Related papers: Correcting a Single Deletion in Reads from a Nanop…
This paper studies codes that correct bursts of deletions. Namely, a code will be called a $b$-burst-deletion-correcting code if it can correct a deletion of any $b$ consecutive bits. While the lower bound on the redundancy of such codes…
A new class of exact-repair regenerating codes is constructed by stitching together shorter erasure correction codes, where the stitching pattern can be viewed as block designs. The proposed codes have the "help-by-transfer" property where…
We consider a neural network (NN) that may experience memory faults and computational errors. In this paper, we propose a novel real-number-based error correction code (ECC) capable of detecting and correcting both memory errors and…
We study the application of polar codes in deletion channels by analyzing the cascade of a binary erasure channel (BEC) and a deletion channel. We show how polar codes can be used effectively on a BEC with a single deletion, and propose a…
Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In…
Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…
Polymer translocation is a promising strategy for the next-generation DNA sequencing technologies. The use of biological and synthetic nano-pores, however, still suffers from serious drawbacks. In particular, the width of the membrane layer…
A rapid and low-cost method to sequence DNA would usher in a revolution in medicine. We propose and theoretically show the feasibility of a protocol for sequencing based on the distributions of transverse electrical currents of…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
This work is driven by a practical question: corrections of Artificial Intelligence (AI) errors. These corrections should be quick and non-iterative. To solve this problem without modification of a legacy AI system, we propose special…
We propose the Insertion-Deletion Transformer, a novel transformer-based neural architecture and training method for sequence generation. The model consists of two phases that are executed iteratively, 1) an insertion phase and 2) a…
Several studies suggest strong correlation between different types of cancer and the relative concentration of short circulating RNA sequences (miRNA). Because of short length and low concentration, miRNA detection is not easy. Standard…
We study segmented burst-deletion channels motivated by the observation that synchronization errors commonly occur in a bursty manner in real-world settings. In this channel model, transmitted sequences are implicitly divided into…
In most error correction coding (ECC) frameworks, the typical error metric is the bit error rate (BER) which measures the number of bit errors. For this metric, the positions of the bits are not relevant to the decoding, and in many noise…
Hollow-core fibers offer superior loss and latency characteristics compared to solid-core alternatives, yet the geometric complexity of nested antiresonance nodeless fibers (NANFs) makes traditional optimization computationally prohibitive.…
Cross-encoder models, which jointly encode and score a query-item pair, are prohibitively expensive for direct k-nearest neighbor (k-NN) search. Consequently, k-NN search typically employs a fast approximate retrieval (e.g. using BM25 or…
A tandem cell is proposed for DNA sequencing in which an exonuclease enzyme cleaves bases (mononucleotides) from a strand of DNA for identification inside a nanopore. It has two nanopores and three compartments with the structure [cis1,…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences.…
With the emergence of new storage and communication methods, the insertion, deletion, and substitution (IDS) channel has attracted considerable attention. However, many topics on the IDS channel and the associated Levenshtein distance…