Related papers: Mutually Uncorrelated Primers for DNA-Based Data S…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
The dynamics of coupled intermittent maps is used to model the correlated structure of genomic sequences. The use of intermittent maps, as opposed to other simple chaotic maps, is particularly suited for the production of long range…
Modern biological science produces vast amounts of genomic sequence data. This is fuelling the need for efficient algorithms for sequence compression and analysis. Data compression and the associated techniques coming from information…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
Sequence alignment is a cornerstone of bioinformatics, widely used to identify similarities between DNA, RNA, and protein sequences and studying evolutionary relationships and functional properties. The Needleman-Wunsch algorithm remains a…
Constrained sequential pattern mining aims at identifying frequent patterns on a sequential database of items while observing constraints defined over the item attributes. We introduce novel techniques for constraint-based sequential…
Sequence classification has numerous applications in various fields. Despite extensive studies in the last decades, many challenges still exist, particularly in pattern-based methods. Existing pattern-based methods measure the…
DNA has been proposed as a chemical platform for computing and data storage, paving the way for building DNA-based computers. Recently, DNA has been hypothesized as an ideal quantum computer with the base pairs working as Josephson…
Deploying TinyML models on low-cost IoT hardware is very challenging, due to limited device memory capacity. Neural processing unit (NPU) hardware address the memory challenge by using model compression to exploit weight quantization and…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
In a distributed information application an encoder compresses an arbitrary vector while a similar reference vector is available to the decoder as side information. For the Hamming-distance similarity measure, and when guaranteed perfect…
Non-uniquely decodable codes can be defined as the codes that cannot be uniquely decoded without additional disambiguation information. These are mainly the class of non-prefix-free codes, where a codeword can be a prefix of other(s), and…
Massive multiuser (MU) multiple-input multiple-output (MIMO) will be a core technology in fifth-generation (5G) wireless systems as it offers significant improvements in spectral efficiency compared to existing multi-antenna technologies.…
In this paper, we design low correlation binary sequences favorable in wireless communication and radar applications. First, we formulate the designing problem as a nonconvex combination optimization problem with flexible correlation…
Using precoding to suppress multi-user interference is a well-known technique to improve spectra efficiency in multiuser multiple-input multiple-output (MU-MIMO) systems, and the pursuit of high performance and low complexity precoding…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
Weak superimposed codes are combinatorial structures related closely to generalized cover-free families, superimposed codes, and disjunct matrices in that they are only required to satisfy similar but less stringent conditions. This class…
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently,…
Developing concurrent software is challenging, especially if it has to run on modern architectures with Weak Memory Models (WMMs) such as ARMv8, Power, or RISC-V. For the sake of performance, WMMs allow hardware and compilers to…