Related papers: Coding for Sequence Reconstruction for Single Edit…
We present a method for the reconstruction of networks, based on the order of nodes visited by a stochastic branching process. Our algorithm reconstructs a network of minimal size that ensures consistency with the data. Crucially, we show…
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…
In this paper, we investigate binary reconstruction codes capable of correcting one deletion and one substitution. We define the \emph{single-deletion single-substitution ball} function $ \mathcal{B} $ as a mapping from a sequence to the…
In the trace reconstruction problem our goal is to learn an unknown string $x\in \{0,1\}^n$ given independent traces of $x$. A trace is obtained by independently deleting each bit of $x$ with some probability $\delta$ and concatenating the…
We extend Ziv and Lempel's model of finite-state encoders to the realm of lossy compression of individual sequences. In particular, the model of the encoder includes a finite-state reconstruction codebook followed by an information lossless…
String edit distances have been used for decades in applications ranging from spelling correction and web search suggestions to DNA analysis. Most string edit distances are variations of the Levenshtein distance and consider only…
Recent work by Smagloy et al. (ISIT 2020) shows that the redundancy of a single-deletion $s$-substitution correcting code is asymptotically at least $(s+1)\log n+o(\log n)$, where $n$ is the length of the codes. They also provide a…
We study a variant of the successive refinement problem with receiver side information where the receivers require identical reconstructions. We present general inner and outer bounds for the rate region for this variant and present a…
In the classical source coding problem, the compressed source is reconstructed at the decoder with respect to some distortion metric. Motivated by settings in which we are interested in more than simply reconstructing the compressed source,…
In this paper, we present a novel communication channel, called the absorption channel, inspired by information transmission in neurons. Our motivation comes from in-vivo nano-machines, emerging medical applications, and brain-machine…
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…
We consider the question of interactive communication, in which two remote parties perform a computation while their communication channel is (adversarially) noisy. We extend here the discussion into a more general and stronger class of…
The repair problem in distributed storage addresses recovery of the data encoded using an erasure code, for instance, a Reed-Solomon (RS) code. We consider the problem of repairing a single node or multiple nodes in RS-coded storage systems…
String similarity, longest common subsequence and shortest edit scripts are the triplets of problem that related to each other. There are different algorithms exist to generate edit script by solving longest common subsequence problem. This…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
An edit refers to a single insertion, deletion, or substitution. This paper aims to construct binary codes that can correct two edits. To do this, a necessary and sufficient condition for a code to be two-edit correctable is provided,…
In this paper we consider the problem of encoding data into \textit{repeat-free} sequences in which sequences are imposed to contain any $k$-tuple at most once (for predefined $k$). First, the capacity of the repeat-free constraint are…
Trace reconstruction is the problem of learning an unknown string $x$ from independent traces of $x$, where traces are generated by independently deleting each bit of $x$ with some deletion probability $q$. In this paper, we initiate the…
We study segmented burst-deletion channels motivated by the observation that synchronization errors commonly occur in a bursty manner in real-world settings. In this channel model, transmitted sequences are implicitly divided into…
A new channel coding approach was proposed in [1] for random multiple access communication over the discrete-time memoryless channel. The coding approach allows users to choose their communication rates independently without sharing the…