Related papers: Variable-Order de Bruijn Graphs
While Graph Neural Networks (GNNs) excel on graph-structured data, their performance is fundamentally limited by the quality of the observed graph, which often contains noise, missing links, or structural properties misaligned with GNNs'…
We investigate a process of joining $k$ random spanning trees on a fixed clique $K_n$. The joined trees may not be disjoint and multiple edges are replaced by one simple edge. This process produces a simple graph $G$ on $n$~vertices with an…
Graph neural networks (GNNs) demonstrate a robust capability for representation learning on graphs with complex structures, showcasing superior performance in various applications. The majority of existing GNNs employ a graph convolution…
Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…
Bipartite graphs are a prevalent modeling tool for real-world networks, capturing interactions between vertices of two different types. Within this framework, bicliques emerge as crucial structures when studying dense subgraphs: they are…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
Goal-conditioned rearrangement of deformable objects (e.g. straightening a rope and folding a cloth) is one of the most common deformable manipulation tasks, where the robot needs to rearrange a deformable object into a prescribed goal…
The crossing number of a graph $G$, $\mathrm{cr}(G)$, is the minimum number of edge crossings arising when drawing a graph on a certain surface. Determining $\mathrm{cr}(G)$ is a problem of great importance in Graph Theory. Its maximum…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
The discrepancy of a binary string is the maximum (absolute) difference between the number of ones and the number of zeroes over all possible substrings of the given binary string. In this note we determine the minimal discrepancy that a…
Numerous subgraph-enhanced graph neural networks (GNNs) have emerged recently, provably boosting the expressive power of standard (message-passing) GNNs. However, there is a limited understanding of how these approaches relate to each other…
We introduce the class of interval $H$-graphs, which is the generalization of interval graphs, particularly interval bigraphs. For a fixed graph $H$ with vertices $a_1,a_2,\dots,a_k$, we say that an input graph $G$ with given partition…
Graph Convolutional Networks (GCNs) have recently become the primary choice for learning from graph-structured data, superseding hash fingerprints in representing chemical compounds. However, GCNs lack the ability to take into account the…
Reducing the cost of sequencing genomes provided by next-generation sequencing technologies has greatly increased the number of genomic projects. As a result, there is a growing need for better assembly and assembly validation methods. One…
Graphs provide a natural representation of relational structure that arises across diverse domains. Despite this ubiquity, graph structure is typically learned in a modality- and task-isolated manner, where graph representations are…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…
We study spreading processes in temporal graphs, i. e., graphs whose connections change over time. These processes naturally model real-world phenomena such as infectious diseases or information flows. More precisely, we investigate how…
An edge-ordered graph is a graph with a total ordering of its edges. A path $P=v_1v_2\ldots v_k$ in an edge-ordered graph is called increasing if $(v_iv_{i+1}) > (v_{i+1}v_{i+2})$ for all $i = 1,\ldots,k-2$; it is called decreasing if…
Given a collection of planar graphs $G_1,\dots,G_k$ on the same set $V$ of $n$ vertices, the simultaneous geometric embedding (with mapping) problem, or simply $k$-SGE, is to find a set $P$ of $n$ points in the plane and a bijection $\phi:…