相关论文: Estimating Genome Reversal Distance by Genetic Alg…

An algorithm is described that adaptively learns a non-linear mutation distribution. It works by training a denoising autoencoder (DA) online at each generation of a genetic algorithm to reconstruct a slowly decaying memory of the best…

We consider the following problem: from a given set of gene families trees on a set of genomes, find a first speciation, that splits these genomes into two subsets, that minimizes the number of gene duplications that happened before this…

Genetic algorithms are high-level heuristic optimization methods which enjoy great popularity thanks to their intuitive description, flexibility, and, of course, effectiveness. The optimization procedure is based on the evolution of…

In the context of the genome rearrangement problem, we analyze two well known models, namely the block transposition and the prefix block transposition models, by exploiting the connection with the notion of permutation pattern. More…

Sorting is one of the most used and well investigated algorithmic problem [1]. Traditional postulation supposes the sorting data archived, and the elementary operation as comparisons of two numbers. In a view of appearance of new processors…

Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…

The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…

Recent developments in integrated photonics technology are opening the way to the fabrication of complex linear optical interferometers. The application of this platform is ubiquitous in quantum information science, from quantum simulation…

We study the problem of reconstructing a signal from its projection on a subspace. The proposed signal reconstruction algorithms utilize a guiding subspace that represents desired properties of reconstructed signals. We show that optimal…

Image restoration algorithms are typically evaluated by some distortion measure (e.g. PSNR, SSIM, IFC, VIF) or by human opinion scores that quantify perceived perceptual quality. In this paper, we prove mathematically that distortion and…

A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…

Permutation resemblance measures the distance of a function from being a permutation. Here we show how to determine the permutation resemblance through linear integer programming techniques. We also present an algorithm for constructing…

We investigate the quantum state discrimination task for sets of linear independent pure states with an intrinsic ordering. This structured discrimination problems allow for a novel scheme that provides a certified level of error, that is,…

Compressed sensing aims to undersample certain high-dimensional signals, yet accurately reconstruct them by exploiting signal characteristics. Accurate reconstruction is possible when the object to be recovered is sufficiently sparse in a…

We explore the fundamental problem of sorting through the lens of learning-augmented algorithms, where algorithms can leverage possibly erroneous predictions to improve their efficiency. We consider two different settings: In the first…

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…

Given a pattern $P$ and a text $T$, both strings over a binary alphabet, the binary jumbled string matching problem consists in telling whether any permutation of $P$ occurs in $T$. The indexed version of this problem, i.e., preprocessing a…

Motivation: Seed filtering is critical in DNA read mapping, a process where billions of DNA fragments (reads) sampled from a donor are mapped onto a reference genome to identify genomic variants of the donor. Read mappers 1) quickly…

We study the problem of sorting under incomplete information, when queries are used to resolve uncertainties. Each of $n$ data items has an unknown value, which is known to lie in a given interval. We can pay a query cost to learn the…

Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…