Related papers: Correcting a Single Deletion in Reads from a Nanop…
This paper introduces a neural polar decoder (NPD) for deletion channels with a constant deletion rate. Existing polar decoders for deletion channels exhibit high computational complexity of $O(N^4)$, where $N$ is the block length. This…
This paper considers the classical error correcting problem which is frequently discussed in coding theory. We wish to recover an input vector $f \in \R^n$ from corrupted measurements $y = A f + e$. Here, $A$ is an $m$ by $n$ (coding)…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. We have created a method for…
We construct deletion error-correcting codes in the oblivious model, where errors are adversarial but oblivious to the encoder's randomness. Oblivious errors bridge the gap between the adversarial and random error models, and are motivated…
We consider the problem of constructing a code capable of correcting a single long tandem duplication error of variable length. As the main contribution of this paper, we present a $q$-ary efficiently encodable code of length $n+1$ and…
In this paper, we study error exponents for a concatataned coding based class of DNA storage codes in which the number of reads performed can be variable. That is, the decoder can sequentially perform reads and choose whether to output the…
High read depth can be used to assemble short sequence repeats. The existing genome assemblers fail in repetitive regions of longer than average read. I propose a new algorithm for a DNA assembly which uses the relative frequency of reads…
We developed a new base caller DeepNano-coral for nanopore sequencing, which is optimized to run on the Coral Edge Tensor Processing Unit, a small USB-attached hardware accelerator. To achieve this goal, we have designed new versions of two…
An indel refers to a single insertion or deletion, while an edit refers to a single insertion, deletion or substitution. In this paper, we investigate codes that combat either a single indel or a single edit and provide linear-time…
This paper explores the possibilities and limitations of error correction by the structural simplicity of error mechanisms. Specifically, we consider channel models, called \emph{samplable additive channels}, in which (a) errors are…
Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…
To increase the information capacity of DNA storage, composite DNA letters were introduced. We propose a novel channel model for composite DNA in which composite sequences are decomposed into ordered standard non-composite sequences. The…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
In this paper, we show that the single deletion correcting Varshamov-Tenengolts code, with minor modifications, can also correct an ordered deletion-erasure pattern where one deletion and at most one erasure occur and the deletion always…
A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length…
Error correction is essential for modern computing systems, enabling information to be processed accurately even in the presence of noise. Here, we demonstrate a new approach which exploits an error correcting phase that emerges in a system…
Reed-Muller codes encode an $m$-variate polynomial of degree $r$ by evaluating it on all points in $\{0,1\}^m$. We denote this code by $RM(m,r)$. The minimal distance of $RM(m,r)$ is $2^{m-r}$ and so it cannot correct more than half that…
Error correction techniques have been used to refine the output sentences from automatic speech recognition (ASR) models and achieve a lower word error rate (WER) than original ASR outputs. Previous works usually use a sequence-to-sequence…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…