Related papers: Read Mapping on de Bruijn graph

Graph Neural Networks (GNN) is an emerging field for learning on non-Euclidean data. Recently, there has been increased interest in designing GNN that scales to large graphs. Most existing methods use "graph sampling" or "layer-wise…

There is a growing interest in designing Graph Neural Networks (GNNs) for seeded graph matching, which aims to match two unlabeled graphs using only topological information and a small set of seed nodes. However, most previous GNNs for this…

Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…

The de Bruijn graph, its sequences, and their various generalizations, have found many applications in information theory, including many new ones in the last decade. In this paper, motivated by a coding problem for emerging memory…

Graph neural networks (GNNs) are prominent for their effectiveness in processing graph data for semi-supervised node classification tasks. Most works of GNNs assume that the observed structure accurately represents the underlying node…

This paper is focused in designing an efficient on-line algorithm to reconstruct a DNA sequence and search the genes in it, we assume that the segment have no mutation or reading error, the algorithm is based on de Bruijn Graph for…

Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…

As one of the core technologies for 5G systems, massive multiple-input multiple-output (MIMO) introduces dramatic capacity improvements along with very high beamforming and spatial multiplexing gains. When developing efficient physical…

Graph Neural Networks (GNNs) have demonstrated remarkable performance in a wide range of tasks, such as node classification, link prediction, and graph classification, by exploiting the structural information in graph-structured data.…

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…

Graph Neural Networks (GNNs) are widely used for learning on graph-structured data, but scaling GNN training to massive graphs remains challenging. To enable scalable distributed training, graphs are divided into smaller partitions that are…

Graph Neural Networks (GNNs) have attracted increasing attention in recent years and have achieved excellent performance in semi-supervised node classification tasks. The success of most GNNs relies on one fundamental assumption, i.e., the…

In genome-scale constraint-based metabolic models, gene deletion strategies are essential for achieving growth-coupled production, where cell growth and target metabolite synthesis occur simultaneously. Despite the inherently networked…

Discovery gene-disease links is important in biology and medicine areas, enabling disease identification and drug repurposing. Machine learning approaches accelerate this process by leveraging biological knowledge represented in ontologies…

Graph Neural Networks (GNNs) are emerging ML models to analyze graph-structure data. Graph Neural Network (GNN) execution involves both compute-intensive and memory-intensive kernels, the latter dominates the total time, being significantly…

The recent advancements in graph neural networks (GNNs) have led to state-of-the-art performances in various applications, including chemo-informatics, question-answering systems, and recommender systems. However, scaling up these methods…

Graph neural networks (GNNs), as a group of powerful tools for representation learning on irregular data, have manifested superiority in various downstream tasks. With unstructured texts represented as concept maps, GNNs can be exploited…

Graph Neural Network (GNN) on streaming graphs has gained increasing popularity. However, its practical deployment remains challenging, as the inference process relies on Runtime Embedding Computation (RTEC) to capture recent graph changes.…

Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a…

Graph Convolutional Networks (GCNs) have emerged as the state-of-the-art method for graph-based learning tasks. However, training GCNs at scale is still challenging, hindering both the exploration of more sophisticated GCN architectures and…