Related papers: On Duplication-Free Codes for Disjoint or Equal-Le…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
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…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
This paper is concerned with the problem of error-free communication over the i.i.d. duplication channel which acts on a transmitted sequence $ x_1 \cdots x_n $ by inserting a random number of copies of each symbol $ x_i $ next to the…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
Non-binary codes correcting multiple deletions have recently attracted a lot of attention. In this work, we focus on multiplicity-free codes, a family of non-binary codes where all symbols are distinct. Our main contribution is a new…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
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…
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…
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…
The set of all $ q $-ary strings that do not contain repeated substrings of length $ \leqslant\! 3 $ (i.e., that do not contain substrings of the form $ a a $, $ a b a b $, and $ a b c a b c $) constitutes a code correcting an arbitrary…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
The construction of asymmetric error correcting codes is a topic that was studied extensively, however, the existing approach for code construction assumes that every codeword should tolerate $t$ asymmetric errors. Our main observation is…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
In this work, we derive upper bounds on the cardinality of tandem duplication and palindromic deletion correcting codes by deriving the generalized sphere packing bound for these error types. We first prove that an upper bound for tandem…
Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…
DNA-based storage is an emerging storage technology that provides high information density and long duration. Due to the physical constraints in the reading and writing processes, error correction in DNA storage poses several interesting…
We find that existing language modeling datasets contain many near-duplicate examples and long repetitive substrings. As a result, over 1% of the unprompted output of language models trained on these datasets is copied verbatim from the…
This paper concerns non-overlapping codes, block codes motivated by synchronisation and DNA-based storage applications. Most existing constructions of these codes do not account for the restrictions posed by the physical properties of…