Related papers: Genomic Compression with Read Alignment at the Dec…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
Recent advancements in deep learning-based image compression are notable. However, prevalent schemes that employ a serial context-adaptive entropy model to enhance rate-distortion (R-D) performance are markedly slow. Furthermore, the…
In the current era, DeoxyriboNucleic Acid (DNA) based data storage emerges as an intriguing approach, garnering substantial academic interest and investigation. This paper introduces a novel deep joint source-channel coding (DJSCC) scheme…
DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…
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…
In distributed optimization problems, a technique called gradient coding, which involves replicating data points, has been used to mitigate the effect of straggling machines. Recent work has studied approximate gradient coding, which…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
We trained and applied an encoder-decoder model to semantically segment breast biopsy images into biologically meaningful tissue labels. Since conventional encoder-decoder networks cannot be applied directly on large biopsy images and the…
A new coding scheme for general N-node relay networks is presented for unicast, multicast, and broadcast. The proposed distributed decode-forward scheme combines and generalizes Marton coding for single-hop broadcast channels and the…
This paper reviews strategies for solving problems encountered when analyzing large genomic data sets and describes the implementation of those strategies in R by packages from the Bioconductor project. We treat the scalable processing,…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
Mobile and embedded machine learning developers frequently have to compromise between two inferior on-device deployment strategies: sacrifice accuracy and aggressively shrink their models to run on dedicated low-power cores; or sacrifice…
Ultrasound image compression by preserving speckle-based key information is a challenging task. In this paper, we introduce an ultrasound image compression framework with the ability to retain realism of speckle appearance despite achieving…
This article introduces a novel communication scheme, termed coded compressed sensing, for unsourced multiple-access communication. The proposed divide-and-conquer approach leverages recent advances in compressed sensing and forward error…
Coded computing has emerged as a promising framework for tackling significant challenges in large-scale distributed computing, including the presence of slow, faulty, or compromised servers. In this approach, each worker node processes a…
In this paper, we study the problem of graph compression with side information at the decoder. The focus is on the situation when an unlabelled graph (which is also referred to as a structure) is to be compressed or is available as side…
Distributed compressed sensing is concerned with representing an ensemble of jointly sparse signals using as few linear measurements as possible. Two novel joint reconstruction algorithms for distributed compressed sensing are presented in…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
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…
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…