Related papers: Random Access in DNA Storage: Algorithms, Construc…
Batched network coding is a variation of random linear network coding which has low computational and storage costs. In order to adapt to random fluctuations in the number of erasures in individual batches, it is not optimal to recode and…
We consider the canonical {\em shared link network} formed by a source node, hosting a library of $m$ information messages (files), connected via a noiseless common link to $n$ destination nodes (users), each with a cache of size M files.…
DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…
The edit distance is a metric of dissimilarity between strings, widely applied in computational biology, speech recognition, and machine learning. Let $e_k(n)$ denote the average edit distance between random, independent strings of $n$…
In the classical interval scheduling type of problems, a set of $n$ jobs, characterized by their start and end time, need to be executed by a set of machines, under various constraints. In this paper we study a new variant in which the jobs…
Finding the minimum value in an unordered database is a common and fundamental task in computer science. However, the optimal classical deterministic algorithm can find the minimum value with a time complexity that grows linearly with the…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
DNA is an attractive medium for digital data storage. When data is stored on DNA, errors occur, which makes error-correcting coding techniques critical for reliable DNA data storage. To reduce the errors, a common technique is to include…
We consider a setting in which a sender wishes to broadcast a block of K data packets to a set of wireless receivers, where each of the receivers has a subset of the data packets already available to it (e.g., from prior transmissions) and…
A primary source of increased read time on NAND flash comes from the fact that in the presence of noise, the flash medium must be read several times using different read threshold voltages for the decoder to succeed. This paper proposes an…
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…
Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors…
In the orthogonal range reporting problem, we are to preprocess a set of $n$ points with integer coordinates on a $U \times U$ grid. The goal is to support reporting all $k$ points inside an axis-aligned query rectangle. This is one of the…
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…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
We present a randomized algorithm for reconstructing directed rooted trees of $n$ nodes and node degree at most $d$, by asking at most $O(dn\log^2 n)$ path queries. Each path query takes as input an origin node and a target node, and…
The selection problem, where one wishes to locate the $k^{th}$ smallest element in an unsorted array of size $n$, is one of the basic problems studied in computer science. The main focus of this work is designing algorithms for solving 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…