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This paper deals with a method for solving Poisson Equation (PE) based on genetic algorithms and grammatical evolution. The method forms generations of solutions expressed in an analytical form. Several examples of PE are tested and in most…
Scheduling problems are generally NP-hard combinatorial problems, and a lot of research has been done to solve these problems heuristically. However, most of the previous approaches are problem-specific and research into the development of…
In this note, we consider the problem of finding a step-by-step transformation between two longest increasing subsequences in a sequence, namely Longest Increasing Subsequence Reconfiguration. We give a polynomial-time algorithm for…
Background: Selecting feature genes to predict phenotypes is one of the typical tasks in analyzing genomics data. Though many general-purpose algorithms were developed for prediction, dealing with highly correlated genes in the prediction…
This thesis investigates the use of problem-specific knowledge to enhance a genetic algorithm approach to multiple-choice optimisation problems.It shows that such information can significantly enhance performance, but that the choice of…
We consider the longest common subsequence problem in the context of subsequences with gap constraints. In particular, following Day et al. 2022, we consider the setting when the distance (i. e., the gap) between two consecutive symbols of…
The genetic algorithm (GA) is an optimization and search technique based on the principles of genetics and natural selection. A GA allows a population composed of many individuals to evolve under specified selection rules to a state that…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
We study possible applications of artificial neural networks to examine the string landscape. Since the field of application is rather versatile, we propose to dynamically evolve these networks via genetic algorithms. This means that we…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
Bioinformatics, as an emerging and rapidly developing interdisciplinary, has become a promising and popular research field in 21st century. Extracting and explaining useful biological information from huge amount of genetic data is an…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
One of the main challenges in Computational Biology is to find the evolutionary distance between two organisms. In the field of comparative genomics, one way to estimate such distance is to find a minimum cost sequence of rearrangements…
Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
Distributions of triplets in some genetic sequences are examined and found to be well described by a 2-parameter Markov process with a sparse transition matrix. The variances of all the relevant parameters are not large, indicating that…
It is a well-known fact that genetic sequences may contain sections with repeated units, called repeats, that differ in length over a population, with a length distribution of geometric type. A simple class of recombination models with…
In this paper, we conduct theoretical analyses on inferring the structure of gene regulatory networks. Depending on the experimental method and data type, the inference problem is classified into 20 different scenarios. For each scenario,…
The present article is the first of a series whose goal is to define a logical formalism in which it is possible to reason about genetics. In this paper, we introduce the main concepts of our language whose domain of discourse consists of a…