Related papers: Deterministic Polynomial-Time Algorithms for Desig…
The Monotone Min-Plus Product problem is a useful primitive that has seen many algorithmic applications over the past decade. In this problem, we are given two $n\times n$ integer matrices $A$ and $B$, where each row of $B$ is a monotone…
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…
An absent word of a word y of length n is a word that does not occur in y. It is a minimal absent word if all its proper factors occur in y. Minimal absent words have been computed in genomes of organisms from all domains of life; their…
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…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
We give a simple combinatorial algorithm to deterministically approximately count the number of satisfying assignments of general constraint satisfaction problems (CSPs). Suppose that the CSP has domain size $q=O(1)$, each constraint…
We give a {\em deterministic} algorithm for approximately computing the fraction of Boolean assignments that satisfy a degree-$2$ polynomial threshold function. Given a degree-2 input polynomial $p(x_1,\dots,x_n)$ and a parameter $\eps >…
Locally Decodable Codes (LDCs) are error-correcting codes $C\colon\Sigma^n\rightarrow \Sigma^m,$ encoding \emph{messages} in $\Sigma^n$ to \emph{codewords} in $\Sigma^m$, with super-fast decoding algorithms. They are important mathematical…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
In this paper, a genetic algorithm, one of the evolutionary algorithms optimization methods, is used for the first time for the problem of finding extremal binary self-dual codes. We present a comparison of the computational times between a…
Given a signed permutation on $n$ elements, we need to sort it with the fewest reversals. This is a fundamental algorithmic problem motivated by applications in comparative genomics, as it allows to accurately model rearrangements in small…
We present $O(m^3)$ algorithms for specifying the support of minimum-weight words of extended binary BCH codes of length $n=2^m$ and designed distance $d(m,s,i):=2^{m-1-s}-2^{m-1-i-s}$ for some values of $m,i,s$, where $m$ may grow to…
A new method for constructing minimum-redundancy binary prefix codes is described. Our method does not explicitly build a Huffman tree; instead it uses a property of optimal prefix codes to compute the codeword lengths corresponding to the…
Twins in a finite word are formed by a pair of identical subwords placed at disjoint sets of positions. We investigate the maximum length of twins in a random word over a $k$-letter alphabet. The obtained lower bounds for small values of…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
The evaluation of the minimum distance of linear block codes remains an open problem in coding theory, and it is not easy to determine its true value by classical methods, for this reason the problem has been solved in the literature with…
In 1996, Karger [Kar96] gave a startling randomized algorithm that finds a minimum-cut in a (weighted) graph in time $O(m\log^3n)$ which he termed near-linear time meaning linear (in the size of the input) times a polylogarthmic factor. In…
In this paper, we introduce the problem of rewriting finite formal languages using syntactic macros such that the rewriting is minimal in size. We present polynomial-time algorithms to solve variants of this problem and show their…
We describe a deterministic algorithm that computes an approximate root of n complex polynomial equations in n unknowns in average polynomial time with respect to the size of the input, in the Blum-Shub-Smale model with square root. It…