Related papers: Random Access in DNA Storage: Algorithms, Construc…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
In the usual trace reconstruction problem, the goal is to exactly reconstruct an unknown string of length $n$ after it passes through a deletion channel many times independently, producing a set of traces (i.e., random subsequences of the…
Quantum Random Access Memory (QRAM) is a critical component for loading classical data into quantum computers. While constructing a practical QRAM presents several challenges, including the impracticality of an infinitely large QRAM size…
We consider query-based data acquisition and the corresponding information recovery problem, where the goal is to recover $k$ binary variables (information bits) from parity measurements of those variables. The queries and the corresponding…
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 consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. In this work, we study the fundamental limits and tradeoffs of DNA-based storage systems under a simple model, motivated by current…
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…
We consider the task of assigning unique integers to a group of processes in an asynchronous distributed system of a total of $n$ processes prone to crashes that communicate through shared read-write registers. In the Renaming problem, an…
DNA-based storage is an emerging storage technology that provides high information density and long duration. Due to the physical constraints in the reading and writing processes, error correction in DNA storage poses several interesting…
Let $\mathcal{D}$ be a collection of $D$ documents, which are strings over an alphabet of size $\sigma$, of total length $n$. We describe a data structure that uses linear space and and reports $k$ most relevant documents that contain a…
DNA-based data storage has been attracting significant attention due to its extremely high data storage density, low power consumption, and long duration compared to conventional data storage media. Despite the recent advancements in DNA…
Min-entropy sampling gives a bound on the min-entropy of a randomly chosen subset of a string, given a bound on the min-entropy of the whole string. K\"onig and Renner showed a min-entropy sampling theorem that holds relative to quantum…
We formulate and analyze a generic sequential resource access problem arising in a variety of engineering fields, where a user disposes a number of heterogeneous computing, communication, or storage resources, each characterized by the…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
The maximum coverage problem is to select $k$ sets from a collection of sets such that the cardinality of the union of the selected sets is maximized. We consider $(1-1/e-\epsilon)$-approximation algorithms for this NP-hard problem in three…
Randomised algorithms often employ methods that can fail and that are retried with independent randomness until they succeed. Randomised data structures therefore often store indices of successful attempts, called seeds. If $n$ such seeds…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Motivated by the philosophy and phenomenal success of compressed sensing, the problem of reconstructing a matrix from a sampling of its entries has attracted much attention recently. Such a problem can be viewed as an information-theoretic…
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…