Related papers: Read Mapping on de Bruijn graph

Graph Neural Networks (GNNs) offer a compact and computationally efficient way to learn embeddings and classifications on graph data. GNN models are frequently large, making distributed minibatch training necessary. The primary contribution…

Recently Graph Neural Network (GNN) has been applied successfully to various NLP tasks that require reasoning, such as multi-hop machine reading comprehension. In this paper, we consider a novel case where reasoning is needed over graphs…

Recently, graph neural networks (GNNs) have been shown powerful capacity at modeling structural data. However, when adapted to downstream tasks, it usually requires abundant task-specific labeled data, which can be extremely scarce in…

Graph neural networks (GNNs) have delivered remarkable results in various fields. However, the rapid increase in the scale of graph data has introduced significant performance bottlenecks for GNN inference. Both computational complexity and…

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…

With the increasing affordability and accessibility of genome sequencing data, de novo genome assembly is an important first step to a wide variety of downstream studies and analyses. Therefore, bioinformatics tools that enable the…

Graph neural networks (GNNs) have struggled to outperform traditional optimization methods on combinatorial problems, limiting their practical impact. We address this gap by introducing a novel chaining procedure for the graph alignment…

Graph Neural Networks (GNNs) are a computationally efficient method to learn embeddings and classifications on graph data. However, GNN training has low computational intensity, making communication costs the bottleneck for scalability.…

Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…

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…

Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics data in a time- and cost-efficient manner. It finished assembling a soil metagenomics dataset with 252Gbps in 44.1 hours and 99.6 hours on a single computing…

We present GNN-Suite, a robust modular framework for constructing and benchmarking Graph Neural Network (GNN) architectures in computational biology. GNN-Suite standardises experimentation and reproducibility using the Nextflow workflow to…

In recent years, Graph Neural Networks (GNNs) have achieved remarkable success in many graph mining tasks. However, scaling them to large graphs is challenging due to the high computational and storage costs of repeated feature propagation…

Algorithms for laying out large graphs have seen significant progress in the past decade. However, browsing large graphs remains a challenge. Rendering thousands of graphical elements at once often results in a cluttered image, and…

Graph Neural Networks (GNNs) have emerged as powerful tools for various graph mining tasks, yet existing scalable solutions often struggle to balance execution efficiency with prediction accuracy. These difficulties stem from iterative…

De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…

Spurred by widening gap between data processing speed and data communication speed in Von-Neumann computing architectures, some bioinformatic applications have harnessed the computational power of Processing-in-Memory (PIM) platforms.…