Related papers: Genomic Compression with Read Alignment at the Dec…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
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…
Recent work identified the fundamental limits on the information requirements in terms of read length and coverage depth required for successful de novo genome reconstruction from shotgun sequencing data, based on the idealistic assumption…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Image compression and reconstruction are crucial for various digital applications. While contemporary neural compression methods achieve impressive compression rates, the adoption of such technology has been largely hindered by the…
Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…
Time series account for a large proportion of the data stored in financial, medical and scientific databases. The efficient storage of time series is important in practical applications. In this paper, we propose a novel compression scheme…
Lossy compression algorithms aim to compactly encode images in a way which enables to restore them with minimal error. We show that a key limitation of existing algorithms is that they rely on error measures that are extremely sensitive to…
We study the problem of the reconstruction of a Gaussian field defined in [0,1] using N sensors deployed at regular intervals. The goal is to quantify the total data rate required for the reconstruction of the field with a given mean square…
We propose a new coding scheme, called the delayed coding (DC) scheme, for channels with insertion, deletion, and substitution (IDS) errors. The proposed scheme employs delayed encoding and non-iterative detection and decoding strategies to…
We consider replication-based distributed storage systems in which each node stores the same quantum of data and each data bit stored has the same replication factor across the nodes. Such systems are referred to as balanced distributed…
Regenerating codes provide an efficient way to recover data at failed nodes in distributed storage systems. It has been shown that regenerating codes can be designed to minimize the per-node storage (called MSR) or minimize the…
Scalable coding, which can adapt to channel bandwidth variation, performs well in today's complex network environment. However, most existing scalable compression methods face two challenges: reduced compression performance and insufficient…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
This paper investigates a unification of distributed source coding, multiple description coding, and source coding with side information at decoders. The equivalence between the multiple-decoder extension of distributed source coding with…
Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
We propose a joint source-channel-network coding scheme, based on compressive sensing principles, for wireless networks with AWGN channels (that may include multiple access and broadcast), with sources exhibiting temporal and spatial…
In the classical source coding problem, the compressed source is reconstructed at the decoder with respect to some distortion metric. Motivated by settings in which we are interested in more than simply reconstructing the compressed source,…