Related papers: Weighted ancestors in suffix trees
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
Over the last decade, deep neural networks have transformed our society, and they are already widely applied in various machine learning applications. State-of-art deep neural networks are becoming larger in size every year to deliver…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
We revisit the Heaviest Induced Ancestors (HIA) problem that was introduced by Gagie, Gawrychowski, and Nekrich [CCCG 2013] and has a number of applications in string algorithms. Let $T_1$ and $T_2$ be two rooted trees whose nodes have…
We consider problems in which we are given a rooted tree as input, and must find a subtree with the same root, optimizing some objective function of the nodes in the subtree. When this function is the sum of constant node weights, the…
The sorting problem is one of the most relevant problems in computer science. Within the scope of modern computer science it has been studied for more than 70 years. In spite of these facts, new sorting algorithms have been developed in…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
A labeled tree (or a trie) is a natural generalization of a string, which can also be seen as a compact representation of a set of strings. This paper considers the labeled tree indexing problem, and provides a number of new results on…
Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…
Suppose that a rooted tree T is given for preprocessing. The Level-Ancestor Problem is to answer quickly queries of the following form. Given a vertex v and an integer i > 0, find the i-th vertex on the path from the root to v. Algorithms…
The Weighted First-Order Model Counting Problem (WFOMC) asks to compute the weighted sum of models of a given first-order logic sentence over a given domain. It can be solved in time polynomial in the domain size for sentences from the…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant requires merging two paths in a single operation. In contrast to the standard…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…
In the past thirty years, numerous algorithms for building the suffix array of a string have been proposed. In 2021, the notion of suffix array was extended from strings to DFAs, and it was shown that the resulting data structure can be…
In order to speed-up classification models when facing a large number of categories, one usual approach consists in organizing the categories in a particular structure, this structure being then used as a way to speed-up the prediction…
Decision trees are well-known due to their ease of interpretability. To improve accuracy, we need to grow deep trees or ensembles of trees. These are hard to interpret, offsetting their original benefits. Shapley values have recently become…