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Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal…
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…
There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…
We initiate a systematic study of utilizing predictions to improve over approximation guarantees of classic algorithms, without increasing the running time. We propose a systematic method for a wide class of optimization problems that ask…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
Text-to-pattern distance is a fundamental problem in string matching, where given a pattern of length $m$ and a text of length $n$, over an integer alphabet, we are asked to compute the distance between pattern and the text at every…
We study a generalization of the recently introduced order-preserving pattern matching, where instead of looking for an exact copy of the pattern, we only require that the relative order between the elements is the same. In our variant, we…
In the problem of $\texttt{Generalised Pattern Matching}\ (\texttt{GPM})$ [STOC'94, Muthukrishnan and Palem], we are given a text $T$ of length $n$ over an alphabet $\Sigma_T$, a pattern $P$ of length $m$ over an alphabet $\Sigma_P$, and a…
In CPM 2017, Amir et al. introduce a problem, named \emph{approximate string cover} (\textbf{ACP}), motivated by many aplications including coding and automata theory, formal language theory, combinatorics and molecular biology. A…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
The notion of $\mathcal{H}$-treewidth, where $\mathcal{H}$ is a hereditary graph class, was recently introduced as a generalization of the treewidth of an undirected graph. Roughly speaking, a graph of $\mathcal{H}$-treewidth at most $k$…
In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, the goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that the length-$m$ substrings of $T$ starting at positions $i$ and $j$…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
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…
The graph invariant EPT-sum has cropped up in several unrelated fields in later years: As an objective function for hierarchical clustering, as a more fine-grained version of the classical edge ranking problem, and, specifically when the…
The kTree problem is a special case of Subgraph Isomorphism where the pattern graph is a tree, that is, the input is an $n$-node graph $G$ and a $k$-node tree $T$, and the goal is to determine whether $G$ has a subgraph isomorphic to $T$.…