Related papers: Approximate Trace Reconstruction
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
The Shortest Common Superstring (SCS) problem asks for the shortest string that contains each of a given set of strings as a substring. Its reverse-complement variant, the Shortest Common Superstring problem with Reverse Complements…
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 $S$…
The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the…
We consider the case in which a robot has to navigate in an unknown environment but does not have enough on-board power or payload to carry a traditional depth sensor (e.g., a 3D lidar) and thus can only acquire a few (point-wise) depth…
The edit distance (a.k.a. the Levenshtein distance) between two strings is defined as the minimum number of insertions, deletions or substitutions of symbols needed to transform one string into another. The problem of computing the edit…
We present an algorithm for approximating the edit distance $\operatorname{ed}(x, y)$ between two strings $x$ and $y$ in time parameterized by the degree to which one of the strings $x$ satisfies a natural pseudorandomness property. The…
In this paper we investigate the \emph{approximate string matching problem} when the allowed edit operations are \emph{non-overlapping unbalanced translocations of adjacent factors}. Such kind of edit operations take place when two adjacent…
As DNA data storage moves closer to practical deployment, minimizing sequencing coverage depth is essential to reduce both operational costs and retrieval latency. This paper addresses the recently studied Random Access Problem, which…
This paper addresses the problem of finding a representation of a subtree distance, which is an extension of the tree metric. We show that a minimal representation is uniquely determined by a given subtree distance, and give a linear time…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
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 edit distance between two rooted ordered trees with $n$ nodes labeled from an alphabet~$\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling…
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…
Constructions of optimal locally repairable codes (LRCs) in the case of $(r+1) \nmid n$ and over small finite fields were stated as open problems for LRCs in [I. Tamo \emph{et al.}, "Optimal locally repairable codes and connections to…
The approximate period recovery problem asks to compute all $\textit{approximate word-periods}$ of a given word $S$ of length $n$: all primitive words $P$ ($|P|=p$) which have a periodic extension at edit distance smaller than $\tau_p$ from…
We show that under mild assumptions for a problem whose solutions admit a dynamic programming-like recurrence relation, we can still find a solution under additional packing constraints, which need to be satisfied approximately. The number…
This paper considers the problem of inferring the structure of a network from indirect observations. Each observation (a "trace") is the unordered set of nodes which are activated along a path through the network. Since a trace does not…
Edit distance is a measure of similarity of two strings based on the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. The edit distance can be computed exactly using a…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…