Related papers: Correcting Contextual Deletions in DNA Nanopore Re…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
When a node in a distributed storage system fails, it needs to be promptly repaired to maintain system integrity. While typical erasure codes can provide a significant storage advantage over replication, they suffer from poor repair…
Error-correcting codes over sets, with applications to DNA storage, are studied. The DNA-storage channel receives a set of sequences, and produces a corrupted version of the set, including sequence loss, symbol substitution, symbol…
This study explores the self-synchronization problem in DNA coding, specifically addressing single-deletion errors without using delimiters between codewords. We aim to identify the beginning of each codeword without using delimiters,…
Erasure coding techniques are getting integrated in networked distributed storage systems as a way to provide fault-tolerance at the cost of less storage overhead than traditional replication. Redundancy is maintained over time through…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
We introduce the Random Subsequence Model, a spin glass model on pairs of random strings $(X,Y) \in \{0,1\}^N \times \{0,1\}^M$ whose partition function counts subsequence embeddings of $Y$ into $X$. We study two variants: the null model,…
This paper tackles the reduction of redundant repeating generation that is often observed in RNN-based encoder-decoder models. Our basic idea is to jointly estimate the upper-bound frequency of each target vocabulary in the encoder and…
In this paper, we model Density Evolution (DE) using Recurrent Neural Networks (RNNs) with the aim of designing capacity-approaching Irregular Low-Density Parity-Check (LDPC) codes for binary erasure channels. In particular, we present a…
It is proved in this work that exhaustively determining bad patterns in arbitrary, finite low-density parity-check (LDPC) codes, including stopping sets for binary erasure channels (BECs) and trapping sets (also known as near-codewords) for…
Dropout has been demonstrated as a simple and effective module to not only regularize the training process of deep neural networks, but also provide the uncertainty estimation for prediction. However, the quality of uncertainty estimation…
We consider the problem of constructing codes that can correct $\delta$ deletions occurring in an arbitrary binary string of length $n$ bits. Varshamov-Tenengolts (VT) codes can correct all possible single deletions $(\delta=1)$ with an…
Motivated by the study of deletion channels, this work presents improved bounds on the number of subsequences obtained from a binary sting X of length n under t deletions. It is known that the number of subsequences in this setting strongly…
In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
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…
Motivated by DNA based data storage system, we investigate the errors that occur when synthesizing DNA strands in parallel, where each strand is appended one nucleotide at a time by the machine according to a template supersequence. If…
Function-correcting codes (FCCs) protect specific function evaluations of a message against errors. This condition imposes a less stringent distance requirement than classical error-correcting codes (ECCs), allowing for reduced redundancy.…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
Analog error-correcting codes (Analog ECCs) for approximate vector-matrix multiplication have been extensively studied as means to achieve fault-tolerant in-memory computation. The theoretical foundations for such coding schemes,…
Code-trained language models have proven to be highly effective for various code intelligence tasks. However, they can be challenging to train and deploy for many software engineering applications due to computational bottlenecks and memory…