Related papers: Upper Bounds to Genome Rearrangement Problem using…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
Superposition is an established decision procedure for a variety of first-order logic theories represented by sets of clauses. A satisfiable theory, saturated by superposition, implicitly defines a minimal term-generated model for the…
Cartesian Genetic Programming (CGP) suffers from a specific limitation: Positional bias, a phenomenon in which mostly genes at the start of the genome contribute to a program output, while genes at the end rarely do. This can lead to an…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
We investigate a family of $(\mu+\lambda)$ Genetic Algorithms (GAs) which creates offspring either from mutation or by recombining two randomly chosen parents. By scaling the crossover probability, we can thus interpolate from a fully…
Genetic programming is a powerful heuristic search technique that is used for a number of real world applications to solve among others regression, classification, and time-series forecasting problems. A lot of progress towards a theoretic…
The Genome Median Problem is an important problem in phylogenetic reconstruction under rearrangement models. It can be stated as follows: given three genomes, find a fourth that minimizes the sum of the pairwise rearrangement distances…
In the evolution of a genome, the gene sequence is sometimes rearranged, for example by transposition of two adjacent gene blocks. In biocombinatorics, one tries to reconstruct these rearrangement incidents from the resulting permutation.…
Given a permutation pi, the application of prefix reversal f^(i) to pi reverses the order of the first i elements of pi. The problem of Sorting By Prefix Reversals (also known as pancake flipping), made famous by Gates and Papadimitriou…
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…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
We use a method for determining the number of preimages of any permutation under the stack-sorting map in order to obtain recursive upper bounds for the numbers $W_t(n)$ and $W_t(n,k)$ of $t$-stack sortable permutations of length $n$ and…
Codes over permutations under the infinity norm have been recently suggested as a coding scheme for correcting limited-magnitude errors in the rank modulation scheme. Given such a code, we show that a simple relabeling operation, which…
Covering alignment problems arise from recent developments in genomics; so called pan-genome graphs are replacing reference genomes, and advances in haplotyping enable full content of diploid genomes to be used as basis of sequence…
We study a problem of best-effort adaptation motivated by several applications and considerations, which consists of determining an accurate predictor for a target domain, for which a moderate amount of labeled samples are available, while…
We consider rank modulation codes for flash memories that allow for handling arbitrary charge-drop errors. Unlike classical rank modulation codes used for correcting errors that manifest themselves as swaps of two adjacently ranked…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
This work studies rearrangement problems involving the sorting of robots or objects in stack-like containers, which can be accessed only from one side. Two scenarios are considered: one where every robot or object needs to reach a…
We design a heuristic method, a genetic algorithm, for the computation of an upper bound of the minimum distance of a linear code over a finite field. By the use of the row reduced echelon form, we obtain a permutation encoding of the…
Most of the attention in statistical compression is given to the space used by the compressed sequence, a problem completely solved with optimal prefix codes. However, in many applications, the storage space used to represent the prefix…