Related papers: Ultrabubble enumeration via a lowest common ancest…

A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph. These correspond to regions of genetic variation and are…

Bidirected graphs are a common generalisation of directed graphs where arcs can also be incoming to both their incident nodes, or outgoing from both their incident nodes. Such arcs allow a walk to change direction. Some algorithms can…

Superbubbles are acyclic induced subgraphs of a digraph with single entrance and exit that naturally arise in the context of genome assembly and the analysis of genome alignments in computational biology. These structures can be computed in…

Snarls and superbubbles are fundamental pangenome decompositions capturing variant sites. These bubble-like structures underpin key tasks in computational pangenomics, including structural-variant genotyping, distance indexing, haplotype…

A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…

The dominant paradigm for learning on graph-structured data is message passing. Despite being a strong inductive bias, the local message passing mechanism suffers from pathological issues such as over-smoothing, over-squashing, and limited…

Hypergraph offers a framework to depict the multilateral relationships in real-world complex data. Predicting higher-order relationships, i.e hyperedge, becomes a fundamental problem for the full understanding of complicated interactions.…

In this paper, we introduce flubbles, a new definition of "bubbles" corresponding to variants in a (pan)genome graph $G$. We then show a characterization for flubbles in terms of equivalence classes regarding cycles in an intermediate data…

We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect…

Unsupervised graph representation learning aims to learn low-dimensional node embeddings without supervision while preserving graph topological structures and node attributive features. Previous graph neural networks (GNN) require a large…

Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…

Alternative splicing creates complex bubbles in splicing graphs where more than two transcript paths compete, challenging methods designed for simple binary events. We present a unified framework that compares paths using distinct exonic…

Graph anomaly detection (GAD) is a critical task in graph machine learning, with the primary objective of identifying anomalous nodes that deviate significantly from the majority. This task is widely applied in various real-world scenarios,…

Bundling of graph edges (node-to-node connections) is a common technique to enhance visibility of overall trends in the edge structure of a large graph layout, and a large variety of bundling algorithms have been proposed. However, with…

Bundle recommendation is an emerging research direction in the recommender system with the focus on recommending customized bundles of items for users. Although Graph Neural Networks (GNNs) have been applied in this problem and achieve…

Graph Neural Networks (GNNs) have emerged as a powerful category of learning architecture for handling graph-structured data. However, existing GNNs typically ignore crucial structural characteristics in node-induced subgraphs, which thus…

Many complex systems involve interactions between more than two agents. Hypergraphs capture these higher-order interactions through hyperedges that may link more than two nodes. We consider the problem of embedding a hypergraph into…

Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…

The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…