相关论文: Computing the Inversion-Indel Distance

This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…

Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities like: exons, introns, intergenic and repeat/unique DNA sequences, in each of the 22 human chromosomes. The purpose…

This paper presents a new deep regression model, which we call DeepDistance, for cell detection in images acquired with inverted microscopy. This model considers cell detection as a task of finding most probable locations that suggest cell…

The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…

In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…

Given two genomes with duplicate genes, \textsc{Zero Exemplar Distance} is the problem of deciding whether the two genomes can be reduced to the same genome without duplicate genes by deleting all but one copy of each gene in each genome.…

Herein it is shown that in order to study the statistical properties of DNA sequences in bacterial chromosomes it suffices to consider only one half of the chromosome because they are similar to its corresponding complementary sequence in…

Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…

Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…

In Digital Holography (DH), it is crucial to extract the object distance from a hologram in order to reconstruct its amplitude and phase. This step is called auto-focusing and it is conventionally solved by first reconstructing a stack of…

Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…

We propose a new distance metric for DNA sequences, which can be defined on any evolutionary Markov model with infinitesimal generator matrix Q. That is the new metric can be defined under existing models such as Jukes-Cantor model,…

Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…

This work continues the study of linear error correcting codes against adversarial insertion deletion errors (insdel errors). Previously, the work of Cheng, Guruswami, Haeupler, and Li \cite{CGHL21} showed the existence of asymptotically…

Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…

This revisit gives a survey on the analytical methods for the inverse exponential Radon transform which has been investigated in the past three decades from both mathematical interests and medical applications such as nuclear medicine…

The majority of medical images, especially those that resemble cells, have similar characteristics. These images, which occur in a variety of shapes, often show abnormalities in the organ or cell region. The convolution operation possesses…

This short note introduces the harmonic indel distance (HID), a new distance between strings where the cost of an insertion or deletion is inversely proportional to the string length. We present a closed-form formula and show that the HID…

Background: Cardiac MRI derived biventricular mass and function parameters, such as end-systolic volume (ESV), end-diastolic volume (EDV), ejection fraction (EF), stroke volume (SV), and ventricular mass (VM) are clinically well…

The Hausdorff Distance (HD) is widely used in evaluating medical image segmentation methods. However, existing segmentation methods do not attempt to reduce HD directly. In this paper, we present novel loss functions for training…