Related papers: Genetic algorithms with permutation-based represen…
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…
We propose an algorithm using the Gaussian elimination method to find the minimal Hamming distance and decode received messages of linear codes. This algorithm is easy to implement as it requires no Gr\"obner bases to compute solutions for…
The design of binary error-correcting codes is a challenging optimization problem with several applications in telecommunications and storage, which has also been addressed with metaheuristic techniques and evolutionary algorithms. Still,…
Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…
Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of…
We consider the problem of designing optimal linear codes (in terms of having the largest minimum distance) subject to a support constraint on the generator matrix. We show that the largest minimum distance can be achieved by a subcode of a…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
In this work we present a general and versatile algorithmic framework for exhaustively generating a large variety of different combinatorial objects, based on encoding them as permutations. This approach provides a unified view on many…
We construct new linear codes with high minimum distance d. In at least 12 cases these codes improve the minimum distance of the previously known best linear codes for fixed parameters n,k. Among these new codes there is an optimal ternary…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
We address the problem of computing distances between rankings that take into account similarities between candidates. The need for evaluating such distances is governed by applications as diverse as rank aggregation, bioinformatics, social…
In this paper we show the usability of the Gray code with constant weight words for computing linear combinations of codewords. This can lead to a big improvement of the computation time for finding the minimum distance of a code. We have…
Optimizing compilers, as well as other translator systems, often work by rewriting expressions according to equivalence preserving rules. Given an input expression and its optimized form, finding the sequence of rules that were applied is a…
A suitable choice of the representation of candidate solutions is crucial for the efficiency of evolutionary algorithms and related metaheuristics. We focus on problems in permutation spaces, which are at the core of numerous practical…
Error correction codes are an integral part of communication applications, boosting the reliability of transmission. The optimal decoding of transmitted codewords is the maximum likelihood rule, which is NP-hard due to the curse of…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
Permutation codes of length $n$ and distance $d$ is a set of permutations on $n$ symbols, where the distance between any two elements in the set is at least $d$. Subgroup permutation codes are permutation codes with the property that the…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…