A Proof of Entropy Minimization for Outputs in Deletion Channels via Hidden Word Statistics

From the output produced by a memoryless deletion channel from a uniformly random input of known length $n$, one obtains a posterior distribution on the channel input. The difference between the Shannon entropy of this distribution and that of the uniform prior measures the amount of information about the channel input which is conveyed by the output of length $m$, and it is natural to ask for which outputs this is extremized. This question was posed in a previous work, where it was conjectured on the basis of experimental data that the entropy of the posterior is minimized and maximized by the constant strings $\texttt{000}\ldots$ and $\texttt{111}\ldots$ and the alternating strings $\texttt{0101}\ldots$ and $\texttt{1010}\ldots$ respectively. In the present work we confirm the minimization conjecture in the asymptotic limit using results from hidden word statistics. We show how the analytic-combinatorial methods of Flajolet, Szpankowski and Vall\'ee for dealing with the hidden pattern matching problem can be applied to resolve the case of fixed output length and $n\rightarrow\infty$, by obtaining estimates for the entropy in terms of the moments of the posterior distribution and establishing its minimization via a measure of autocorrelation.Comment: 11 pages, 2 figure

Matrix models and stochastic growth in Donaldson-Thomas theory

We show that the partition functions which enumerate Donaldson-Thomas invariants of local toric Calabi-Yau threefolds without compact divisors can be expressed in terms of specializations of the Schur measure. We also discuss the relevance of the Hall-Littlewood and Jack measures in the context of BPS state counting and study the partition functions at arbitrary points of the Kaehler moduli space. This rewriting in terms of symmetric functions leads to a unitary one-matrix model representation for Donaldson-Thomas theory. We describe explicitly how this result is related to the unitary matrix model description of Chern-Simons gauge theory. This representation is used to show that the generating functions for Donaldson-Thomas invariants are related to tau-functions of the integrable Toda and Toeplitz lattice hierarchies. The matrix model also leads to an interpretation of Donaldson-Thomas theory in terms of non-intersecting paths in the lock-step model of vicious walkers. We further show that these generating functions can be interpreted as normalization constants of a corner growth/last-passage stochastic model.Comment: 31 pages; v2: comments and references added; v3: presentation improved, comments added; final version to appear in Journal of Mathematical Physic

The Optimisation of Stochastic Grammars to Enable Cost-Effective Probabilistic Structural Testing

The effectiveness of probabilistic structural testing depends on the characteristics of the probability distribution from which test inputs are sampled at random. Metaheuristic search has been shown to be a practical method of optimis- ing the characteristics of such distributions. However, the applicability of the existing search-based algorithm is lim- ited by the requirement that the software’s inputs must be a fixed number of numeric values. In this paper we relax this limitation by means of a new representation for the probability distribution. The repre- sentation is based on stochastic context-free grammars but incorporates two novel extensions: conditional production weights and the aggregation of terminal symbols represent- ing numeric values. We demonstrate that an algorithm which combines the new representation with hill-climbing search is able to effi- ciently derive probability distributions suitable for testing software with structurally-complex input domains

Fractals from genomes: exact solutions of a biology-inspired problem

This is a review of a set of recent papers with some new data added. After a brief biological introduction a visualization scheme of the string composition of long DNA sequences, in particular, of bacterial complete genomes, will be described. This scheme leads to a class of self-similar and self-overlapping fractals in the limit of infinitely long constotuent strings. The calculation of their exact dimensions and the counting of true and redundant avoided strings at different string lengths turn out to be one and the same problem. We give exact solution of the problem using two independent methods: the Goulden-Jackson cluster method in combinatorics and the method of formal language theory.Comment: 24 pages, LaTeX, 5 PostScript figures (two in color), psfi

Quenched Averages for self-avoiding walks and polygons on deterministic fractals

We study rooted self avoiding polygons and self avoiding walks on deterministic fractal lattices of finite ramification index. Different sites on such lattices are not equivalent, and the number of rooted open walks W_n(S), and rooted self-avoiding polygons P_n(S) of n steps depend on the root S. We use exact recursion equations on the fractal to determine the generating functions for P_n(S), and W_n(S) for an arbitrary point S on the lattice. These are used to compute the averages $, ,$ and $<log W_n(S)>$ over different positions of S. We find that the connectivity constant $\mu$, and the radius of gyration exponent $\nu$ are the same for the annealed and quenched averages. However, $~ n log \mu + (\alpha_q -2) log n$, and $~ n log \mu + (\gamma_q -1)log n$, where the exponents $\alpha_q$ and $\gamma_q$ take values different from the annealed case. These are expressed as the Lyapunov exponents of random product of finite-dimensional matrices. For the 3-simplex lattice, our numerical estimation gives $\alpha_q \simeq 0.72837 \pm 0.00001$; and $\gamma_q \simeq 1.37501 \pm 0.00003$, to be compared with the annealed values $\alpha_a = 0.73421$ and $\gamma_a = 1.37522$.Comment: 17 pages, 10 figures, submitted to Journal of Statistical Physic