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DNA rearrangement processes recombine gene segments that are organized on the chromosome in a variety of ways. The segments can overlap, interleave or one may be a subsegment of another. We use directed graphs to represent segment…

In the graph clustering problem with a planted solution, the input is a graph on $n$ vertices partitioned into $k$ clusters, and the task is to infer the clusters from graph structure. A standard assumption is that clusters induce…

The task of data integration for multi-omics data has emerged as a powerful strategy to unravel the complex biological underpinnings of cancer. Recent advancements in graph neural networks (GNNs) offer an effective framework to model…

Graphical models or networks describe the statistical dependence among multiple variables and are widely used in biology (e.g., gene regulatory networks). Under appropriate assumptions, directed edges may represent causal relationships. A…

While Graph Neural Networks (GNNs) are powerful models for learning representations on graphs, most state-of-the-art models do not have significant accuracy gain beyond two to three layers. Deep GNNs fundamentally need to address: 1).…

In graphical modelling, a bi-directed graph encodes marginal independences among random variables that are identified with the vertices of the graph. We show how to transform a bi-directed graph into a maximal ancestral graph that (i)…

Graphs are used widely to model complex systems, and detecting anomalies in a graph is an important task in the analysis of complex systems. Graph anomalies are patterns in a graph that do not conform to normal patterns expected of the…

We define the crossing graph of a given embedded graph (such as a road network) to be a graph with a vertex for each edge of the embedding, with two crossing graph vertices adjacent when the corresponding two edges of the embedding cross…

A nut graph is a simple graph whose kernel is spanned by a single full vector (i.e. the adjacency matrix has a single zero eigenvalue and all non-zero kernel eigenvectors have no zero entry). We classify generalisations of nut graphs to nut…

The genus of a graph is a topological invariant that measures the minimum genus of a surface on which the graph can be embedded without any edges crossing. Graph genus plays a fundamental role in topological graph theory, used to classify…

A graph $H$ is an induced subgraph of a graph $G$ if a graph isomorphic to $H$ can be obtained from $G$ by deleting vertices. Recently, there has been significant interest in understanding the unavoidable induced subgraphs for graphs of…

Ordered binary decision diagrams (OBDDs) are an efficient data structure for representing and manipulating Boolean formulas. With respect to different variable orders, the OBDDs' sizes may vary from linear to exponential in the number of…

This paper is devoted to signal processing on point-clouds by means of neural networks. Nowadays, state-of-the-art in image processing and computer vision is mostly based on training deep convolutional neural networks on large datasets.…

There is a growing need for methods which can capture uncertainties and answer queries over graph-structured data. Two common types of uncertainty are uncertainty over the attribute values of nodes and uncertainty over the existence of…

Grid diagrams with their relatively simple mathematical formalism provide a convenient way to generate and model projections of various knots. It has been an open question whether these 2D diagrams can be used to model a complex 3D process…

In evolutionary computation, it is commonly assumed that a search algorithm acquires knowledge about a problem instance by sampling solutions from the search space and evaluating them with a fitness function. This is necessarily inefficient…

Graphs are a powerful data structure to represent relational data and are widely used to describe complex real-world data structures. Probabilistic Graphical Models (PGMs) have been well-developed in the past years to mathematically model…

Knowledge hypergraphs generalize knowledge graphs using hyperedges to connect multiple entities and depict complicated relations. Existing methods either transform hyperedges into an easier-to-handle set of binary relations or view…

Graph clustering has been popularly studied in recent years. However, most existing graph clustering methods focus on node-level clustering, i.e., grouping nodes in a single graph into clusters. In contrast, graph-level clustering, i.e.,…

Hypergraphs generalize classical graphs by allowing a single edge to connect multiple vertices, providing a natural language for modeling higher-order interactions. Superhypergraphs extend this paradigm further by accommodating nested,…