Related papers: Codes for DNA Sequence Profiles
The possibility of detecting mutations in a DNA from force measurements (as a first step towards sequence analysis) is discussed theoretically based on exact calculations. The force signal is associated with the domain wall separating the…
We study the theoretical problem of synthesizing multiple DNA strands under spatial constraints, motivated by large-scale DNA synthesis technologies. In this setting, strands are arranged in an array and synthesized according to a fixed…
In this paper, we formally define and analyze the class of noisy permutation channels. The noisy permutation channel model constitutes a standard discrete memoryless channel (DMC) followed by an independent random permutation that reorders…
We study the channel coding problem when errors and uncertainty occur in the encoding process. For simplicity we assume the channel between the encoder and the decoder is perfect. Focusing on linear block codes, we model the encoding…
Distributed storage systems often introduce redundancy to increase reliability. When coding is used, the repair problem arises: if a node storing encoded information fails, in order to maintain the same level of reliability we need to…
The goal of a denoising algorithm is to reconstruct a signal from its noise-corrupted observations. Perfect reconstruction is seldom possible and performance is measured under a given fidelity criterion. In a recent work, the authors…
Using a mild variant of polar codes we design linear compression schemes compressing Hidden Markov sources (where the source is a Markov chain, but whose state is not necessarily observable from its output), and to decode from Hidden Markov…
Sequencing by synthesis is the underlying technology for many next-generation DNA sequencing platforms. We developed a new model, the fixed flow cycle model, to derive the distributions of sequence length for a given number of flow cycles…
In the problem of blind reconstruction of channel codes, the receiver does not have the knowledge of the channel code used at the transmitter and the aim is to identify this unknown channel code corresponding to the given received sequence.…
The design of codes for communicating reliably over a statistically well defined channel is an important endeavor involving deep mathematical research and wide-ranging practical applications. In this work, we present the first family of…
Sequencing by synthesis is used in many next-generation DNA sequencing technologies. Some of the technologies, especially those exploring the principle of single-molecule sequencing, allow incomplete nucleotide incorporation in each cycle.…
We investigate time encoding as an alternative method to classical sampling, and address the problem of reconstructing classes of non-bandlimited signals from time-based samples. We consider a sampling mechanism based on first filtering the…
We introduce a novel method to analyse complete genomes and recognise some distinctive features by means of an adaptive compression algorithm, which is not DNA-oriented. We study the Information Content as a function of the number of…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…
DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…
Neural Audio Codecs, initially designed as a compression technique, have gained more attention recently for speech generation. Codec models represent each audio frame as a sequence of tokens, i.e., discrete embeddings. The discrete and…
We propose a novel coding scheme for DNA-based storage systems, called the shift-interleave (SI) coding, designed to correct insertion, deletion, and substitution (IDS) errors, as well as sequence losses. The SI coding scheme employs…
Current techniques in sequencing a genome allow a service provider (e.g. a sequencing company) to have full access to the genome information, and thus the privacy of individuals regarding their lifetime secret is violated. In this paper, we…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
In the Levenshtein's sequence reconstruction problem a codeword is transmitted through $N$ channels and in each channel a set of errors is introduced to the transmitted word. In previous works, the restriction that each channel provides a…