Related papers: Multi-strand Reconstruction from Substrings
The problem of reconstructing a string from its error-prone copies, the trace reconstruction problem, was introduced by Vladimir Levenshtein two decades ago. While there has been considerable theoretical work on trace reconstruction,…
We study the problem of the reconstruction of a Gaussian field defined in [0,1] using N sensors deployed at regular intervals. The goal is to quantify the total data rate required for the reconstruction of the field with a given mean square…
In the deletion channel, an important problem is to determine the number of subsequences derived from a string $U$ of length $n$ when subjected to $t$ deletions. It is well-known that the number of subsequences in the setting exhibits a…
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused on predicting splice site junctions or de novo assembly of…
The central problem in sequence reconstruction is to find the minimum number of distinct channel outputs required to uniquely reconstruct the transmitted sequence. According to Levenshtein's work in 2001, this number is determined by the…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
We describe properties and constructions of constraint-based codes for DNA-based data storage which account for the maximum repetition length and AT/GC balance. We present algorithms for computing the number of sequences with maximum…
Channel estimation poses significant challenges in millimeter-wave massive multiple-input multiple-output systems, especially when the base station has fewer radio-frequency chains than antennas. To address this challenge, one promising…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the…
The labeled stochastic block model is a random graph model representing networks with community structure and interactions of multiple types. In its simplest form, it consists of two communities of approximately equal size, and the edges…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
In the trace reconstruction problem, an unknown bit string $x \in \{0,1\}^n$ is observed through the deletion channel, which deletes each bit of $x$ with some constant probability $q$, yielding a contracted string $\widetilde{x}$. How many…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
We consider an \emph{approximate} version of the trace reconstruction problem, where the goal is to recover an unknown string $s\in\{0,1\}^n$ from $m$ traces (each trace is generated independently by passing $s$ through a probabilistic…
Image reconstruction from undersampled k-space data plays an important role in accelerating the acquisition of MR data, and a lot of deep learning-based methods have been exploited recently. Despite the achieved inspiring results, the…
For a string $S$, a palindromic substring $S[i..j]$ is said to be a \emph{shortest unique palindromic substring} ($\mathit{SUPS}$) for an interval $[s, t]$ in $S$, if $S[i..j]$ occurs exactly once in $S$, the interval $[i, j]$ contains $[s,…
Music source separation is the task of isolating the instrumental tracks from a music song. Despite its spectacular recent progress, the trend towards more complex architectures and training protocols exacerbates reproducibility issues. The…
Analysis of large-scale sequential data has been one of the most crucial tasks in areas such as bioinformatics, text, and audio mining. Existing string kernels, however, either (i) rely on local features of short substructures in the…
In this paper, we study the Random Access Problem in DNA storage, which addresses the challenge of retrieving a specific information strand from a DNA-based storage system. In this framework, the data is represented by $k$ information…