Related papers: On the Variance of the Optimal Alignments Score fo…
The comparison of alternative rankings of a set of items is a general and prominent task in applied statistics. Predictor variables are ranked according to magnitude of association with an outcome, prediction models rank subjects according…
This study focuses on an alignment-free sequence comparison method: the number of words of length k shared between two sequences, also known as the D_2 statistic. The advantages of the use of this statistic over alignment-based methods are…
For words of length n, generated by independent geometric random variables, we consider the average value and the average position of the r-th left-to-right maximum counted from the right, for fixed r and n->oo. This complements previous…
In testing the independence of two Gaussian populations, one computes the distribution of the sample canonical correlation coefficients, given that the actual correlation is zero. The "Laplace transform" of this distribution is not only an…
We relate the computational complexity of finite strings to universal representations of their underlying symmetries. First, Boolean functions are classified using the universal covering topologies of the circuits which enumerate them. A…
Various approaches to alignment-free sequence comparison are based on the length of exact or inexact word matches between two input sequences. Haubold {\em et al.} (2009) showed how the average number of substitutions between two DNA…
We use some of the largest order statistics of the random projections of a reference signal to construct a binary embedding that is adapted to signals correlated with such signal. The embedding is characterized from the analytical…
Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…
Score matching is an estimation procedure that has been developed for statistical models whose probability density function is known up to proportionality but whose normalizing constant is intractable, so that maximum likelihood is…
A synchronizing word of a deterministic finite complete automaton is a word whose action maps every state to a single one. Finding a shortest or a short synchronizing word is a central computational problem in the theory of synchronizing…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…
More than 120 algorithms have been developed for exact string matching within the last 40 years. We show by experiments that the \naive{} algorithm exploiting SIMD instructions of modern CPUs (with symbols compared in a special order) is…
We investigate the weight distribution of random binary linear codes. For $0<\lambda<1$ and $n\to\infty$ pick uniformly at random $\lambda n$ vectors in $\mathbb{F}_2^n$ and let $C \le \mathbb{F}_2^n$ be the orthogonal complement of their…
A theory of systems with long-range correlations based on the consideration of binary N-step Markov chains is developed. In our model, the conditional probability that the i-th symbol in the chain equals zero (or unity) is a linear function…
Linearizing two partial orders to maximize the number of adjacencies and minimize the number of breakpoints is APX-hard. This holds even if one of the two partial orders is already a linear order and the other is an interval order, or if…
$V$-order is a global order on strings related to Unique Maximal Factorization Families (UMFFs), which are themselves generalizations of Lyndon words. $V$-order has recently been proposed as an alternative to lexicographical order in the…
We discuss a new stochastic ordering for the sequence of independent random variables. It generalizes the stochastic precedence order that is defined for two random variables to the case $n>2$. All conventional stochastic orders are…
A binary word is symmetric if it is a palindrome or an antipalindrome. We define a new measure of asymmetry of a binary word equal to the minimal number of letters of the word whose deleting from the word yields a symmetric word and obtain…
We study mixed long-range percolation on the square lattice. Each vertical edge of unit length is independently open with probability $\varepsilon$, and each horizontal edge of length $i$ is independently open with probability $p_i$. Also,…
We consider the problem of finding $A_2(n,\{d_1,d_2\})$ defined as the maximal size of a binary (non-linear) code of length $n$ with two distances $d_1$ and $d_2$. Binary codes with distances $d$ and $d+2$ of size…