Related papers: Levenshtein's Sequence Reconstruction Problem and …
DNA is an attractive candidate for data storage. Its millennial durability and nanometer scale offer exceptional data density and longevity. Its relevance to medical applications also drives advances in DNA-related biotechnology. To protect…
Consider the case where consecutive blocks of N letters of a semi-infinite individual sequence X over a finite-alphabet are being compressed into binary sequences by some one-to-one mapping. No a-priori information about X is available at…
The emerging field of DNA storage employs strands of DNA bases (A/T/C/G) as a storage medium for digital information to enable massive density and durability. The DNA storage pipeline includes: (1) encoding the raw data into sequences of…
DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…
The image reconstruction process in medical imaging can be treated as solving an inverse problem. The inverse problem is usually solved using time-consuming iterative algorithms with sparsity or other constraints. Recently, deep neural…
DNA data storage is rapidly emerging as a promising solution for long-term data archiving, largely due to its exceptional durability. However, the synthesis of DNA strands remains a significant bottleneck in terms of cost and speed. To…
The DNA storage channel is considered, in which the $M$ Deoxyribonucleic acid (DNA) molecules comprising each codeword are stored without order, sampled $N$ times with replacement, and then sequenced over a discrete memoryless channel. For…
Deep learning models have shown state-of-the-art performance in many inverse reconstruction problems. However, it is not well understood what properties of the latent representation may improve the generalization ability of the network.…
Motivated by DNA storage in living organisms, and by known biological mutation processes, we study the reverse-complement string-duplication system. We fully classify the conditions under which the system has full expressiveness, for all…
Over the past years, the ever-growing trend on data storage demand, more specifically for "cold" data (i.e. rarely accessed), has motivated research for alternative systems of data storage. Because of its biochemical characteristics,…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Synthetic sequence-controlled polymers promise to transform polymer science by combining the chemical versatility of synthetic polymers with the precise sequence-mediated functionality of biological proteins. However, design of these…
Data storage is one of the main computing issues of this century. Not only storage devices are converging to strict physical limits, but also the amount of data generated by users is growing at an unbelievable rate. To face these…
This paper addresses the problem of learning binary hash codes for large scale image search by proposing a novel hashing method based on deep neural network. The advantage of our deep model over previous deep model used in hashing is that…
The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow…
As a possible implementation of data storage using DNA, multiple strands of DNA are stored in a liquid container so that, in the future, they can be read by an array of DNA readers in parallel. These readers will sample the strands with…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication setting in which a sender transmits a codeword and the receiver observes K independent noisy versions of this codeword. In this work, we study…
Recent advances in DNA sequencing technology and DNA storage systems have rekindled the interest in deletion channels. Multiple recent works have looked at variants of sequence reconstruction over a single and over multiple deletion…