Related papers: Shift-Interleave Coding for DNA-Based Storage: Cor…
Fast, reliable and inexpensive DNA sequencing is an important pursuit in healthcare, especially in personalized medicine with possible deep societal impacts. Despite significant progress of various nanopore-based sequencing configurations,…
DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…
Polar codes are a class of capacity-achieving codes for the binary-input discrete memoryless channels (B-DMCs). However, when applied in channels with intersymbol interference (ISI), the codes may perform poorly with BCJR equalization and…
Erasure coding techniques are used to increase the reliability of distributed storage systems while minimizing storage overhead. Also of interest is minimization of the bandwidth required to repair the system following a node failure. In a…
In this paper, we study error exponents for a concatataned coding based class of DNA storage codes in which the number of reads performed can be variable. That is, the decoder can sequentially perform reads and choose whether to output the…
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 data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Regenerating codes enable trading off repair bandwidth for storage in distributed storage systems (DSS). Due to their distributed nature, these systems are intrinsically susceptible to attacks, and they may also be subject to multiple…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have…
Cryptographic check values (digital signatures, MACs and H-MACs) are useful only if they are free of errors. For that reason all of errors in cryptographic check values should be corrected after the transmission over a noisy channel before…
Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures during…
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…
Neural text generation models are typically trained by maximizing log-likelihood with the sequence cross entropy (CE) loss, which encourages an exact token-by-token match between a target sequence with a generated sequence. Such training…
Generative retrieval, a promising new paradigm in information retrieval, employs a seq2seq model to encode document features into parameters and decode relevant document identifiers (IDs) based on search queries. Existing generative…
The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow…
Biological sequence analysis relies on the ability to denoise the imprecise output of sequencing platforms. We consider a common setting where a short sequence is read out repeatedly using a high-throughput long-read platform to generate…
We construct $s$-interleaved linearized Reed--Solomon (ILRS) codes and variants and propose efficient decoding schemes that can correct errors beyond the unique decoding radius in the sum-rank metric. The proposed interpolation-based scheme…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…