Related papers: Hardness of Covering Alignment: Phase Transition i…
A pangenome captures the genetic diversity across multiple individuals simultaneously, providing a more comprehensive reference for genome analysis than a single linear genome, which may introduce allele bias. A widely adopted pangenome…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
In this paper, we study a dynamic analogue of the Path Cover problem, which can be solved in polynomial-time in directed acyclic graphs. A temporal digraph has an arc set that changes over discrete time-steps, if the underlying digraph (the…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
We provide a novel new approach for aligning geometric models using a dual graph structure where local features are mapping probabilities. Alignment of non-rigid structures is one of the most challenging computer vision tasks due to the…
Graph alignment refers to the problem of finding a bijective mapping across vertices of two graphs such that, if two nodes are connected in the first graph, their images are connected in the second graph. This problem arises in many fields…
The coverage depth problem in DNA data storage is about computing the expected number of reads needed to recover all encoded strands. Given a generator matrix of a linear code, this quantity equals the expected number of randomly drawn…
An exact-match overlap graph of $n$ given strings of length $\ell$ is an edge-weighted graph in which each vertex is associated with a string and there is an edge $(x,y)$ of weight $\omega = \ell - |ov_{max}(x,y)|$ if and only if $\omega…
In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs…
We investigate here the computational complexity of three natural problems in directed acyclic graphs. We prove their NP Completeness and consider their restrictions to linear orders.
Graph-based semi-supervised learning, which can exploit the connectivity relationship between labeled and unlabeled data, has been shown to outperform the state-of-the-art in many artificial intelligence applications. One of the most…
Correspondence homomorphisms are both a generalization of standard homomorphisms and a generalization of correspondence colourings. For a fixed target graph $H$, the problem is to decide whether an input graph $G$, with each edge labeled by…
We introduce and study the complexity of Path Packing. Given a graph $G$ and a list of paths, the task is to embed the paths edge-disjoint in $G$. This generalizes the well known Hamiltonian-Path problem. Since Hamiltonian Path is…
We study the {\sc Graph Relabeling Problem}--given an undirected, connected, simple graph $G = (V,E)$, two labelings $L$ and $L'$ of $G$, and label {\em flip} or {\em mutation} functions determine the complexity of transforming or evolving…
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…
Graph neural networks (GNNs) have achieved impressive impressions for graph-related tasks. However, most GNNs are primarily studied under the cases of signal domain with supervised training, which requires abundant task-specific labels and…
Planar graphs can be represented as intersection graphs of different types of geometric objects in the plane, e.g., circles (Koebe, 1936), line segments (Chalopin \& Gon{\c{c}}alves, 2009), \textsc{L}-shapes (Gon{\c{c}}alves et al, 2018).…
Graph neural networks (GNNs) and message passing neural networks (MPNNs) have been proven to be expressive for subgraph structures in many applications. Some applications in heterogeneous graphs require explicit edge modeling, such as…
Let H be a graph, and let C_H(G) be the number of (subgraph isomorphic) copies of H contained in a graph G. We investigate the fundamental problem of estimating C_H(G). Previous results cover only a few specific instances of this general…
Hypergraphs tackle the limitations of traditional graphs by introducing {\em hyperedges}. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges. Also, the underlying message-passing…