Related papers: On the Reverse-Complement String-Duplication Syste…
The discrepancy of a binary string is the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. In this note we determine the minimal discrepancy that a…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
Deterministic two-way transducers capture the class of regular functions. The efficiency of composing two-way transducers has a direct implication in algorithmic problems related to reactive synthesis, where transformation specifications…
We construct codes over the ring $\mathbb{F}_2+u\mathbb{F}_2$ with $u^2=0$. These code are designed for use in DNA computing applications. The codes obtained satisfy the reverse complement constraint, the $GC$ content constraint and avoid…
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…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
In this paper we study codes for correcting deletable errors in binary words, where each bit is either retained, substituted, erased or deleted and the total number of errors is much smaller compared to the length of the codeword. We…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
Generation of an (arbitrarily) long string of bits unique to a given finite-length numerical seed is of great value in the field of random number generation, computer simulations, and other areas of computer science. Extending this idea…
This paper presents a storage-efficient learning model titled Recursive Binary Neural Networks for sensing devices having a limited amount of on-chip data storage such as < 100's kilo-Bytes. The main idea of the proposed model is to…
String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…
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…
We study the complexity of the problem of searching for a set of patterns that separate two given sets of strings. This problem has applications in a wide variety of areas, most notably in data mining, computational biology, and in…
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…
Motivated by applications in DNA-based storage and communication systems, we study deletion and insertion errors simultaneously in a burst. In particular, we study a type of error named $t$-deletion-$s$-insertion-burst ($(t,s)$-burst for…
Tandem duplication is an evolutionary process whereby a segment of DNA is replicated and proximally inserted. The different configurations that can arise from this process give rise to some interesting combinatorial questions. Firstly, we…
Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data,…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
Recently, DNA storage has surfaced as a promising alternative for data storage, presenting notable benefits in terms of storage capacity, cost-effectiveness in maintenance, and the capability for parallel replication. Mathematically, the…