Related papers: Near-Optimal Trace Reconstruction for Mildly Separ…
The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…
This paper investigates graph clustering in the planted cluster model in the presence of {\em small clusters}. Traditional results dictate that for an algorithm to provably correctly recover the clusters, {\em all} clusters must be…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
The problem of reconstructing strings from substring information has found many applications due to its importance in genomic data sequencing and DNA- and polymer-based data storage. One practically important and challenging paradigm…
We study the problem of cutting a length-$n$ string of positive real numbers into $k$ pieces so that every piece has sum at least $b$. The problem can also be phrased as transforming such a string into a new one by merging adjacent numbers.…
Suppose we wish to recover a signal x in C^n from m intensity measurements of the form |<x,z_i>|^2, i = 1, 2,..., m; that is, from data in which phase information is missing. We prove that if the vectors z_i are sampled independently and…
The restoration lemma by Afek, Bremler-Barr, Kaplan, Cohen, and Merritt [Dist. Comp. '02] proves that, in an undirected unweighted graph, any replacement shortest path avoiding a failing edge can be expressed as the concatenation of two…
Random graph matching refers to recovering the underlying vertex correspondence between two random graphs with correlated edges; a prominent example is when the two random graphs are given by Erd\H{o}s-R\'{e}nyi graphs $G(n,\frac{d}{n})$.…
Sparse recovery can recover sparse signals from a set of underdetermined linear measurements. Motivated by the need to monitor large-scale networks from a limited number of measurements, this paper addresses the problem of recovering sparse…
Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
Graph reconstruction can efficiently detect the underlying topology of massive networks such as the Internet. Given a query oracle and a set of nodes, the goal is to obtain the edge set by performing as few queries as possible. An algorithm…
We consider the problem of finding a sparse solution for an underdetermined linear system of equations when the known parameters on both sides of the system are subject to perturbation. This problem is particularly relevant to…
Determining whether an unordered collection of overlapping substrings (called shingles) can be uniquely decoded into a consistent string is a problem that lies within the foundation of a broad assortment of disciplines ranging from…
In this work, we study the Biclique-Free Vertex Deletion problem: Given a graph $G$ and integers $k$ and $i \le j$, find a set of at most $k$ vertices that intersects every (not necessarily induced) biclique $K_{i, j}$ in $G$. This is a…
We introduce an algorithm for the uniform generation of infinite traces, i.e., infinite words up to commutation of some letters. The algorithm outputs on-the-fly approximations of a theoretical infinite trace, the latter being distributed…
The problem of reconstructing a source sequence with the presence of decoder side-information that is mis-synchronized to the source due to deletions is studied in a distributed source coding framework. Motivated by practical applications,…
Recently we presented the first algorithm for maintaining the set of nodes reachable from a source node in a directed graph that is modified by edge deletions with $o(mn)$ total update time, where $m$ is the number of edges and $n$ is the…
In this article, we show that each semidefinite relaxation of a ball-constrained noncommutative polynomial optimization problem can be cast as a semidefinite program with a constant trace matrix variable. We then demonstrate how this…
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…