Related papers: Insertion and Deletion Correction in Polymer-based…
Text datasets can be represented using models that do not preserve text structure, or using models that preserve text structure. Our hypothesis is that depending on the dataset nature, there can be advantages using a model that preserves…
Distributed data storage systems are essential to deal with the need to store massive volumes of data. In order to make such a system fault-tolerant, some form of redundancy becomes crucial, incurring various overheads - most prominently in…
This paper mainly focuses on the problem of lossy compression storage from the perspective of message importance when the reconstructed data pursues the least distortion within limited total storage size. For this purpose, we transform this…
Compression is a crucial solution for data reduction in modern scientific applications due to the exponential growth of data from simulations, experiments, and observations. Compression with progressive retrieval capability allows users to…
The idea of using fragment embedding to circumvent the high computational scaling of accurate electronic structure methods while retaining high accuracy has been a long-standing goal for quantum chemists. Traditional fragment embedding…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…
In recent years, the emergence of DNA storage systems has led to a widespread focus on the research of codes correcting insertions, deletions, and classic substitutions. During the initial investigation, Levenshtein discovered the VT codes…
Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any arbitrary k of n nodes. However regenerating codes possess in addition, the ability to repair a…
This paper addresses the problem of simultaneous signal recovery and dictionary learning based on compressive measurements. Multiple signals are analyzed jointly, with multiple sensing matrices, under the assumption that the unknown signals…
Synthetic DNA can in principle be used for the archival storage of arbitrary data. Because errors are introduced during DNA synthesis, storage, and sequencing, an error-correcting code (ECC) is necessary for error-free recovery of the data.…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Ensemble methods are among the state-of-the-art predictive modeling approaches. Applied to modern big data, these methods often require a large number of sub-learners, where the complexity of each learner typically grows with the size of…
In continuation to earlier works where the problem of joint information embedding and lossless compression (of the composite signal) was studied in the absence \cite{MM03} and in the presence \cite{MM04} of attacks, here we consider the…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
We propose two extensions to existing importance sampling based methods for lossy compression. First, we introduce an importance sampling based compression scheme that is a variant of ordered random coding (Theis and Ahmed, 2022) and is…
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…
Tandem duplication 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 et al. (2017) proposed the study of codes that correct tandem…
In DNA-based data storage, DNA codes with biochemical constraints and error correction are designed to protect data reliability. Single-stranded DNA sequences with secondary structure avoidance (SSA) help to avoid undesirable secondary…
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…
In syntax-guided synthesis, one of the challenges is to reduce the enormous size of the search space. We observe that most search spaces are not just flat sets of programs, but can be endowed with a structure that we call an oriented…