Related papers: Correcting Contextual Deletions in DNA Nanopore Re…
This paper investigates the problem of correcting multiple criss-cross insertions and deletions in arrays. More precisely, we study the unique recovery of $n \times n$ arrays affected by $t$-criss-cross deletions defined as any combination…
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…
The well-known trace reconstruction problem is the problem of inferring an unknown source string $x \in \{0,1\}^n$ from independent "traces", i.e. copies of $x$ that have been corrupted by a $\delta$-deletion channel which independently…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
Large language models produce repetitive output when prompted independently across many batches, a phenomenon we term cross-batch mode collapse: the progressive loss of output diversity when a language model is prompted repeatedly without…
Motivated by communication channels in which the transmitted sequences are subject to random permutations, as well as by certain DNA storage systems, we study the error control problem in settings where the information is stored/transmitted…
One of the primary sequencing methods gaining prominence in DNA storage is nanopore sequencing, attributed to various factors. In this work, we consider a simplified model of the sequencer, characterized as a channel. This channel takes a…
We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…
Fault tolerance in Deep Neural Networks (DNNs) deployed on resource-constrained systems presents unique challenges for high-accuracy applications with strict timing requirements. Memory bit-flips can severely degrade DNN accuracy, while…
Data synchronization is a fundamental problem with applications in diverse fields such as cloud storage, genomics, and distributed systems. This paper addresses the challenge of synchronizing two files, one of which is a subsequence of the…
DNA emerges as a promising medium for the exponential growth of digital data due to its density and durability. This study extends recent research by addressing the \emph{coverage depth problem} in practical scenarios, exploring optimal…
In this paper, we present a novel way for solving the main problem of designing the capacity approaching irregular low-density parity-check (LDPC) code ensemble over binary erasure channel (BEC). The proposed method is much simpler, faster,…
We derive an upper bound on the capacity of non-binary deletion channels. Although binary deletion channels have received significant attention over the years, and many upper and lower bounds on their capacity have been derived, such…
In recent years we have witnessed an increase on the development of methods for submodular optimization, which have been motivated by the wide applicability of submodular functions in real-world data-science problems. In this paper, we…
We present a finite blocklength performance bound for a DNA storage channel with insertions, deletions, and substitutions. The considered bound -- the dependency testing (DT) bound, introduced by Polyanskiy et al. in 2010 -- provides an…
Recently, network error correction coding (NEC) has been studied extensively. Several bounds in classical coding theory have been extended to network error correction coding, especially the Singleton bound. In this paper, following the…
In distributed storage systems, erasure codes with locality $r$ is preferred because a coordinate can be recovered by accessing at most $r$ other coordinates which in turn greatly reduces the disk I/O complexity for small $r$. However, the…
This paper presents new lower and upper bounds for the optimal compression of binary prefix codes in terms of the most probable input symbol, where compression efficiency is determined by the nonlinear codeword length objective of…
Neural Differential Equations (NDEs) excel at modeling continuous-time dynamics, effectively handling challenges such as irregular observations, missing values, and noise. Despite their advantages, NDEs face a fundamental challenge in…
Cyclic redundancy check (CRC) codes check if a codeword is correctly received. This paper presents an algorithm to design CRC codes that are optimized for the code-specific error behavior of a specified feedforward convolutional code. The…