Related papers: On the Reverse-Complement String-Duplication Syste…
The analysis of the decoding failure rate of the bit-flipping algorithm has received increasing attention. For a binary linear code we consider the minimum number of rows in a parity-check matrix such that the bit-flipping algorithm is able…
We design, implement and test a simple algorithm which computes the approximate entropy of a finite binary string of arbitrary length. The algorithm uses a weighted average of the Shannon Entropies of the string and all but the last binary…
Consider a binary word being transmitted through a communication channel that introduces deletable errors where each bit of the word is either retained, flipped, erased or deleted. The simplest code for correcting \emph{all} possible…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
We study a character-based phylogeny reconstruction problem when an incomplete set of data is given. More specifically, we consider the situation under the directed perfect phylogeny assumption with binary characters in which for some…
We show that iterative coding systems can not surpass capacity using only quantities which naturally appear in density evolution. Although the result in itself is trivial, the method which we apply shows that in order to achieve capacity…
Recurrence rate, determinism, average line length, and entropy of line lengths are measures of complexity in recurrence quantification analysis, that help to understand the structure, predictability and complexity of dynamical systems. In…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…
In this work, we propose constructions that correct duplications of multiple consecutive symbols. These errors are known as tandem duplications, where a sequence of symbols is repeated; respectively as palindromic duplications, where a…
In this paper we consider the problem of encoding data into \textit{repeat-free} sequences in which sequences are imposed to contain any $k$-tuple at most once (for predefined $k$). First, the capacity of the repeat-free constraint are…
Motivated by applications in polymer-based data storage we introduced the new problem of characterizing the code rate and designing constant-weight binary $B_2$-sequences. Binary $B_2$-sequences are collections of binary strings of length…
The number of zeros and the number of ones in a binary string are referred to as the composition of the string, and the prefix-suffix compositions of a string are a multiset formed by the compositions of the prefixes and suffixes of all…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by…
While achieving a compression ratio of 2.0 bits/base, the new algorithm codes non-N bases in fixed length. It dramatically reduces the time of coding and decoding than previous DNA compression algorithms and some universal compression…
Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in…
We consider the problem of designing low-redundancy codes in settings where one must correct deletions in conjunction with substitutions or adjacent transpositions; a combination of errors that is usually observed in DNA-based data storage.…