Related papers: Upper Bounds to Genome Rearrangement Problem using…
A distributed computing system is a collection of processors that communicate either by reading and writing from a shared memory or by sending messages over some communication network. Most prior biologically inspired distributed computing…
On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…
Combinatorial designs provide an interesting source of optimization problems. Among them, permutation codes are particularly interesting given their applications in powerline communications, flash memories, and block ciphers. This paper…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
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…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
We define a new problem in comparative genomics, denoted PQ-Tree Search, that takes as input a PQ-tree $T$ representing the known gene orders of a gene cluster of interest, a gene-to-gene substitution scoring function $h$, integer…
This paper investigates the influence of genotype size on evolutionary algorithms' performance. We consider genotype compression (where genotype is smaller than phenotype) and expansion (genotype is larger than phenotype) and define…
We introduce a framework for the design of finite element methods for two-dimensional moving boundary problems with prescribed boundary evolution that have arbitrarily high order of accuracy, both in space and in time. At the core of our…
Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to…
Thresholding--the pruning of nodes or edges based on their properties or weights--is an essential preprocessing tool for extracting interpretable structure from complex network data, yet existing methods face several key limitations.…
We consider the problem of factoring permutations as a product of special types of transpositions, namely, those transpositions involving two positions with bounded distances. In particular, we investigate the minimum number, $\delta$, such…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Preference learning in Large Language Models (LLMs) has advanced significantly, yet existing methods remain limited by modest performance gains, high computational costs, hyperparameter sensitivity, and insufficient modeling of global…
A permutation on an alphabet $ \Sigma $, is a sequence where every element in $ \Sigma $ occurs precisely once. Given a permutation $ \pi $= ($\pi_{1} $, $ \pi_{2} $, $ \pi_{3} $,....., $ \pi_{n} $) over the alphabet $ \Sigma $ =$\{ $0, 1,…
Optimization problems consist of either maximizing or minimizing an objective function. Instead of looking for a maximum solution (resp. minimum solution), one can find a minimum maximal solution (resp. maximum minimal solution). Such…
The first step in any genome assembly algorithm entails the conversion from the domain of strings and overlaps to the language of graphs and paths, typically using one of the two conventional methods: de Bruijn graphs or overlap graphs.…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…