Related papers: Coded trace reconstruction
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. Motivated by…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
Erasure coding is a storage-efficient alternative to replication for achieving reliable data backup in distributed storage systems. During the storage process, traditional erasure codes require a unique source node to create and upload all…
Regenerating codes are a class of codes proposed for providing reliability of data and efficient repair of failed nodes in distributed storage systems. In this paper, we address the fundamental problem of handling errors and erasures during…
DNA data storage systems encode digital data into DNA strands, enabling dense and durable storage. Efficient data retrieval depends on coverage depth, a key performance metric. We study the random access coverage depth problem and focus on…
In the trace reconstruction problem, one seeks to reconstruct a binary string $s$ from a collection of traces, each of which is obtained by passing $s$ through a deletion channel. It is known that $\exp(\tilde O(n^{1/5}))$ traces suffice to…
DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…
In the search for highly efficient decoders for short LDPC codes approaching maximum likelihood performance, a relayed decoding strategy, specifically activating the ordered statistics decoding process upon failure of a neural min-sum…
We consider the design of regenerating codes for distributed storage systems that enjoy the property of local, exact and uncoded repair, i.e., (a) upon failure, a node can be regenerated by simply downloading packets from the surviving…
The deletion channel takes as input a bit string $\mathbf{x} \in \{0,1\}^n$, and deletes each bit independently with probability $q$, yielding a shorter string. The trace reconstruction problem is to recover an unknown string $\mathbf{x}$…
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 the (deletion-channel) trace reconstruction problem, there is an unknown $n$-bit source string $x$. An algorithm is given access to independent traces of $x$, where a trace is formed by deleting each bit of~$x$ independently with…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple…
We initiate the study of DNA-based distributed storage systems, where information is encoded across multiple DNA data storage containers to achieve robustness against container failures. In this setting, data are distributed over $M$…
Data storage systems are more reliable than their individual components. In order to build highly reliable systems out of less reliable parts, systems introduce redundancy. In replicated systems, objects are simply copied several times with…
Permutation codes and multi-permutation codes have been widely considered due to their various applications, especially in flash memory. In this paper, we consider permutation codes and multi-permutation codes against a burst of stable…
There has been considerable recent interest in "cloud storage" wherein a user asks a server to store a large file. One issue is whether the user can verify that the server is actually storing the file, and typically a challenge-response…
We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…
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…
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 unique string…