Is G close in cut-distance to a typical Gn,r? Via a beautiful new framework for large deviation principles in Gn,p, Chatterjee and Varadhan gave bounds on the replica symmetric phase, the region of p,r where the answer is positive. They further showed that for any small enough p there are at least two phase transitions as r varies. We settle this question by identifying the replica symmetric phase for triangles and more generally for any fixed d-regular graph. By analyzing the variational problem arising from the framework of Chatterjee and Varadhan we show that the replica symmetry phase consists of all p,r such that rd,hpr lies on the convex minorant of xi¾?hpx1 d where hp is the rate function of a binomial with parameter p. In particular, the answer for triangles involves hpx rather than the natural guess of hpx1 3 where symmetry was previously known. Analogous results are obtained for linear hypergraphs as well as the setting where the largest eigenvalue of G Gn,p is conditioned to exceed the typical value of the largest eigenvalue of Gn,r. Building on the work of Chatterjee and Diaconis 2012 we obtain additional results on a class of exponential random graphs including a new range of parameters where symmetry breaking occurs. En route we give a short alternative proof of a graph homomorphism inequality due to Kahn 2001 and Galvin and Tet ali 2004. © 2014 Wiley Periodicals, Inc. Random Struct. Alg., 47, 109-146, 2015 We consider the set of all graphs on n labeled vertices with prescribed degrees D = (d1,…,dn). For a wide class of tame degree sequences D we obtain a computationally efficient asymptotic formula approximating the number of graphs within a relative error which approaches 0 as n grows. As a corollary, we prove that the structure of a random graph with a given tame degree sequence D is well described by a certain maximum entropy matrix computed from D. We also establish an asymptotic formula for the number of bipartite graphs with prescribed degrees of vertices, or, equivalently, for the number of 0-1 matrices with prescribed row and column sums. © 2012 Wiley Periodicals, Inc. Random Struct. Alg., 2013 We study random r-uniform n vertex hypergraphs with fixed degree sequence d = (d1…,dn), maximum degree D = o(n1 24) and total degree tn, where t is bounded. We give the size, number of edges and degree sequence of the k ≥ 2) up to a whp error of O(n2 3 D4 3 log n). In the case of graphs (r = 2) we give further structural details such as the number of tree components and, for the case of smooth degree sequences, the size of the mantle. We give various examples, such as the cores of r-uniform hypergraphs with a near Poisson degree sequence, and an improved upper bound for the first linear dependence among the columns in the independent column model of random Boolean matrices. © 2004 Wiley Periodicals, Inc. Random Struct. Alg., 25, 2004 We consider the Erdős–Renyi random graph G(n, p) inside the critical window, that is when p = 1 n + λn −4 3, for some fixed ( R ) . We prove that the sequence of connected components of G(n, p), considered as metric spaces using the graph distance rescaled by n −1 3, converges towards a sequence of continuous compact metric spaces. The result relies on a bijection between graphs and certain marked random walks, and the theory of continuum random trees. Our result gives access to the answers to a great many questions about distances in critical random graphs. In particular, we deduce that the diameter of G(n, p) rescaled by n −1 3 converges in distribution to an absolutely continuous random variable with finite mean. We consider the random graph induced by the random key predistribution scheme of Eschenauer and Gligor under the assumption of full visibility. We show the existence of a zero-one law for the absence of isolated nodes, and complement it by a Poisson convergence for the number of isolated nodes. Leveraging earlier results and analogies with Erdos-Renyi graphs, we explore similar results for the property of graph connectivity. Suppose we are given a bipartite graph with vertex set X, Y, |X| = n , |Y| = N , each point in X (Y) has degree D(d) fixed, respectively, moreover, each pair of points x, x' ∈ X has at most D (log n) 3 (common) neighbours. Let t (X, Y) denote the minimum number of vertices of Y needed to cover all vertices of X. We prove (Theorem 1.1) that t (X, Y) d n tends to 1 as n tends to infinity. This result has many applications: Theorem [5]. Suppose k > r > 1 are fixed, n → ∞. Then there exists a collection of (1 + o (1)) × ( n r ) ( k r ) k -subsets of an n -set so that each r -subset is contained in at least one member of the collection. Analogues and