Related papers: A step towards neural genome assembly

Graph Neural Networks (GNNs) have been generalized to process the heterogeneous graphs by various approaches. Unfortunately, these approaches usually model the heterogeneity via various complicated modules. This paper aims to propose a…

Graph neural networks (GNNs) based methods have achieved impressive performance on node clustering task. However, they are designed on the homophilic assumption of graph and clustering on heterophilic graph is overlooked. Due to the lack of…

Graph spectral analysis can yield meaningful embeddings of graphs by providing insight into distributed features not directly accessible in nodal domain. Recent efforts in graph signal processing have proposed new decompositions-e.g., based…

The recent introduction of Graph Neural Networks (GNNs) and their growing popularity in the past few years has enabled the application of deep learning algorithms to non-Euclidean, graph-structured data. GNNs have achieved state-of-the-art…

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of…

The computation of distance measures between nodes in graphs is inefficient and does not scale to large graphs. We explore dense vector representations as an effective way to approximate the same information: we introduce a simple yet…

Graph neural networks (GNNs) face significant challenges with class imbalance, leading to biased inference results. To address this issue in heterogeneous graphs, we propose a novel framework that combines Graph Neural Network (GNN) and…

Sampling random nodes is a fundamental algorithmic primitive in the analysis of massive networks, with many modern graph mining algorithms critically relying on it. We consider the task of generating a large collection of random nodes in…

Previous AutoML pruning works utilized individual layer features to automatically prune filters. We analyze the correlation for two layers from the different blocks which have a short-cut structure. It shows that, in one block, the deeper…

The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…

The complicated syntax structure of natural language is hard to be explicitly modeled by sequence-based models. Graph is a natural structure to describe the complicated relation between tokens. The recent advance in Graph Neural Networks…

In this study, we introduce a domain-decomposition-based distributed training and inference approach for message-passing neural networks (MPNN). Our objective is to address the challenge of scaling edge-based graph neural networks as the…

Graph neural networks have achieved state-of-the-art accuracy for graph node classification. However, GNNs are difficult to scale to large graphs, for example frequently encountering out-of-memory errors on even moderate size graphs. Recent…

Because of its wide application, critical nodes identification has become an important research topic at the micro level of network science. Influence maximization is one of the main problems in critical nodes mining and is usually handled…

Subgraph pattern detection aims to uncover complex interaction structures in graphs. However, state-of-the-art graph neural network (GNN)-based solutions assume centralized access to the entire graph. When graphs are instead distributed…

Graph Neural Networks (GNNs) are a form of deep learning that enable a wide range of machine learning applications on graph-structured data. The learning of GNNs, however, is known to pose challenges for memory-constrained devices such as…

Combinatorial optimization problems near algorithmic phase transitions represent a fundamental challenge for both classical algorithms and machine learning approaches. Among them, graph coloring stands as a prototypical constraint…

Message Passing Neural Networks (MPNNs) model local relations effectively but struggle to propagate information over long distances. Graph Transformers (GTs) mitigate this via global self-attention, yet their quadratic cost in the number of…

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…

Developing automated and semi-automated solutions for reconstructing wiring diagrams of the brain from electron micrographs is important for advancing the field of connectomics. While the ultimate goal is to generate a graph of neuron…