Related papers: Single-Error Detection and Correction for Duplicat…
The sequence reconstruction problem involves a model where a sequence is transmitted over several identical channels. This model investigates the minimum number of channels required for the unique reconstruction of the transmitted sequence.…
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…
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 explores the possibilities and limitations of error correction by the structural simplicity of error mechanisms. Specifically, we consider channel models, called \emph{samplable additive channels}, in which (a) errors are…
Transceivers used for telecommunications transmit and receive specific modulation patterns that are represented as sequences of complex numbers. Classifying modulation patterns is challenging because noise and channel impairments affect the…
Given a set of aligned sequences of independent noisy observations, we are concerned with detecting intervals where the mean values of the observations change simultaneously in a subset of the sequences. The intervals of changed means are…
A distributed binary hypothesis testing (HT) problem involving two parties, one referred to as the observer and the other as the detector is studied. The observer observes a discrete memoryless source (DMS) and communicates its observations…
We develop statistically based methods to detect single nucleotide DNA mutations in next generation sequencing data. Sequencing generates counts of the number of times each base was observed at hundreds of thousands to billions of genome…
We consider the problem of joint source and channel coding of structured data such as natural language over a noisy channel. The typical approach to this problem in both theory and practice involves performing source coding to first…
We consider the problem of storing and retrieving information from synthetic DNA media. The mathematical basis of the problem is the construction and design of sequences that may be discriminated based on their collection of substrings…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
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…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Evolving genomes increase a number of their genes by gene duplications. To escape degradation in a functionless pseudogene, any gene duplicate needs to be guarded by negative (purifying) selection from otherwise inevitable fixation of…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
The Levenshtein sequence reconstruction problem studies the reconstruction of a transmitted sequence from multiple erroneous copies of it. A fundamental question in this field is to determine the minimum number of erroneous copies required…
Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Detecting covert channels among legitimate traffic represents a severe challenge due to the high heterogeneity of networks. Therefore, we propose an effective covert channel detection method, based on the analysis of DNS network data…
The one-bit deletion and duplication channel is investigated. An input to this channel consists of a block of bits which experiences either a deletion, or a duplication, or remains unchanged. For this channel a capacity expression is…