strengthenings of this result are deduced. E.g. for vector spaces, orthogonal or simplectic geometries, random collections of k -sets with constant probabilities, etc. Theorem 3.3. Suppose G is a graph on v vertices and e edges and ℛ is a random graph on n vertices and edge probability e ( v 2 ). Then there exists a collection of (1 + o (1))( n 2 ) ( v 2 ) induced subgraphs of ℛ on v vertices, isomorphic to G and such that each edge (non-edge) of ℛ is covered by an edge (non-edge) of a graph in the collection. Random regular graphs play a central role in combinatorics and theoretical computer science. In this paper, we analyze a simple algorithm introduced by Steger and Wormald [10] and prove that it produces an asymptotically uniform random regular graph in a polynomial time. Precisely, for fixed d and n with d = O(n1 3−e), it is shown that the algorithm generates an asymptotically uniform random d-regular graph on n vertices in time O(nd2). This confirms a conjecture of Wormald. The key ingredient in the proof is a recently developed concentration inequality by the second author. The algorithm works for relatively large d in practical (quadratic) time and can be used to derive many properties of uniform random regular graphs. In this paper we establish a substantially improved lower bound on the k-color ability threshold of the random graph G(n, m) with n vertices and m edges. The new lower bound is ≈ 1.39 less than the 2k ln (k)-ln (k) first-moment upper bound (and approximately 0.39 less than the 2k ln (k) - ln(k) - 1 physics conjecture). By comparison, the best previous bounds left a gap of about 2+ln(k), unbounded in terms of the number of colors [Achlioptas, Naor: STOC 2004]. Furthermore, we prove that, in a precise sense, our lower bound marks the so-called condensation phase transition predicted on the basis of physics arguments [: PNAS 2007]. Our proof technique is a novel approach to the second moment method, inspired by physics conjectures on the geometry of the set of k-colorings of the random graph. We initiate the probabilistic analysis of linear programming (LP) decoding of low-density parity-check (LDPC) codes. Specifically, we show that for a random LDPC code ensemble, the linear programming decoder of Feldman succeeds in correcting a constant fraction of errors with high probability. The fraction of correctable errors guaranteed by our analysis surpasses previous nonasymptotic results for LDPC codes, and in particular, exceeds the best previous finite-length result on LP decoding by a factor greater than ten. This improvement stems in part from our analysis of probabilistic bit-flipping channels, as opposed to adversarial channels. At the core of our analysis is a novel combinatorial characterization of LP decoding success, based on the notion of a flow on the Tanner graph of the code. An interesting by-product of our analysis is to establish the existence of ldquoprobabilistic expansionrdquo in random bipartite graphs, in which one requires only that almost every (as opposed to every) set of a certain size expands, for sets much larger than in the classical worst case setting. Random graphs with a given degree sequence are a useful model capturing several features absent in the classical Erd˝os-Renyi model, such as dependent edges and non-binomial degrees. In this paper, we use a characterization due to Erd˝os and Gallai to develop a sequential algorithm for generating a random labeled graph with a given degree sequence. The algorithm is easy to implement and allows surprisingly ecient sequential importance sampling. Applications are given, in- cluding simulating a biological network and estimating the number of graphs with a given degree sequence. 1. Introduction. Random graphs with given vertex degrees have recently attracted great interest as a model for many real-world complex networks, including the World Wide Web, peer-to-peer networks, social networks, and biological networks. Newman (58) contains an excellent survey of these networks, with extensive references. A common approach to simulating these systems is to study (empirically or theoretically) the degrees of the vertices in instances of the network, and then to generate a random graph with the appropriate degrees. Graphs with prescribed degrees also appear in random matrix theory and string theory, which can call for large simulations based on random k-regular graphs. Throughout, we are concerned with generating simple graphs, i.e., no loops or multiple edges are allowed (the problem becomes considerably easier if loops and multiple edges are allowed). The main result of this paper is a new sequential importance sampling algorithm for generating