Related papers: Trace Reconstruction with Bounded Edit Distance

Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…

This study investigates whether reoptimization can help in solving the closest substring problem. We are dealing with the following reoptimization scenario. Suppose, we have an optimal l-length closest substring of a given set of sequences…

In this paper, we design new sublinear-time algorithms for solving the gap edit distance problem and for embedding edit distance to Hamming distance. For the gap edit distance problem, we give an $\tilde{O}(\frac{n}{k}+k^2)$-time greedy…

The goal of ordinal embedding is to represent items as points in a low-dimensional Euclidean space given a set of constraints in the form of distance comparisons like "item $i$ is closer to item $j$ than item $k$". Ordinal constraints like…

This paper studies reconstruction of strings based upon their substrings spectrum. Under this paradigm, it is assumed that all substrings of some fixed length are received and the goal is to reconstruct the string. While many existing works…

Suppose that a sequence of numbers $x_n$ (a `signal') is transmitted through a noisy channel. The receiver observes a noisy version of the signal with additive random fluctuations, $x_n + \xi_n$, where $\xi_n$ is a sequence of independent…

Edit distance similarity search, also called approximate pattern matching, is a fundamental problem with widespread database applications. The goal of the problem is to preprocess $n$ strings of length $d$, to quickly answer queries $q$ of…

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 $u$…

We consider the following k-sparse recovery problem: design an m x n matrix A, such that for any signal x, given Ax we can efficiently recover x' satisfying ||x-x'||_1 <= C min_{k-sparse} x"} ||x-x"||_1. It is known that there exist…

The edit distance of two strings is the minimum number of insertions, deletions, and substitutions needed to transform one string into the other. The textbook algorithm determines the edit distance of length-$n$ strings in $O(n^2)$ time,…

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 paper investigates the number of quantum queries made to solve the problem of reconstructing an unknown string from its substrings in a certain query model. More concretely, the goal of the problem is to identify an unknown string $S$…

We give cell-probe bounds for the computation of edit distance, Hamming distance, convolution and longest common subsequence in a stream. In this model, a fixed string of $n$ symbols is given and one $\delta$-bit symbol arrives at a time in…

This paper considers the model problem of reconstructing an object from incomplete frequency samples. Consider a discrete-time signal $f \in \C^N$ and a randomly chosen set of frequencies $\Omega$ of mean size $\tau N$. Is it possible to…

We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…

Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the…

We study the closeness of an experimental unitary bosonic network with only partially indistinguishable bosons in an arbitrary mixed input state, in particular an experimental realization of the Boson Sampling, to the ideal bosonic network,…

Recently, a number of reconstruction algorithms have been presented for residual strain tomography from Bragg-edge neutron transmission measurements. In this paper, we examine whether strain tomography can also be achieved from diffraction…

Edit distance, also known as Levenshtein distance, is an essential way to compare two strings that proved to be particularly useful in the analysis of genetic sequences and natural language processing. However, edit distance is a discrete…

The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…