Related papers: On the Reverse-Complement String-Duplication Syste…
We discuss the generalization of recently discovered BPS configurations, corresponding to the planar string networks, to non-planar ones by considering the U-duality symmetry of type II string theory in various dimensions. As an explicit…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
Diagonal lines in symbolic recurrence plots are closely related to the identification and characterization of specific biprolongable words within a sequence. In this paper we focus on the recurrence plot of a fixed point of a uniform binary…
On the string of finite length, a (genomic) transposition is defined as the operation of exchanging two consecutive substrings. The minimum number of transpositions needed to transform one into the other is the transposition distance, that…
We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
Knowledge of the input format of binary executables is important for finding bugs and vulnerabilities, such as generating data for fuzzing or manual reverse engineering. This paper presents an algorithm to recover the structure and semantic…
In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…
Detecting and measuring repetitiveness of strings is a problem that has been extensively studied in data compression and text indexing. However, when the data are structured in a non-linear way, like in the context of two-dimensional…
Distribution matching transforms independent and Bernoulli(1/2) distributed input bits into a sequence of output symbols with a desired distribution. Fixed-to-fixed length, invertible, and low complexity encoders and decoders based on…
Let S be a finite, ordered alphabet, and let x = x_1 x_2 ... x_n be a string over S. A "secondary index" for x answers alphabet range queries of the form: Given a range [a_l,a_r] over S, return the set I_{[a_l;a_r]} = {i |x_i \in [a_l;…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
The biggest challenge when using DNA as a storage medium is maintaining its stability. The relative occurrence of Guanine (G) and Cytosine (C) is essential for the longevity of DNA. In addition to that, reverse complementary base pairs…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $\Delta$, the {\em exact string matching} problem consists of finding all occurrences of…
Labeling of DNA molecules is a fundamental technique for DNA visualization and analysis. This process was mathematically modeled in [1], where the received sequence indicates the positions of the used labels. In this work, we develop error…
We identify string corrections to the EM memory effect. Though largely negligible in the low-energy limit, the effect become relevant in high-energy collisions and in extreme events. We illustrate our findings in a simple unoriented bosonic…
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…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
Self-synchronization under the presence of additive noise can be achieved by allocating a certain number of bits of each codeword as markers for synchronization. Difference systems of sets are combinatorial designs which specify the…
Based on the extended binary image of non-binary LDPC codes, we propose a method for generating extra redundant bits, such as to decreases the coding rate of a mother code. The proposed method allows for using the same decoder, regardless…