Related papers: Permutation Recovery Problem against Deletion Erro…
Large pools of synthetic DNA molecules have been recently used to reliably store significant volumes of digital data. While DNA as a storage medium has enormous potential because of its high storage density, its practical use is currently…
Motivated by applications in DNA-based storage, we introduce the new problem of code design in the Damerau metric. The Damerau metric is a generalization of the Levenshtein distance which, in addition to deletions, insertions and…
DNA replication stands as one of the fundamental biological processes crucial for cellular functioning. Recent experimental developments enable the study of replication dynamics at the single-molecule level for complete genomes,…
In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
We investigate the problem of maintaining an encoded distributed storage system when some nodes contain adversarial errors. Using the error-correction capabilities that are built into the existing redundancy of the system, we propose a…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…
Effective and reliable data retrieval is critical for the feasibility of DNA storage, and the development of random access efficiency plays a key role in its practicality and reliability. In this paper, we study the Random Access Problem,…
Disaggregated memory leverages recent technology advances in high-density, byte-addressable non-volatile memory and high-performance interconnects to provide a large memory pool shared across multiple compute nodes. Due to higher memory…
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…
A network coding-based scheme is proposed to improve the energy efficiency of distributed storage systems in WSNs (wireless sensor networks), which mainly focuses on two problems: firstly, consideration is given to effective distributed…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
The recently developed dynamic discretization discovery (DDD) is a powerful method that allows many time-dependent problems to become more tractable. While DDD has been applied to a variety of problems, one particular challenge has been to…
The surge in demand for cost-effective, durable long-term archival media, coupled with density limitations of contemporary magnetic media, has resulted in synthetic DNA emerging as a promising new alternative. Despite its benefits, storing…
The existence of label noise imposes significant challenges (e.g., poor generalization) on the training process of deep neural networks (DNN). As a remedy, this paper introduces a permutation layer learning approach termed PermLL to…
Motivated by DNA-based storage applications, we study the problem of reconstructing a coded sequence from multiple traces. We consider the model where the traces are outputs of independent deletion channels, where each channel deletes each…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
Motivation: Next generation methods of DNA sequencing produce relatively high rate of reading errors, which interfere with de novo genome assembly of newly sequenced organisms and particularly affect the quality of SNP detection important…
Distributed storage systems and associated storage codes can efficiently store a large amount of data while ensuring that data is retrievable in case of node failure. The study of such systems, particularly the design of storage codes over…
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…