Related papers: Approximate Trace Reconstruction
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…
We present novel randomized approximation schemes for the Edit Distance (ED) problem and the Longest Common Subsequence (LCS) problem that, for any constant $\epsilon>0$, compute a $(1+\epsilon)$-approximation for ED and a…
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…
We present the first dynamic algorithms for Dyck and tree edit distances with subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a well-parenthesized expression, while tree edit distance quantifies…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and 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 $u$…
In the trace reconstruction problem an unknown string ${\bf x}=(x_0,\dots,x_{n-1})\in\{0,1,...,m-1\}^n$ is observed through the deletion channel, which deletes each $x_k$ with a certain probability, yielding a contracted string…
Mean-based reconstruction is a fundamental, natural approach to worst-case trace reconstruction over channels with synchronization errors. It is known that $\exp(O(n^{1/3}))$ traces are necessary and sufficient for mean-based worst-case…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
We develop a new framework for generalizing approximation algorithms from the structural graph algorithm literature so that they apply to graphs somewhat close to that class (a scenario we expect is common when working with real-world…
The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…
We consider the problem of reconstructing an undirected graph $G$ on $n$ vertices given multiple random noisy subgraphs or "traces". Specifically, a trace is generated by sampling each vertex with probability $p_v$, then taking the…
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…
Edit distance is an important measure of string similarity. It counts the number of insertions, deletions and substitutions one has to make to a string $x$ to get a string $y$. In this paper we design an almost linear-size sketching scheme…
We study approximation algorithms for the following three string measures that are widely used in practice: edit distance (ED), longest common subsequence (LCS), and longest increasing sequence (LIS). All three problems can be solved…
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…
The network inference problem consists of reconstructing the edge set of a network given traces representing the chronology of infection times as epidemics spread through the network. This problem is a paradigmatic representative of…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. A simple dynamic…
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,…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…