Related papers: Upper Bounds to Genome Rearrangement Problem using…
In this paper we study the adaptive prefix coding problem in cases where the size of the input alphabet is large. We present an online prefix coding algorithm that uses $O(\sigma^{1 / \lambda + \epsilon}) $ bits of space for any constants…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
We present a new method for proving lower bounds on the expected running time of evolutionary algorithms. It is based on fitness-level partitions and an additional condition on transition probabilities between fitness levels. The method is…
We address the problem of reasoning on graph transformations featuring actions such as \emph{addition} and \emph{deletion} of nodes and edges, node \emph{merging} and \emph{cloning}, node or edge \emph{labelling} and edge…
Genetic programming (GP) is an evolutionary computation technique to solve problems in an automated, domain-independent way. Rather than identifying the optimum of a function as in more traditional evolutionary optimization, the aim of GP…
A permutation array $A$ is a set of permutations on a finite set $\Omega$, say of size $n$. Given distinct permutations $\pi, \sigma\in \Omega$, we let $hd(\pi, \sigma) = |\{ x\in \Omega: \pi(x) \ne \sigma(x) \}|$, called the Hamming…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
A permutation $\pi$ over alphabet $\Sigma = {1,2,3,\ldots,n}$, is a sequence where every element $x$ in $\Sigma$ occurs exactly once. $S_n$ is the symmetric group consisting of all permutations of length $n$ defined over $\Sigma$. $I_n$ =…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Explaining to what extent the real power of genetic algorithms lies in the ability of crossover to recombine individuals into higher quality solutions is an important problem in evolutionary computation. In this paper we show how the…
We study the combination of two recent coding approaches, in the context of DNA based data storage. Composite DNA alphabets leverage properties of the DNA synthesis and sequencing process. A composite symbol does not represent a single…
This work discusses single-objective constrained genetic algorithm with floating-point, integer, binary and permutation representation. Floating-point genetic algorithm tuning with use of test functions is done and leads to a…
A heapable sequence is a sequence of numbers that can be arranged in a "min-heap data structure". Finding a longest heapable subsequence of a given sequence was proposed by Byers, Heeringa, Mitzenmacher, and Zervas (ANALCO 2011) as a…
We describe a new algorithm, termed subspace evolution and transfer (SET), for solving low-rank matrix completion problems. The algorithm takes as its input a subset of entries of a low-rank matrix, and outputs one low-rank matrix…
The all-pairs shortest path problem is the first non-artificial problem for which it was shown that adding crossover can significantly speed up a mutation-only evolutionary algorithm. Recently, the analysis of this algorithm was refined and…
Despite the impressive growth of the abilities of multilingual language models, such as XLM-R and mT5, it has been shown that they still face difficulties when tackling typologically-distant languages, particularly in the low-resource…
This paper studies the underlying combinatorial structure of a class of object rearrangement problems, which appear frequently in applications. The problems involve multiple, similar-geometry objects placed on a flat, horizontal surface,…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
An algorithm is presented for unranking permutations in transposition order: Given a seed s\in N, the algorithm produces a permutation P(s) that differs from the permutation P(s+1) by the transposition of two elements.
We study sorting by queues that can rearrange their content by applying permutations from a predefined set. These new sorting devices are called shuffle queues and we investigate those of them corresponding to sets of permutations defining…