相关论文: Incorporating indel channels into average-case ana…
Fault tolerance is a major concern in distributed computational settings. In the classic master-worker setting, a server (the master) needs to perform some heavy computation which it may distribute to $m$ other machines (workers) in order…
In this work, we study linear error-correcting codes against adversarial insertion-deletion (indel) errors. While most constructions for the indel model are nonlinear, linear codes offer compact representations, efficient encoding, and…
In the trace reconstruction problem, one observes the output of passing a binary string $s \in \{0,1\}^n$ through a deletion channel $T$ times and wishes to recover $s$ from the resulting $T$ "traces." Most of the literature has focused on…
A fundamental problem in wireless networks is the maximum link scheduling problem: given a set $L$ of links, compute the largest possible subset $L'\subseteq L$ of links that can be scheduled simultaneously without interference. This…
Owing to its several merits over other DNA sequencing technologies, nanopore sequencers hold an immense potential to revolutionize the efficiency of DNA storage systems. However, their higher error rates necessitate further research to…
Consider two remote nodes having binary sequences $X$ and $Y$, respectively. $Y$ is an edited version of ${X}$, where the editing involves random deletions, insertions, and substitutions, possibly in bursts. The goal is for the node with…
In the standard trace reconstruction problem, the goal is to \emph{exactly} reconstruct an unknown source string $\mathsf{x} \in \{0,1\}^n$ from independent "traces", which are copies of $\mathsf{x}$ that have been corrupted by a…
The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be exactly computed thanks to a pioneering approach of Hannenhalli and Pevzner from 1995. In…
We consider the problem of single link failure in an elastic optical network, (also known as flex-grid WDM network). The task is to reroute optical connections that go through the broken link using free capacity of other links of the…
In the trace reconstruction problem, one attempts to reconstruct a fixed but unknown string $x$ of length $n$ from a given number of traces $\tilde{x}$ drawn iid from the application of a noisy process (such as the deletion channel) to $x$.…
The Shortest Common Superstring (SCS) problem is a fundamental task in sequence analysis. In genome assembly, however, the double-stranded nature of DNA implies that each fragment may occur either in its original orientation or as its…
The process of DNA-based data storage (DNA storage for short) can be mathematically modelled as a communication channel, termed DNA storage channel, whose inputs and outputs are sets of unordered sequences. To design error correcting codes…
We present the squirrel parser, a PEG packrat parser that directly handles all forms of left recursion with optimal error recovery, while maintaining linear time complexity in the length of the input even in the presence of an arbitrary…
This paper considers the problem of channel coding with a given (possibly suboptimal) maximum-metric decoding rule. A cost-constrained random-coding ensemble with multiple auxiliary costs is introduced, and is shown to achieve error…
A binary string transmitted via a memoryless i.i.d. deletion channel is received as a subsequence of the original input. From this, one obtains a posterior distribution on the channel input, corresponding to a set of candidate…
In this paper, we present improved decoding algorithms for expander-based Tanner codes. We begin by developing a randomized linear-time decoding algorithm that, under the condition that $ \delta d_0 > 2 $, corrects up to $ \alpha n $ errors…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
Let $G = (V,E,\ell)$ be a $n$-node $m$-edge weighted undirected graph, where $\ell: E \rightarrow (0,\infty)$ is a real \emph{length} function defined on its edges, and let $g$ denote the girth of $G$, i.e., the length of its shortest…
The merit factor problem is of practical importance to manifold domains, such as digital communications engineering, radars, system modulation, system testing, information theory, physics, chemistry. However, the merit factor problem is…
Given two strings $S$ and $P$, the Episode Matching problem is to find the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997) , where $n,m$ are…