Related papers: Efficient repeat finding via suffix arrays
We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…
Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…
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 $X$…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
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…
We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of…
Searches for phrases and word sets in large text arrays by means of additional indexes are considered. Their use may reduce the query-processing time by an order of magnitude in comparison with standard inverted files.
The fundamental question considered in algorithms on strings is that of indexing, that is, preprocessing a given string for specific queries. By now we have a number of efficient solutions for this problem when the queries ask for an exact…
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…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…
With the development of connected filters for the last decade, many algorithms have been proposed to compute the max-tree. Max-tree allows to compute the most advanced connected operators in a simple way. However, no fair comparison of…
Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…
Decision trees have been a very popular class of predictive models for decades due to their interpretability and good performance on categorical features. However, they are not always robust and tend to overfit the data. Additionally, if…
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main…
The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…
We consider the problems of computing maximal palindromes and distinct palindromes in a trie. A trie is a natural generalization of a string, which can be seen as a single-path tree. There is a linear-time offline algorithm to compute…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…