random graphs with a given degree sequence. The idea is to build up the graph sequentially, at each stage choosing an edge from a list of candidates with probability proportional to the degrees. Most previously studied algorithms for this problem sometimes either get stuck or produce loops or multiple edges in the output, which is handled by starting over and trying again. Often for such algorithms, the probability of a restart being needed on a trial rapidly approaches 1 as the degree parameters grow, resulting in an enormous number of trials being needed on average to obtain a simple graph. A major advantage of our algorithm is that it never gets stuck. This is achieved using the Erd˝os- Gallai characterization, which is explained in Section 2, and a carefully chosen order of edge selection. Abstract The paper studies effective approximate solutions to combinatorial counting and unform generation problems. Using a technique based on the simulation of ergodic Markov chains, it is shown that, for self-reducible structures, almost uniform generation is possible in polynomial time provided only that randomised approximate counting to within some arbitrary polynomial factor is possible in polynomial time. It follows that, for self-reducible structures, polynomial time randomised algorithms for counting to within factors of the form (1 + n − β ) are available either for all β ϵ R or for no β ϵ R . A substantial part of the paper is devoted to investigating the rate of convergence of finite ergodic Markov chains, and a simple but powerful characterisation of rapid convergence for a broad class of chains based on a structural property of the underlying graph is established. Finally, the general techniques of the paper are used to derive an almost uniform generation procedure for labelled graphs with a given degree sequence which is valid over a much wider range of degrees than previous methods: this in turn leads to randomised approximate counting algorithms for these graphs with very good asymptotic behaviour. Starting around the late 1950s, several research communities began relating the geometry of graphs to stochastic processes on these graphs. This book, twenty years in the making, ties together research in the field, encompassing work on percolation, isoperimetric inequalities, eigenvalues, transition probabilities, and random walks. Written by two leading researchers, the text emphasizes intuition, while giving complete proofs and more than 850 exercises. Many recent developments, in which the authors have played a leading role, are discussed, including percolation on trees and Cayley graphs, uniform spanning forests, the mass-transport technique, and connections on random walks on graphs to embedding in Hilbert space. This state-of-the-art account of probability on networks will be indispensable for graduate students and researchers alike. Let G be a fixed connected multigraph with no loops. A random n-lift of G is obtained by replacing each vertex of G by a set of n vertices (where these sets are pairwise disjoint) and replacing each edge by a randomly chosen perfect matching between the n-sets corresponding to the endpoints of the edge. Let XG be the number of perfect matchings in a random lift of G. We study the distribution of XG in the limit as n tends to infinity, using the small subgraph conditioning method. We present several results including an asymptotic formula for the expectation of XG when G is d-regular, d ≥ 3. The interaction of perfect matchings with short cycles in random lifts of regular multigraphs is also analysed. Partial calculations are performed for the second moment of XG, with full details given for two example multigraphs, including the complete graph K4. To assist in our calculations we provide a theorem for estimating a summation over multiple dimensions using Laplace's method. This result is phrased as a summation over lattice points, and may prove useful in future applications. We consider the following probabilistic model of a graph on n labeled vertices. First choose a random graph G(n, 1 2), and then choose randomly a subset Q of vertices of size k and force it to be a clique by joining every pair of vertices of Q by an edge. The problem is to give a polynomial time algorithm for finding this hidden clique almost surely for various values of k. This question was posed independently, in various variants, by Jerrum and by Kucera. In this paper we present an efficient algorithm for all k>cn0.5, for any fixed c>0, thus improving the trivial case k>cn0.5(log n)0.5. The algorithm is based on the spectral properties of the graph. © 1998 John Wiley & Sons, Inc. Random Struct. Alg., 13: 457–466, 1998