Related papers: The Geometry of Codes for Random Access in DNA Sto…
The coverage depth problem in DNA data storage is about minimizing the expected number of reads until all data is recovered. When they exist, MDS codes offer the best performance in this context. This paper focuses on the scenario where the…
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 study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
We provide a static data structure for distance estimation which supports {\it adaptive} queries. Concretely, given a dataset $X = \{x_i\}_{i = 1}^n$ of $n$ points in $\mathbb{R}^d$ and $0 < p \leq 2$, we construct a randomized data…
Random geometric graphs are random graph models defined on metric spaces. Such a model is defined by first sampling points from a metric space and then connecting each pair of sampled points with probability that depends on their distance,…
A random access code (RAC) encodes an $L$-bit string into a $k$-bit message, where $L>k$, such that any requested bit can be decoded with high probability; a quantum RAC (QRAC) replaces the message with $k$ qubits. This paper provides a…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Erasure list decoding was introduced to correct a larger number of erasures with output of a list of possible candidates. In the present paper, we consider both random linear codes and algebraic geometry codes for list decoding erasure…
Although the expenses associated with DNA sequencing have been rapidly decreasing, the current cost of sequencing information stands at roughly $120/GB, which is dramatically more expensive than reading from existing archival storage…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…
The problem of fast items retrieval from a fixed collection is often encountered in most computer science areas, from operating system components to databases and user interfaces. We present an approach based on hash tables that focuses on…
Leveraging recent progress in physical-layer network coding we propose a new approach to random access: When packets collide, it is possible to recover a linear combination of the packets at the receiver. Over many rounds of transmission,…
Large models and enormous data are essential driving forces of the unprecedented successes achieved by modern algorithms, especially in scientific computing and machine learning. Nevertheless, the growing dimensionality and model…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
We present an approach to random access that is based on three elements: physical-layer network coding, signature codes and tree splitting. Upon occurrence of a collision, physical-layer network coding enables the receiver to decode the sum…
Random access codes are a type of communication task that is widely used in quantum information science. The optimal average success probability that can be achieved through classical strategies is known for any random access code. However,…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…