Related papers: Sorting Genomes by Prefix Double-Cut-and-Joins
Highly-concurrent system models with vast state spaces like Chemical Reaction Networks (CRNs) that model biological and chemical systems pose a formidable challenge to cutting-edge formal analysis tools. Although many symbolic approaches…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Pancake flipping, a famous open problem in computer science, can be formalised as the problem of sorting a permutation of positive integers using as few prefix reversals as possible. In that context, a prefix reversal of length k reverses…
We consider the following problem: Given an undirected (mixed) network and a set of ordered source-target, or cause-effect pairs, direct all edges so as to maximize the number of pairs that admit a directed source-target path. This is…
Ranking bit patterns -- finding the index of a given pattern in an ordered sequence -- is a major bottleneck scaling up numerical quantum many-body calculations, as fermionic and hard-core bosonic states translate naturally to bit patterns.…
In this thesis, we present fast deterministic algorithm to find small cuts in distributed networks. Finding small min-cuts for a network is essential for ensuring the quality of service and reliability. Throughout this thesis, we use the…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while…
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…
Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of 'linked selection' on levels of genetic diversity is key to making reliable inference about demography, building a null model in…
Subgraph matching is a fundamental problem in graph analysis with a wide range of applications. However, due to its inherent NP-hardness, enumerating subgraph matches efficiently on large real-world graphs remains highly challenging. Most…
We study permutations over the set of $\ell$-grams, that are feasible in the sense that there is a sequence whose $\ell$-gram frequency has the same ranking as the permutation. Codes, which are sets of feasible permutations, protect…
In this paper, a genetic algorithm, one of the evolutionary algorithms optimization methods, is used for the first time for the problem of finding extremal binary self-dual codes. We present a comparison of the computational times between a…
A tandem duplication denotes the process of inserting a copy of a segment of DNA adjacent to its original position. More formally, a tandem duplication can be thought of as an operation that converts a string $S = AXB$ into a string $T =…
Deep neural networks (DNNs) are nowadays witnessing a major success in solving many pattern recognition tasks including skeleton-based classification. The deployment of DNNs on edge-devices, endowed with limited time and memory resources,…
In this thesis we propose new methods for crossover operator namely: cut on worst gene (COWGC), cut on worst L+R gene (COWLRGC) and Collision Crossovers. And also we propose several types of mutation operator such as: worst gene with random…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
This article introduces a new DNA sequence compression algorithm which is based on LUT and LZ77 algorithm. Combined a LUT-based pre-coding routine and LZ77 compression routine,this algorithm can approach a compression ratio of 1.9bits…
An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable…