Related papers: A step towards neural genome assembly

We address the problem of learning on sets of features, motivated by the need of performing pooling operations in long biological sequences of varying sizes, with long-range dependencies, and possibly few labeled data. To address this…

Graph Neural Networks (GNNs) have emerged as powerful tools for learning on graph-structured data, but often struggle to balance local and global information. While graph Transformers aim to address this by enabling long-range interactions,…

Currently the state of the art network models are based or depend on Discrete Event Simulation (DES). While DES is highly accurate, it is also computationally costly and cumbersome to parallelize, making it unpractical to simulate high…

Graph learning from data represents a canonical problem that has received substantial attention in the literature. However, insufficient work has been done in incorporating prior structural knowledge onto the learning of underlying…

As one of the most fundamental tasks in graph theory, subgraph matching is a crucial task in many fields, ranging from information retrieval, computer vision, biology, chemistry and natural language processing. Yet subgraph matching problem…

This paper describes a new method for representing embedding tables of graph neural networks (GNNs) more compactly via tensor-train (TT) decomposition. We consider the scenario where (a) the graph data that lack node features, thereby…

Topological deep learning is a rapidly growing field that pertains to the development of deep learning models for data supported on topological domains such as simplicial complexes, cell complexes, and hypergraphs, which generalize many…

In this paper, we explore a novel model reusing task tailored for graph neural networks (GNNs), termed as "deep graph reprogramming". We strive to reprogram a pre-trained GNN, without amending raw node features nor model parameters, to…

Deep neural networks have been applied to a wide range of problems across different application domains with great success. Recently, research into combinatorial optimization problems in particular has generated much interest in the machine…

Designing effective graph neural networks (GNNs) with message passing has two fundamental challenges, i.e., determining optimal message-passing pathways and designing local aggregators. Previous methods of designing optimal pathways are…

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…

Graph convolutional network (GCN) is an emerging neural network approach. It learns new representation of a node by aggregating feature vectors of all neighbors in the aggregation process without considering whether the neighbors or…

Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…

Deep learning models have demonstrated remarkable results for various computer vision tasks, including the realm of medical imaging. However, their application in the medical domain is limited due to the requirement for large amounts of…

Motivated by applications in social and biological network analysis, we introduce a new form of agnostic clustering termed~\emph{motif correlation clustering}, which aims to minimize the cost of clustering errors associated with both edges…

A hallmark of graph neural networks is their ability to distinguish the isomorphism class of their inputs. This study derives hardness results for the classification variant of graph isomorphism in the message-passing model (MPNN). MPNN…

The network embedding problem that maps nodes in a graph to vectors in Euclidean space can be very useful for addressing several important tasks on a graph. Recently, graph neural networks (GNNs) have been proposed for solving such a…

A novel Gromov-Wasserstein learning framework is proposed to jointly match (align) graphs and learn embedding vectors for the associated graph nodes. Using Gromov-Wasserstein discrepancy, we measure the dissimilarity between two graphs and…

Hypergraphs serve as an effective model for depicting complex connections in various real-world scenarios, from social to biological networks. The development of Hypergraph Neural Networks (HGNNs) has emerged as a valuable method to manage…

Graph convolutional networks (GCNs) are powerful deep neural networks for graph-structured data. However, GCN computes the representation of a node recursively from its neighbors, making the receptive field size grow exponentially with the…