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The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. In this paper we…
The NP-complete Permutation Pattern Matching problem asks whether a permutation P (the pattern) can be matched into a permutation T (the text). A matching is an order-preserving embedding of P into T. In the Generalized Permutation Pattern…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
A pattern p (i.e., a string of variables and terminals) matches a word w, if w can be obtained by uniformly replacing the variables of p by terminal words. The respective matching problem, i.e., deciding whether or not a given pattern…
We propose an online algorithm for tracking a multidimensional time-varying parameter of a time series, which is also allowed to be a predictable process with respect to the underlying time series. The algorithm is driven by a gain…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
Width parameterizations of SAT, such as tree-width and path-width, enable the study of computationally more tractable and practical SAT instances. We give two simple algorithms. One that runs simultaneously in time-space…
Byte-pair encoding (BPE) is a ubiquitous algorithm in the subword tokenization process of language models as it provides multiple benefits. However, this process is solely based on pre-training data statistics, making it hard for the…
We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…
In this paper, we present a novel heuristic algorithm for the stable but NP-complete deformation-based edit distance on merge trees. Our key contribution is the introduction of a user-controlled look-ahead parameter that allows to trade off…
We propose a way of characterizing the algorithms computing a Walsh-Hadamard transform that consist of a sequence of arrays of butterflies ($I_{2^{n-1}}\otimes \text{DFT}_2$) interleaved by linear permutations. Linear permutations are those…
Bigraphs are a versatile modelling formalism that allows easy expression of placement and connectivity relations in a graphical format. System evolution is user defined as a set of rewrite rules. This paper presents a practical, yet…
We study the "set parameterized matching" problem, a generalization of the classical parameterized matching problem introduced by Baker. In set parameterized matching, both the pattern and text are sequences where each position contains a…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
In quantum computing, the efficient optimization of Pauli string decompositions is a crucial aspect for the compilation of quantum circuits for many applications, such as chemistry simulations and quantum machine learning. In this paper, we…
Many computational problems admit fast algorithms on special inputs, however, the required properties might be quite restrictive. E.g., many graph problems can be solved much faster on interval or cographs, or on graphs of small…
Fixed parameter tractable algorithms for bounded treewidth are known to exist for a wide class of graph optimization problems. While most research in this area has been focused on exact algorithms, it is hard to find decompositions of…
A $k$-mismatch square is a string of the form $XY$ where $X$ and $Y$ are two equal-length strings that have at most $k$ mismatches. Kolpakov and Kucherov [Theor. Comput. Sci., 2003] defined two notions of $k$-mismatch repeats, called…
In the field of parameterized complexity theory, the study of graph width measures has been intimately connected with the development of width-based model checking algorithms for combinatorial properties on graphs. In this work, we…
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an…