Related papers: Algorithms of self-synchronizing single-deletion-c…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
In this paper, we consider the outer channel for DNA-based data storage. When transmitting over the outer channel, each DNA string is treated as a unit/symbol that would be either correctly received, or erased, or corrupted by uniformly…
Reliability is an important requirement for both communication and storage systems. Due to continuous scale down of technology multiple adjacent bits error probability increases. The data may be corrupted due soft errors. Error correction…
Quantum low-density parity-check codes are promising candidates for low-overhead fault-tolerant quantum computing, but degeneracy is known to impair the convergence of belief-propagation (BP) decoding of these codes. In this work, we show…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is…
Model diffing methods aim to identify how fine-tuning changes a model's internal representations. Crosscoders approach this by learning shared dictionaries of interpretable latent directions between base and fine-tuned models. However,…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
We introduce a fully constructive characterisation of holographic quantum error-correcting codes. That is, given a code and an erasure error we give a recipe to explicitly compute the terms in the RT formula. Using this formalism, we employ…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
We consider the `one-shot frame synchronization problem' where a decoder wants to locate a sync pattern at the output of a channel on the basis of sequential observations. We assume that the sync pattern of length N starts being emitted at…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
We consider the problem of constructing deletion correcting codes over a binary alphabet and take a graph theoretic view. An $n$-bit $s$-deletion correcting code is an independent set in a particular graph. We propose constructing such a…
Existing approaches for grammatical error correction (GEC) largely rely on supervised learning with manually created GEC datasets. However, there has been little focus on verifying and ensuring the quality of the datasets, and on how…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
We study the problem of compressing a source sequence in the presence of side-information that is related to the source via insertions, deletions and substitutions. We propose a simple algorithm to compress the source sequence when the…
Due to the ability to provide superior error-correction performance, the successive cancellation list (SCL) algorithm is widely regarded as one of the most promising decoding algorithms for polar codes with short-to-moderate code lengths.…
Erasure correcting codes are widely used to ensure data persistence in distributed storage systems. This paper addresses the simultaneous repair of multiple failures in such codes. We go beyond existing work (i.e., regenerating codes by…
In this work, we introduce convolutional codes for network-error correction in the context of coherent network coding. We give a construction of convolutional codes that correct a given set of error patterns, as long as consecutive errors…
Polar codes asymptotically achieve the symmetric capacity of memoryless channels, yet their error-correcting performance under successive-cancellation (SC) decoding for short and moderate length codes is worse than that of other modern…