Related papers: Substring Density Estimation from Traces
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…
We study how well one can recover sparse principal components of a data matrix using a sketch formed from a few of its elements. We show that for a wide class of optimization problems, if the sketch is close (in the spectral norm) to the…
Given a set of integers, one can easily construct the set of their pairwise distances. We consider the inverse problem: given a set of pairwise distances, find the integer set which realizes the pairwise distance set. This problem arises in…
In the Shortest Superstring problem we are given a set of strings $S=\{s_1, \ldots, s_n\}$ and integer $\ell$ and the question is to decide whether there is a superstring $s$ of length at most $\ell$ containing all strings of $S$ as…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication scenario where the sender transmits a codeword from some codebook and the receiver obtains multiple noisy reads of the codeword. The common…
For an undirected tree with $n$ edges labelled by single letters, we consider its substrings, which are labels of the simple paths between pairs of nodes. We prove that there are $O(n^{1.5})$ different palindromic substrings. This solves an…
Based on unique decoding of the polynomial residue code with non-pairwise coprime moduli, a polynomial with degree less than that of the least common multiple (lcm) of all the moduli can be accurately reconstructed when the number of…
In the pooled data problem the goal is to efficiently reconstruct a binary signal from additive measurements. Given a signal $\sigma \in \{ 0,1 \}^n$, we can query multiple entries at once and get the total number of non-zero entries in the…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
It is now well understood that (1) it is possible to reconstruct sparse signals exactly from what appear to be highly incomplete sets of linear measurements and (2) that this can be done by constrained L1 minimization. In this paper, we…
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…
We address the problem of reconstructing a set of points on a line or a loop from their unassigned noisy pairwise distances. When the points lie on a line, the problem is known as the turnpike; when they are on a loop, it is known as the…
We consider the \textit{phase retrieval} problem of recovering a sparse signal $\mathbf{x}$ in $\mathbb{R}^d$ from intensity-only measurements in dimension $d \geq 2$. Phase retrieval can be equivalently formulated as the problem of…
The problem of finding locally dense components of a graph is an important primitive in data analysis, with wide-ranging applications from community mining to spam detection and the discovery of biological network modules. In this paper we…
In this paper, we define the reoptimization variant of the closest substring problem (CSP) under sequence addition. We show that, even with the additional information we have about the problem instance, the problem of finding a closest…
We consider state reconstruction from the measurement statistics of phase space observables generated by photon number states. The results are obtained by inverting certain infinite matrices. In particular, we obtain reconstruction…
Reconstructing continuous signals from a small number of discrete samples is a fundamental problem across science and engineering. In practice, we are often interested in signals with 'simple' Fourier structure, such as bandlimited,…
This note presents a unified analysis of the recovery of simple objects from random linear measurements. When the linear functionals are Gaussian, we show that an s-sparse vector in R^n can be efficiently recovered from 2s log n…
For a given $n$, what is the smallest number $k$ such that every sequence of length $n$ is determined by the multiset of all its $k$-subsequences? This is called the $k$-deck problem for sequence reconstruction, and has been generalized to…