Related papers: A Fixed-Parameter Algorithm for Minimum Common Str…
Computing an optimal chain of fragments is a classical problem in string algorithms, with important applications in computational biology. There exist two efficient dynamic programming algorithms solving this problem, based on different…
Divide and Conquer is a well known algorithmic procedure for solving many kinds of problem. In this procedure, the problem is partitioned into two parts until the problem is trivially solvable. Finding the distance of the closest pair is an…
This paper deals with the estimation of the modes of an univariate mixture when the number of components is known and when the component density are well separated. We propose an algorithm based on the minimization of the "kp" criterion we…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
Define a building blocks set to be a collection of n cubes (each with six sides) where each side is assigned one letter and one color from a palette of m colors. We propose a novel problem of assigning letters and colors to each face so as…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Longest Common Substring (LCS) is an important text processing problem, which has recently been investigated in the quantum query model. The decisional version of this problem, LCS with threshold $d$, asks whether two length-$n$ input…
In this paper, we extend the notion of gapped strings to elastic-degenerate strings. An elastic-degenerate string can been seen as an ordered collection of k > 1 seeds (substrings/subpatterns) interleaved by elastic-degenerate symbols such…
A balanced partition is a clustering of a graph into a given number of equal-sized parts. For instance, the Bisection problem asks to remove at most k edges in order to partition the vertices into two equal-sized parts. We prove that…
The study of genetic map linearization leads to a combinatorial hard problem, called the {\em minimum breakpoint linearization} (MBL) problem. It is aimed at finding a linearization of a partial order which attains the minimum breakpoint…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show…
State minimization of combinatorial filters is a fundamental problem that arises, for example, in building cheap, resource-efficient robots. But exact minimization is known to be NP-hard. This paper conducts a more nuanced analysis of this…
Given a set of numbers, the balanced partioning problem is to divide them into two subsets, so that the sum of the numbers in each subset are as nearly equal as possible, subject to the constraint that the cardinalities of the subsets be…
We consider running-time optimization for band-joins in a distributed system, e.g., the cloud. To balance load across worker machines, input has to be partitioned, which causes duplication. We explore how to resolve this tension between…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
We consider the following problem: for a given graph $G$ and two integers $k$ and $d$, can we apply a fixed graph operation at most $k$ times in order to reduce a given graph parameter $\pi$ by at least $d$? We show that this problem is…
Motivated by a historical combinatorial problem that resembles the well-known Josephus problem, we investigate circular partition algorithms and formulate problems in deterministic finite automata with practical algorithms. The historical…
Mixed-integer optimisation problems can be computationally challenging. Here, we introduce and analyse two efficient algorithms with a specific sequential design that are aimed at dealing with sampled problems within this class. At each…