Related papers: Switch chain mixing times through triangle counts
We introduce a Markov Chain Monte Carlo algorithm which samples from the space of spanning trees of complete graphs using local rewiring operations only. The probability distribution of graphs of this kind is shown to depend on the…
In statistical mechanical investigations on complex networks, it is useful to employ random graphs ensembles as null models, to compare with experimental realizations. Motivated by transcription networks, we present here a simple way to…
Random unimodular lattice triangulations have been recently used as an embedded random graph model, which exhibit a crossover behaviour between an ordered, large-world and a disordered, small-world behaviour. Using the ergodic Pachner flips…
The Curveball algorithm is a variation on well-known switch-based Markov chain approaches for uniformly sampling binary matrices with fixed row and column sums. Instead of a switch, the Curveball algorithm performs a so-called binomial…
Directed acyclic graphs are the basic representation of the structure underlying Bayesian networks, which represent multivariate probability distributions. In many practical applications, such as the reverse engineering of gene regulatory…
We investigate the mixing properties of a finite Markov chain in random environment defined as a mixture of a deterministic chain and a chain whose state space has been permuted uniformly at random. This work is the counterpart of a…
Full Bayesian computational inference for model determination in undirected graphical models is currently restricted to decomposable graphs, except for problems of very small scale. In this paper we develop new, more efficient methodology…
Establishing cutoff, an abrupt transition from "not mixed" to "well mixed", is a classical topic in the theory of mixing times for Markov chains. Interest has grown recently in determining not only the existence of cutoff and the order of…
In this paper we consider a simple Markov chain for bipartite graphs with given degree sequence on $n$ vertices. We show that the mixing time of this Markov chain is bounded above by a polynomial in $n$ in case of {\em semi-regular} degree…
Randomising networks using a naive `accept-all' edge-swap algorithm is generally biased. Building on recent results for nondirected graphs, we construct an ergodic detailed balance Markov chain with non-trivial acceptance probabilities for…
The configuration model generates random graphs with any given degree distribution, and thus serves as a null model for scale-free networks with power-law degrees and unbounded degree fluctuations. For this setting, we study the local…
We consider sampling and enumeration problems for Markov equivalence classes. We create and analyze a Markov chain for uniform random sampling on the DAGs inside a Markov equivalence class. Though the worst case is exponentially slow…
We introduce and study a class of exchangeable random graph ensembles. They can be used as statistical null models for empirical networks, and as a tool for theoretical investigations. We provide general theorems that carachterize the…
We analyze the properties of degree-preserving Markov chains based on elementary edge switchings in undirected and directed graphs. We give exact yet simple formulas for the mobility of a graph (the number of possible moves) in terms of its…
We study the problem of generating connected random graphs with no self-loops or multiple edges and that, in addition, have a given degree sequence. The generation method we focus on is the edge-switching Markov-chain method, whose…
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…
The standard coalescent is widely used in evolutionary biology and population genetics to model the ancestral history of a sample of molecular sequences as a rooted and ranked binary tree. In this paper, we present a representation of the…
Global variational approximation methods in graphical models allow efficient approximate inference of complex posterior distributions by using a simpler model. The choice of the approximating model determines a tradeoff between the…
We start by introducing avoidance coupling of Markov chains, with an overview of existing results. We then introduce and motivate a new notion, uniform avoidance coupling. We show that the only Markovian avoidance coupling on a cycle is of…
Consider a connected graph $G=(E,V)$ with $N=|V|$ vertices. The main purpose of this paper is to explore the question of uniform sampling of a subtree of $G$ with $n$ nodes, for some $n\leq N$ (the spanning tree case correspond to $n=N$,…