Related papers: Coded trace reconstruction
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…
The {\em insertion-deletion channel} takes as input a binary string $x \in\{0, 1\}^n$, and outputs a string $\widetilde{x}$ where some of the bits have been deleted and others inserted independently at random. In the {\em trace…
The errors occurring in DNA-based storage are correlated in nature, which is a direct consequence of the synthesis and sequencing processes. In this paper, we consider the memory-$k$ nanopore channel model recently introduced by Hamoum et…
Universal compression of patterns of sequences generated by independently identically distributed (i.i.d.) sources with unknown, possibly large, alphabets is investigated. A pattern is a sequence of indices that contains all consecutive…
This paper studies the fundamental problem of data persistency for a general family of redundancy schemes in distributed storage systems, called replicated erasure codes. Namely, we analyze two strategies of replicated erasure codes…
Erasure codes are being increasingly used in distributed-storage systems in place of data-replication, since they provide the same level of reliability with much lower storage overhead. We consider the problem of constructing explicit…
To equip DNA-based data storage with random-access capabilities, Yazdi et al. (2018) prepended DNA strands with specially chosen address sequences called primers and provided certain design criteria for these primers. We provide explicit…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
Reverse engineering of binary executables is a critical problem in the computer security domain. On the one hand, malicious parties may recover interpretable source codes from the software products to gain commercial advantages. On the…
The explosion in the volumes of data being stored online has resulted in distributed storage systems transitioning to erasure coding based schemes. Yet, the codes being deployed in practice are fairly short. In this work, we address what we…
The population recovery problem asks one to recover an unknown distribution over $n$-bit strings given access to independent noisy samples of strings drawn from the distribution. Recently, Ban et al. [BCF+19] studied the problem where the…
The goal of the trace reconstruction problem is to recover a string $x\in\{0,1\}^n$ given many independent {\em traces} of $x$, where a trace is a subsequence obtained from deleting bits of $x$ independently with some given probability…
We consider the problem of efficient construction of q-ary 2-deletion correcting codes with low redundancy. We show that our construction requires less redundancy than any existing efficiently encodable q-ary 2-deletion correcting codes.…
In this paper, we investigate the problem of designing $(n, N; \mathcal{B})$-reconstruction codes for $N\in \{14,11,9,5\}$, where $\mathcal{B}$ is the single-deletion single-substitution ball function that maps a sequence to the set of all…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
In a large-scale and distributed matrix multiplication problem $C=A^{\intercal}B$, where $C\in\mathbb{R}^{r\times t}$, the coded computation plays an important role to effectively deal with "stragglers" (distributed computations that may…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…