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The LCP array is an important tool in stringology, allowing to speed up pattern matching algorithms and enabling compact representations of the suffix tree. Recently, Conte et al. [DCC 2023] and Cotumaccio et al. [SPIRE 2023] extended the…
We study the problem of learning an unknown graph via group queries on node subsets, where each query reports whether at least one edge is present among the queried nodes. In general, learning arbitrary graphs with $n$ nodes and $k$ edges…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Graph Neural Networks (GNNs) as deep learning models working on graph-structure data have achieved advanced performance in many works. However, it has been proved repeatedly that, not all edges in a graph are necessary for the training of…
This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that…
We address the problem of enumerating all maximal clique-partitions of an undirected graph and present an algorithm based on the observation that every maximal clique-partition can be produced from the maximal clique-cover of the graph by…
Hypergraphs, increasingly utilised to model complex and diverse relationships in modern networks, have gained significant attention for representing intricate higher-order interactions. Among various challenges, cohesive subgraph discovery…
We present practical algorithms for generating universal cycles uniformly at random. In particular, we consider universal cycles for shorthand permutations, subsets and multiset permutations, weak orders, and orientable sequences.…
Motivation: Data volumes generated by next-generation sequencing technolo- gies is now a major concern, both for storage and transmission. This triggered the need for more efficient methods than general purpose compression tools, such as…
Every binary De~Bruijn sequence of order n satisfies a recursion 0=x_n+x_0+g(x_{n-1}, ..., x_1). Given a function f on (n-1) bits, let N(f; r) be the number of functions generating a De Bruijn sequence of order n which are obtained by…
Subgraph matching, a cornerstone of relational pattern detection in domains ranging from biochemical systems to social network analysis, faces significant computational challenges due to the dramatically growing search space. Existing…
Canonical orderings and their relatives such as st-numberings have been used as a key tool in algorithmic graph theory for the last decades. Recently, a unifying concept behind all these orders has been shown: they can be described by a…
Graphs and various graph-like combinatorial structures, such as preorders and hypergraphs, are ubiquitous in programming. This paper focuses on representing graphs in a purely functional programming language like Haskell. There are several…
In the area of distributed graph algorithms a number of network's entities with local views solve some computational task by exchanging messages with their neighbors. Quite unfortunately, an inherent property of most existing distributed…
Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very…
Graph Neural Networks (GNNs) have emerged as a dominant paradigm for graph classification. Specifically, most existing GNNs mainly rely on the message passing strategy between neighbor nodes, where the expressivity is limited by the…
A de Bruijn sequence of order $k$ over a finite alphabet is a cyclic sequence with the property that it contains every possible $k$-sequence as a substring exactly once. Orthogonal de Bruijn sequences are collections of de Bruijn sequences…
A generalized de Bruijn digraph generalizes a de Bruijn digraph to the case where the number of vertices need not be a pure power of an integer. Hamiltonian cycles in these digraphs thus generalize regular de~Bruijn cycles, and we will thus…
De Bruijn tori, or perfect maps, are two-dimensional periodic arrays of letters from a finite alphabet, where each possible pattern of shape (m,n) appears exactly once in a single period. While the existence of certain de Bruijn tori, such…
A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…