Badding Practise in Cennerfield?

Many years ago I heard a recorded lecture entitled Good Speech. I have forgotten the advice it contained, but if that speaker were here today I think he would have to start all over again. I think he would suggest a new approach to vowel sounds. A, E, I, O, U are our written vowels, but our sounding vowels are thirteen in number, and are used in this sentence

Uniqueness thresholds on trees versus graphs

Counter to the general notion that the regular tree is the worst case for decay of correlation between sets and nodes, we produce an example of a multi-spin interacting system which has uniqueness on the $d$-regular tree but does not have uniqueness on some infinite $d$-regular graphs.Comment: Published in at http://dx.doi.org/10.1214/07-AAP508 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

Rapid Mixing of Gibbs Sampling on Graphs that are Sparse on Average

In this work we show that for every $d < \infty$ and the Ising model defined on $G(n,d/n)$, there exists a $\beta_d > 0$, such that for all $\beta < \beta_d$ with probability going to 1 as $n \to \infty$, the mixing time of the dynamics on $G(n,d/n)$ is polynomial in $n$. Our results are the first polynomial time mixing results proven for a natural model on $G(n,d/n)$ for $d > 1$ where the parameters of the model do not depend on $n$. They also provide a rare example where one can prove a polynomial time mixing of Gibbs sampler in a situation where the actual mixing time is slower than n \polylog(n). Our proof exploits in novel ways the local treelike structure of Erd\H{o}s-R\'enyi random graphs, comparison and block dynamics arguments and a recent result of Weitz. Our results extend to much more general families of graphs which are sparse in some average sense and to much more general interactions. In particular, they apply to any graph for which every vertex $v$ of the graph has a neighborhood $N(v)$ of radius $O(\log n)$ in which the induced sub-graph is a tree union at most $O(\log n)$ edges and where for each simple path in $N(v)$ the sum of the vertex degrees along the path is $O(\log n)$. Moreover, our result apply also in the case of arbitrary external fields and provide the first FPRAS for sampling the Ising distribution in this case. We finally present a non Markov Chain algorithm for sampling the distribution which is effective for a wider range of parameters. In particular, for $G(n,d/n)$ it applies for all external fields and $\beta < \beta_d$, where $d \tanh(\beta_d) = 1$ is the critical point for decay of correlation for the Ising model on $G(n,d/n)$.Comment: Corrected proof of Lemma 2.

Universality of cutoff for the Ising model

On any locally-finite geometry, the stochastic Ising model is known to be contractive when the inverse-temperature $\beta$ is small enough, via classical results of Dobrushin and of Holley in the 1970's. By a general principle proposed by Peres, the dynamics is then expected to exhibit cutoff. However, so far cutoff for the Ising model has been confirmed mainly for lattices, heavily relying on amenability and log Sobolev inequalities. Without these, cutoff was unknown at any fixed $\beta>0$, no matter how small, even in basic examples such as the Ising model on a binary tree or a random regular graph. We use the new framework of information percolation to show that, in any geometry, there is cutoff for the Ising model at high enough temperatures. Precisely, on any sequence of graphs with maximum degree $d$, the Ising model has cutoff provided that $\beta<\kappa/d$ for some absolute constant $\kappa$ (a result which, up to the value of $\kappa$, is best possible). Moreover, the cutoff location is established as the time at which the sum of squared magnetizations drops to 1, and the cutoff window is $O(1)$, just as when $\beta=0$. Finally, the mixing time from almost every initial state is not more than a factor of $1+\epsilon_\beta$ faster then the worst one (with $\epsilon_\beta\to0$ as $\beta\to 0$), whereas the uniform starting state is at least $2-\epsilon_\beta$ times faster.Comment: 26 pages, 2 figures. Companion paper to arXiv:1401.606

Phase transition in the sample complexity of likelihood-based phylogeny inference

Reconstructing evolutionary trees from molecular sequence data is a fundamental problem in computational biology. Stochastic models of sequence evolution are closely related to spin systems that have been extensively studied in statistical physics and that connection has led to important insights on the theoretical properties of phylogenetic reconstruction algorithms as well as the development of new inference methods. Here, we study maximum likelihood, a classical statistical technique which is perhaps the most widely used in phylogenetic practice because of its superior empirical accuracy. At the theoretical level, except for its consistency, that is, the guarantee of eventual correct reconstruction as the size of the input data grows, much remains to be understood about the statistical properties of maximum likelihood in this context. In particular, the best bounds on the sample complexity or sequence-length requirement of maximum likelihood, that is, the amount of data required for correct reconstruction, are exponential in the number, $n$, of tips---far from known lower bounds based on information-theoretic arguments. Here we close the gap by proving a new upper bound on the sequence-length requirement of maximum likelihood that matches up to constants the known lower bound for some standard models of evolution. More specifically, for the $r$-state symmetric model of sequence evolution on a binary phylogeny with bounded edge lengths, we show that the sequence-length requirement behaves logarithmically in $n$ when the expected amount of mutation per edge is below what is known as the Kesten-Stigum threshold. In general, the sequence-length requirement is polynomial in $n$. Our results imply moreover that the maximum likelihood estimator can be computed efficiently on randomly generated data provided sequences are as above.Comment: To appear in Probability Theory and Related Field