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Suffix trees are an important data structure at the core of optimal solutions to many fundamental string problems, such as exact pattern matching, longest common substring, matching statistics, and longest repeated substring. Recent lines…
Point feature map labeling is a geometric problem, in which a set of input points must be labeled with a set of disjoint rectangles (the bounding boxes of the label texts). Typically, labeling models either use internal labels, which must…
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…
The topic of this paper are integer programming models in which a subset of 0/1-variables encode a partitioning of a set of objects into disjoint subsets. Such models can be surprisingly hard to solve by branch-and-cut algorithms if the…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
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…
The problem of inferring unknown graph edges from numerical data at a graph's nodes appears in many forms across machine learning. We study a version of this problem that arises in the field of \emph{landscape genetics}, where genetic…
The Fibonacci heap is a classic data structure that supports deletions in logarithmic amortized time and all other heap operations in O(1) amortized time. We explore the design space of this data structure. We propose a version with the…
Rectangular layouts, subdivisions of an outer rectangle into smaller rectangles, have many applications in visualizing spatial information, for instance in rectangular cartograms in which the rectangles represent geographic or political…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
The entities in directed networks arising from real-world interactions are often naturally organized under some hierarchical structure. Given a directed, weighted, graph with edges and node labels, we introduce ranking problem where the…
In this article the authors continue the discussion in \cite{ALM} about inverse problems for second order elliptic and hyperbolic equations on metric trees from boundary measurements. In the present paper we prove the identifiability of…
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 give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
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…
An important problem in multi-label classification is to capture label patterns or underlying structures that have an impact on such patterns. This paper addresses one such problem, namely how to exploit hierarchical structures over labels.…
We investigate linear and additive codes in partially ordered Hamming-like spaces that satisfy the extension property, meaning that automorphisms of ideals extend to automorphisms of the poset. The codes are naturally described in terms of…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
In this paper, we revisit the much studied problem of Pattern Matching with Swaps (Swap Matching problem, for short). We first present a graph-theoretic model, which opens a new and so far unexplored avenue to solve the problem. Then, using…