Related papers: Identifying bubble-like subgraphs in linear-time v…
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…
Pangenomics uses graph-based models to represent and study the genetic variation between individuals of the same species or between different species. In such variation graphs, a path through the graph represents one individual genome.…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
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…
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…
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…
Finding dense substructures in a graph is a fundamental graph mining operation, with applications in bioinformatics, social networks, and visualization to name a few. Yet most standard formulations of this problem (like clique, quasiclique,…
Subgraph counting aims to count the occurrences of a subgraph template T in a given network G. The basic problem of computing structural properties such as counting triangles and other subgraphs has found applications in diverse domains.…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
As neural interfaces become more advanced, there has been an increase in the volume and complexity of neural data recordings. These interfaces capture rich information about neural dynamics that call for efficient, real-time processing…
We study the classic problem of subgraph counting, where we wish to determine the number of occurrences of a fixed pattern graph $H$ in an input graph $G$ of $n$ vertices. Our focus is on bounded degeneracy inputs, a rich family of graph…
An SPQR-tree is a data structure that efficiently represents all planar embeddings of a biconnected planar graph. It is a key tool in a number of constrained planarity testing algorithms, which seek a planar embedding of a graph subject to…
We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced…
Subgraph-based graph representation learning (SGRL) has been recently proposed to deal with some fundamental challenges encountered by canonical graph neural networks (GNNs), and has demonstrated advantages in many important data science…
Inspired by the operation of biological brains, Spiking Neural Networks (SNNs) have the unique ability to detect information encoded in spatio-temporal patterns of spiking signals. Examples of data types requiring spatio-temporal processing…
Graph classification is essential for understanding complex biological systems, where molecular structures and interactions are naturally represented as graphs. Traditional graph neural networks (GNNs) perform well on static tasks but…
The design and analysis of communication systems typically rely on the development of mathematical models that describe the underlying communication channel. However, in some systems, such as molecular communication systems where chemical…
Bipartite graphs are ubiquitous in many domains, e.g., e-commerce platforms, social networks, and academia, by modeling interactions between distinct entity sets. Within these graphs, the butterfly motif, a complete 2*2 biclique, represents…
We study the problem of graph structure identification, i.e., of recovering the graph of dependencies among time series. We model these time series data as components of the state of linear stochastic networked dynamical systems. We assume…
For $p,q\ge2$ the $\{p,q\}$-tiling graph is the (finite or infinite) planar graph $T_{p,q}$ where all faces are cycles of length $p$ and all vertices have degree $q$. We give algorithms for the problem of recognizing (induced) subgraphs of…