Related papers: Suffix Tree of Alignment: An Efficient Index for S…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
Long document classification presents challenges in capturing both local and global dependencies due to their extensive content and complex structure. Existing methods often struggle with token limits and fail to adequately model…
Comparing observed behavior (event data generated during process executions) with modeled behavior (process models), is an essential step in process mining analyses. Alignments are the de-facto standard technique for calculating conformance…
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
This paper introduces a data structure, called simplex tree, to represent abstract simplicial complexes of any dimension. All faces of the simplicial complex are explicitly stored in a trie whose nodes are in bijection with the faces of the…
We present a simple algorithm for computing the document array given a string collection and its suffix array as input. Our algorithm runs in linear time using constant additional space for strings from constant alphabets.
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
Approximate pattern matching is a natural and well-studied problem on strings: Given a text $T$, a pattern $P$, and a threshold $k$, find (the starting positions of) all substrings of $T$ that are at distance at most $k$ from $P$. We…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
We consider the following generalization of the binary search problem. A search strategy is required to locate an unknown target node $t$ in a given tree $T$. Upon querying a node $v$ of the tree, the strategy receives as a reply an…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
We show how, given a straight-line program with $g$ rules for a binary string $B$ of length $n$, in $O(g^{2 / 3} n^{4 / 3})$ time we can build a linear-space index such that, given $m$ and $c$, in O(1) time we can determine whether there is…
The directed acyclic word graph (DAWG) of a string $y$ of length $n$ is the smallest (partial) DFA which recognizes all suffixes of $y$ with only $O(n)$ nodes and edges. In this paper, we show how to construct the DAWG for the input string…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 47:15--32, 2015]) are compact indices for texts over an alphabet $[0,\sigma)$ that support rank, select and access queries in $O(\lg \sigma)$ time.…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
The classic string indexing problem is to preprocess a string $S$ into a compact data structure that supports efficient subsequent pattern matching queries, that is, given a pattern string $P$, report all occurrences of $P$ within $S$. In…