Related papers: Weighted ancestors in suffix trees
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
We consider the problem of constructing a sparse suffix tree (or suffix array) for $b$ suffixes of a given text $T$ of size $n$, using only $O(b)$ words of space during construction time. Breaking the naive bound of $\Omega(nb)$ time for…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
We consider the problem of augmenting an $n$-vertex tree with one shortcut in order to minimize the diameter of the resulting graph. The tree is embedded in an unknown space and we have access to an oracle that, when queried on a pair of…
For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…
In this paper, we introduce a new representation for ordered trees, the weight sequence representation. We then use this to construct new representations for both rooted trees and free trees, namely the canonical weight sequence…
The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…
We consider weighted particle systems in which new generations are re-sampled from current particles with probabilities proportional to their weights. This covers a broad class of sequential Monte Carlo methods, widely used in applied…
We consider preprocessing a set $S$ of $n$ points in convex position in the plane into a data structure supporting queries of the following form: given a point $q$ and a directed line $\ell$ in the plane, report the point of $S$ that is…
Indexing highly repetitive texts - such as genomic databases, software repositories and versioned text collections - has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive texts…
Selection of an architectural prior well suited to a task (e.g. convolutions for image data) is crucial to the success of deep neural networks (NNs). Conversely, the weight priors within these architectures are typically left vague,…
We present an improved solution to the Weighted Job Scheduling (WJS) problem. While the classical dynamic programming (DP) solution for $n$ jobs runs in $O(n \log(n))$ time due to comparison-based sorting and per-job binary search, we…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
We show that the compressed suffix array and the compressed suffix tree for a string of length $n$ over an integer alphabet of size $\sigma\leq n$ can both be built in $O(n)$ (randomized) time using only $O(n\log\sigma)$ bits of working…
We revisit the mergeable dictionaries with shift problem, where the goal is to maintain a family of sets subject to search, split, merge, make-set, and shift operations. The search, split, and make-set operations are the usual well-known…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Consider a forest that evolves via $link$ operations that make the root of one tree the child of a node in another tree. Intermixed with $link$ operations are $nca$ operations, which return the nearest common ancestor of two given nodes…
In this paper we propose a dynamic data structure that supports efficient algorithms for updating and querying singly connected Bayesian networks (causal trees and polytrees). In the conventional algorithms, new evidence in absorbed in time…
We show how to construct a dynamic ordered dictionary, supporting insert/delete/rank/select on a set of $n$ elements from a universe of size $U$, that achieves the optimal amortized expected time complexity of $O(1 + \log n / \log \log U)$,…
We revisit the classic problem of simplex range searching and related problems in computational geometry. We present a collection of new results which improve previous bounds by multiple logarithmic factors that were caused by the use of…