Related papers: Genetic algorithms with permutation-based represen…
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…
Multi-parameter persistent homology is a recent branch of topological data analysis. In this area, data sets are investigated through the lens of homology with respect to two or more scale parameters. The high computational cost of many…
In this paper the ensemble of codes formed by a serial concatenation of a repetition code with multiple accumulators connected through random interleavers is considered. Based on finite length weight enumerators for these codes, asymptotic…
Genetic algorithm (GA) is typically used to solve nonlinear model predictive control's optimization problem. However, the size of the search space in which the GA searches for the optimal control inputs is crucial for its applicability to…
We propose a novel scheme that allows MIMO system to modulate a set of permutation matrices to send more information bits, extending our initial work on the topic. This system is called Permutation Matrix Modulation (PMM). The basic idea is…
The paper deals with the problem of deciding if two finite-dimensional linear subspaces over an arbitrary field are identical up to a permutation of the coordinates. This problem is referred to as the permutation code equivalence. We show…
A Genome rearrangement problem studies large-scale mutations on a set of DNAs in living organisms. Various rearrangements like reversals, transpositions, translocations, fissions, fusions, and combinations and different variations have been…
Motivation The Burrows-Wheeler transform (BWT) is the foundation of many algorithms for compression and indexing of text data, but the cost of computing the BWT of very large string collections has prevented these techniques from being…
$\newcommand{\eps}{\varepsilon}$ In this paper, we consider two important problems defined on finite metric spaces, and provide efficient new algorithms and approximation schemes for these problems on inputs given as graph shortest path…
In this paper it is considered rule reduct generation problem, based on Rough Set Theory. Rule Reduct Generation (RG) and Modified Rule Generation (MRG) algorithms are well-known. Alternative to these algorithms Pruning Algorithm of…
Sampling a random permutation with restricted positions, or equivalently approximating the permanent of a 0-1 matrix, is a fundamental problem in computer science, with several notable results achieved over the years. However, existing…
Hashing methods aim to learn a set of hash functions which map the original features to compact binary codes with similarity preserving in the Hamming space. Hashing has proven a valuable tool for large-scale information retrieval. We…
Recent interest on permutation rank modulation shows the Kendall tau metric as an important distance metric. This note documents our first efforts to obtain upper bounds on optimal code sizes (for said metric) ala Delsarte's approach. For…
Dimensionality reduction (DR) is an important technique for data exploration and knowledge discovery. However, most of the main DR methods are either linear (e.g., PCA), do not provide an explicit mapping between the original data and its…
Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…
Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…
In this study, a new $\Delta$-evaluation method is introduced for solving a column permutation problem defined on a sparse binary matrix with the consecutive ones property. This problem models various $\mathcal{NP}$-hard problems in graph…
Genetic information is encoded in a linear sequence of nucleotides, represented by letters ranging from thousands to billions. Mutations refer to changes in the DNA or RNA nucleotide sequence. Thus, mutation detection is vital in all areas…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
This paper investigates the construction of linear network codes for broadcasting a set of data packets to a number of users. The links from the source to the users are modeled as independent erasure channels. Users are allowed to inform…