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Register a new userFast mixing of a randomized shift-register Markov chain
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We present a Markov chain on the $n$-dimensional hypercube ${0,1}^n$ which satisfies $t_{{rm mix}}(epsilon) = n[1 + o(1)]$. This Markov chain alternates between random and deterministic moves and we prove that the chain has cut-off with a window of size at most $O(n^{0.5+delta})$ where $delta>0$. The deterministic moves correspond to a linear shift register.
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In network modeling of complex systems one is often required to sample random realizations of networks that obey a given set of constraints, usually in form of graph measures. A much studied class of problems targets uniform sampling of simple graphs with given degree sequence or also with given degree correlations expressed in the form of a joint degree matrix. One approach is to use Markov chains based on edge switches (swaps) that preserve the constraints, are irreducible (ergodic) and fast mixing. In 1999, Kannan, Tetali and Vempala (KTV) proposed a simple swap Markov chain for sampling graphs with given degree sequence and conjectured that it mixes rapidly (in poly-time) for arbitrary degree sequences. While the conjecture is still open, it was proven for special degree sequences, in particular, for those of undirected and directed regular simple graphs, of half-regular bipartite graphs, and of graphs with certain bounded maximum degrees. Here we prove the fast mixing KTV conjecture for novel, exponentially large classes of irregular degree sequences. Our method is based on a canonical decomposition of degree sequences into split graph degree sequences, a structural theorem for the space of graph realizations and on a factorization theorem for Markov chains. After introducing bipartite splitted degree sequences, we also generalize the canonical split graph decomposition for bipartite and directed graphs.
RNA motifs typically consist of short, modular patterns that include base pairs formed within and between modules. Estimating the abundance of these patterns is of fundamental importance for assessing the statistical significance of matches in genomewide searches, and for predicting whether a given function has evolved many times in different species or arose from a single common ancestor. In this manuscript, we review in an integrated and self-contained manner some basic concepts of automata theory, generating functions and transfer matrix methods that are relevant to pattern analysis in biological sequences. We formalize, in a general framework, the concept of Markov chain embedding to analyze patterns in random strings produced by a memoryless source. This conceptualization, together with the capability of automata to recognize complicated patterns, allows a systematic analysis of problems related to the occurrence and frequency of patterns in random strings. The applications we present focus on the concept of synchronization of automata, as well as automata used to search for a finite number of keywords (including sets of patterns generated according to base pairing rules) in a general text.
A joint degree matrix (JDM) specifies the number of connections between nodes of given degrees in a graph, for all degree pairs and uniquely determines the degree sequence of the graph. We consider the space of all balanced realizations of an arbitrary JDM, realizations in which the links between any two degree groups are placed as uniformly as possible. We prove that a swap Markov Chain Monte Carlo (MCMC) algorithm in the space of all balanced realizations of an {em arbitrary} graphical JDM mixes rapidly, i.e., the relaxation time of the chain is bounded from above by a polynomial in the number of nodes $n$. To prove fast mixing, we first prove a general factorization theorem similar to the Martin-Randall method for disjoint decompositions (partitions). This theorem can be used to bound from below the spectral gap with the help of fast mixing subchains within every partition and a bound on an auxiliary Markov chain between the partitions. Our proof of the general factorization theorem is direct and uses conductance based methods (Cheeger inequality).
We consider a Markov chain that iteratively generates a sequence of random finite words in such a way that the $n^{mathrm{th}}$ word is uniformly distributed over the set of words of length $2n$ in which $n$ letters are $a$ and $n$ letters are $b$: at each step an $a$ and a $b$ are shuffled in uniformly at random among the letters of the current word. We obtain a concrete characterization of the Doob-Martin boundary of this Markov chain. Writing $N(u)$ for the number of letters $a$ (equivalently, $b$) in the finite word $u$, we show that a sequence $(u_n)_{n in mathbb{N}}$ of finite words converges to a point in the boundary if, for an arbitrary word $v$, there is convergence as $n$ tends to infinity of the probability that the selection of $N(v)$ letters $a$ and $N(v)$ letters $b$ uniformly at random from $u_n$ and maintaining their relative order results in $v$. We exhibit a bijective correspondence between the points in the boundary and ergodic random total orders on the set ${a_1, b_1, a_2, b_2, ldots }$ that have distributions which are separately invariant under finite permutations of the indices of the $a$s and those of the $b$s. We establish a further bijective correspondence between the set of such random total orders and the set of pairs $(mu, u)$ of diffuse probability measures on $[0,1]$ such that $frac{1}{2}(mu+ u)$ is Lebesgue measure: the restriction of the random total order to ${a_1, b_1, ldots, a_n, b_n}$ is obtained by taking $X_1, ldots, X_n$ (resp. $Y_1, ldots, Y_n$) i.i.d. with common distribution $mu$ (resp. $ u$), letting $(Z_1, ldots, Z_{2n})$ be ${X_1, Y_1, ldots, X_n, Y_n}$ in increasing order, and declaring that the $k^{mathrm{th}}$ smallest element in the restricted total order is $a_i$ (resp. $b_j$) if $Z_k = X_i$ (resp. $Z_k = Y_j$).
We give qualitative and quantitative improvements to theorems which enable significance testing in Markov Chains, with a particular eye toward the goal of enabling strong, interpretable, and statistically rigorous claims of political gerrymandering. Our results can be used to demonstrate at a desired significance level that a given Markov Chain state (e.g., a districting) is extremely unusual (rather than just atypical) with respect to the fragility of its characteristics in the chain. We also provide theorems specialized to leverage quantitative improvements when there is a product structure in the underlying probability space, as can occur due to geographical constraints on districtings.
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