Related papers: Correcting a Single Deletion in Reads from a Nanop…
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…
Nanopore sequencing is an emerging DNA sequencing technology that has been proposed for use in DNA storage systems. We propose the noisy nanopore channel model for nanopore sequencing. This model captures duplications, inter-symbol…
The noise model of deletions poses significant challenges in coding theory, with basic questions like the capacity of the binary deletion channel still being open. In this paper, we study the harder model of worst-case deletions, with a…
While high-dimensional embedding vectors are being increasingly employed in various tasks like Retrieval-Augmented Generation and Recommendation Systems, popular dimensionality reduction (DR) methods such as PCA and UMAP have rarely been…
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…
Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
An insdel refers to a deletion or an insertion, and an edit refers to an insdel or a substitution. In this paper, we consider the segmented single-insdel (resp. single-edit) channel, where the channel's input bit stream is partitioned into…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Nanopore sequencing is a widely-used high-throughput genome sequencing technology that can sequence long fragments of a genome into raw electrical signals at low cost. Nanopore sequencing requires two computationally-costly processing steps…
Segmentation of nanoscale electron microscopy (EM) images is crucial but still challenging in connectomics research. One reason for this is that none of the existing segmentation methods are error-free, so they require proofreading, which…
We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of…
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 shotgun sequencing process involves fragmenting a long DNA sequence (input string) into numerous shorter, unordered, and overlapping segments (referred to as \emph{reads}). The reads are sequenced, and later aligned to reconstruct the…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
The problem of correcting deletions and insertions has recently received significantly increased attention due to the DNA-based data storage technology, which suffers from deletions and insertions with extremely high probability. In this…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried…
Codes correcting bursts of deletions and localized deletions have garnered significant research interest in recent years. One of the primary objectives is to construct codes with minimal redundancy. Currently, the best known constructions…
Error correcting codes play a central role in digital communication, ensuring that transmitted information can be accurately reconstructed despite channel impairments. Recently, autoencoder (AE) based approaches have gained attention for…