Related papers: Deterministic Polynomial-Time Algorithms for Desig…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
Huffman coding finds an optimal prefix code for a given probability mass function. Consider situations in which one wishes to find an optimal code with the restriction that all codewords have lengths that lie in a user-specified set of…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
This paper presents a model-based, unsupervised algorithm for recovering word boundaries in a natural-language text from which they have been deleted. The algorithm is derived from a probability model of the source that generated the text.…
We present two variations of Duval's algorithm for computing the Lyndon factorization of a word. The first algorithm is designed for the case of small alphabets and is able to skip a significant portion of the characters of the string, for…
We study the amount of reliable information that can be stored in a DNA-based storage system composed of short DNA molecules. In this regime, Shomorony and Heckel (2022) put forward a conjecture on the scaling of the number of information…
We give a deterministic, polynomial-time algorithm for approximately counting the number of {0,1}-solutions to any instance of the knapsack problem. On an instance of length n with total weight W and accuracy parameter eps, our algorithm…
Given a satisfiable 3-SAT formula, how hard is it to find an assignment to the variables that has Hamming distance at most n/2 to a satisfying assignment? More generally, consider any polynomial-time verifier for any NP-complete language. A…
The picture-hanging puzzle, popularized by Demaine et al. (2014), asks for a way to wrap a wire around $n$ nails such that the picture hangs as long as fewer than $k$ nails are removed, but falls as soon as any $k$ are removed. Solutions…
The problem of k-minimisation for a DFA M is the computation of a smallest DFA N (where the size |M| of a DFA M is the size of the domain of the transition function) such that their recognized languages differ only on words of length less…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
An elastic-degenerate (ED) string is a sequence of $n$ sets of strings of total length $N$, which was recently proposed to model a set of similar sequences. The ED string matching (EDSM) problem is to find all occurrences of a pattern of…
Let $g: \{-1,1\}^k \to \{-1,1\}$ be any Boolean function and $q_1,\dots,q_k$ be any degree-2 polynomials over $\{-1,1\}^n.$ We give a \emph{deterministic} algorithm which, given as input explicit descriptions of $g,q_1,\dots,q_k$ and an…
We give a new general approach for designing exact exponential-time algorithms for subset problems. In a subset problem the input implicitly describes a family of sets over a universe of size n and the task is to determine whether the…
Many problems are NP-hard and, unless P = NP, do not admit polynomial-time exact algorithms. The fastest known exact algorithms exactly usually take time exponential in the input size. Much research effort has gone into obtaining faster…
In this paper, we study arbitrary regular factorial languages over a finite alphabet $\Sigma$. For the set of words $L(n)$ of the length $n$ belonging to a regular factorial language $L$, we investigate the depth of decision trees solving…
In this paper we study the problem of deterministic factorization of sparse polynomials. We show that if $f \in \mathbb{F}[x_{1},x_{2},\ldots ,x_{n}]$ is a polynomial with $s$ monomials, with individual degrees of its variables bounded by…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
A decision problem is called parameterized if its input is a pair of strings. One of these strings is referred to as a parameter. The problem: given a propositional logic program P and a non-negative integer k, decide whether P has a stable…
Over the past 30 years numerous algorithms have been designed for symmetry breaking problems in the LOCAL model, such as maximal matching, MIS, vertex coloring, and edge-coloring. For most problems the best randomized algorithm is at least…