Related papers: Trace Reconstruction with Bounded Edit Distance
We consider the following basic inference problem: there is an unknown high-dimensional vector $w \in \mathbb{R}^n$, and an algorithm is given access to labeled pairs $(x,y)$ where $x \in \mathbb{R}^n$ is a measurement and $y = w \cdot x +…
DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
How efficiently can we find an unknown graph using distance queries between its vertices? We assume that the unknown graph is connected, unweighted, and has bounded degree. The goal is to find every edge in the graph. This problem admits a…
Characterizing the differential excision of mRNA is critical for understanding the functional complexity of a cell or tissue, from normal developmental processes to disease pathogenesis. Most transcript reconstruction methods infer…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
Reconstructing a finite set of curves from an unordered set of sample points is a well studied topic. There has been less effort that considers how much better the reconstruction can be if tangential information is given as well. We show…
Tandem duplication in DNA is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain {\em et al.} (2016) proposed the study of codes that…
The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $\Sigma$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to…
For any $T \geq 1$, there are constants $R=R(T) \geq 1$ and $\zeta=\zeta(T)>0$ and a randomized algorithm that takes as input an integer $n$ and two strings $x,y$ of length at most $n$, and runs in time $O(n^{1+\frac{1}{T}})$ and outputs an…
In phase retrieval we want to recover an unknown signal $\boldsymbol x\in\mathbb C^d$ from $n$ quadratic measurements of the form $y_i = |\langle{\boldsymbol a}_i,{\boldsymbol x}\rangle|^2+w_i$ where $\boldsymbol a_i\in \mathbb C^d$ are…
The edit distance $ed(X,Y)$ of two strings $X,Y\in \Sigma^*$ is the minimum number of character edits (insertions, deletions, and substitutions) needed to transform $X$ into $Y$. Its weighted counterpart $ed^w(X,Y)$ minimizes the total cost…
We study the problem of approximating edit distance in sublinear time. This is formalized as the $(k,k^c)$-Gap Edit Distance problem, where the input is a pair of strings $X,Y$ and parameters $k,c>1$, and the goal is to return YES if…
The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two…
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…
The text-to-pattern Hamming distances problem asks to compute the Hamming distances between a given pattern of length $m$ and all length-$m$ substrings of a given text of length $n\ge m$. We focus on the $k$-mismatch version of the problem,…
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are…
This paper deals with the problem of reconstructing a band-limited signal when a finite subset of its samples and of its derivative are missing. The technique used, due to P.J.S.G. Ferreira, is based on the use of a particular frame for…
Given two strings of length $n$ over alphabet $\Sigma$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in…
Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…