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Sequence classification algorithms, such as SVM, require a definition of distance (similarity) measure between two sequences. A commonly used notion of similarity is the number of matches between $k$-mers ($k$-length subsequences) in the…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
This paper shows that a simple algorithm produces the {\em all-prefixes-LCSs-graph} in $O(mn)$ time for two input sequences of size $m$ and $n$. Given any prefix $p$ of the first input sequence and any prefix $q$ of the second input…
The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the…
We study the random-link matching problem on random regular graphs, alongside with two relaxed versions of the problem, namely the fractional matching and the so-called "loopy" fractional matching. We estimated the asymptotic average…
In this paper, we consider the ``Shortest Superstring Problem''(SSP) or the ``Shortest Common Superstring Problem''(SCS). The problem is as follows. For a positive integer $n$, a sequence of n strings $S=(s^1,\dots,s^n)$ is given. We should…
Stochastic search algorithms are among the most sucessful approaches for solving hard combinatorial problems. A large class of stochastic search approaches can be cast into the framework of Las Vegas Algorithms (LVAs). As the run-time…
The convolution between a text string $S$ of length $N$ and a pattern string $P$ of length $m$ can be computed in $O(N \log m)$ time by FFT. It is known that various types of approximate string matching problems are reducible to…
The Shortest Superstring Problem (SSP) consists, for a set of strings S = {s_1,...,s_n}, to find a minimum length string that contains all s_i, 1 <= i <= k, as substrings. This problem is proved to be NP-Complete and APX-hard. Guaranteed…
The skew of a binary string is the difference between the number of zeroes and the number of ones, while the length of the string is the sum of these two numbers. We consider certain suffixes of the lexicographically-least de Bruijn…
Chromy (1979) proposed a unequal probability sampling algorithm, which enables to select a sample in one pass of the sampling frame only. This is the default sequential method used in the SURVEYSELECT procedure of the SAS software. In this…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
Random $k$-SAT is the single most intensely studied example of a random constraint satisfaction problem. But despite substantial progress over the past decade, the threshold for the existence of satisfying assignments is not known precisely…
Random linear codes (RLCs) are well known to have nice combinatorial properties and near-optimal parameters in many different settings. However, getting explicit constructions matching the parameters of RLCs is challenging, and RLCs are…
In the Dictionary-based String Matching (DSM) problem, a retrieval system has access to a source sequence and stores the position of a certain number of strings in a posting table. When a user inquires the position of a string, the…
The Random Sequential Adsorption (RSA) problem holds crucial theoretical and practical significance, serving as a pivotal framework for understanding and optimizing particle packing in various scientific and technological applications. Here…
A classical limit theorem of stochastic process theory concerns the sample cumulative distribution function (CDF) from independent random variables. If the variables are uniformly distributed then these centered CDFs converge in a suitable…
This article considers stochastic algorithms for efficiently solving a class of large scale non-linear least squares (NLS) problems which frequently arise in applications. We propose eight variants of a practical randomized algorithm where…
The article starts with generalizations of some classical results and new truncation error upper bounds in the sampling theorem for bandlimited stochastic processes. Then, it investigates $L_p([0,T])$ and uniform approximations of…