Related papers: Partial DNA Assembly: A Rate-Distortion Perspectiv…
The sequence in which a complex product is assembled directly impacts the ease and efficiency of the assembly process, whether executed by a human or a robot. A sequence that gives the assembler the greatest freedom of movement is therefore…
One of the main challenges in current research on segmentation in cardiac ultrasound is the lack of large and varied labeled datasets and the differences in annotation conventions between datasets. This makes it difficult to design robust…
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…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
The line spectral estimation problem consists in recovering the frequencies of a complex valued time signal that is assumed to be sparse in the spectral domain from its discrete observations. Unlike the gridding required by the classical…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Scanning transmission electron microscopy (STEM) has become the technique of choice for quantitative characterization of atomic structure of materials, where the minute displacements of atomic columns from high-symmetry positions can be…
The so called long range correlation properties of DNA sequences are studied using the variance analyses of the density distribution of a single or a group of nucleotides in a model independent way. This new method which was suggested…
Assessing the complexity of functions computed by a neural network helps us understand how the network will learn and generalize. One natural measure of complexity is how the network distorts length - if the network takes a unit-length…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it…
Graphs are used to represent and analyze data in domains as diverse as physics, biology, chemistry, planetary science, and the social sciences. Across domains, random graph models relate generative processes to expected graph properties,…
We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…
We present a framework for the design of optimal assembly algorithms for shotgun sequencing under the criterion of complete reconstruction. We derive a lower bound on the read length and the coverage depth required for reconstruction in…
The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to…
The detection of local genomic signals using high-throughput DNA sequencing data can be cast as a problem of scanning a Poisson random field for local changes in the rate of the process. We propose a likelihood-based framework for for such…
We deal with the random combinatorial structures called assemblies. By weakening the logarithmic condition which assures regularity of the number of components of a given order, we extend the notion of logarithmic assemblies. Using the…
Acquiring annotated data at scale with rare diseases or conditions remains a challenge. It would be extremely useful to have a method that controllably synthesizes images that can correct such underrepresentation. Assuming a proper latent…
Consider a Gaussian memoryless multiple source with $m$ components with joint probability distribution known only to lie in a given class of distributions. A subset of $k \leq m$ components are sampled and compressed with the objective of…