Related papers: Read Mapping on de Bruijn graph

Recently graph neural network (GNN) based algorithms were proposed to solve a variety of combinatorial optimization problems, including Maximum Cut problem, Maximum Independent Set problem and similar other…

As powerful tools for representation learning on graphs, graph neural networks (GNNs) have facilitated various applications from drug discovery to recommender systems. Nevertheless, the effectiveness of GNNs is immensely challenged by…

Heterogeneous graphs, which contain nodes and edges of multiple types, are prevalent in various domains, including bibliographic networks, social media, and knowledge graphs. As a fundamental task in analyzing heterogeneous graphs,…

Multi-hop reading comprehension across multiple documents attracts much attention recently. In this paper, we propose a novel approach to tackle this multi-hop reading comprehension problem. Inspired by human reasoning processing, we…

Graph neural networks (GNNs) have emerged as powerful tools for processing relational data in applications. However, GNNs suffer from the problem of oversmoothing, the property that the features of all nodes exponentially converge to the…

Graph Neural Networks (GNNs) are gaining extensive attention for their application in graph data. However, the black-box nature of GNNs prevents users from understanding and trusting the models, thus hampering their applicability. Whereas…

Searching on bipartite graphs is basal and versatile to many real-world Web applications, e.g., online recommendation, database retrieval, and query-document searching. Given a query node, the conventional approaches rely on the similarity…

We developed pgMAP, an analysis pipeline to map gRNA sequencing reads from dual-targeting CRISPR screens. pgMAP output includes a dual gRNA read counts table and quality control metrics including the proportion of correctly-paired reads and…

Extensive research has been conducted, over recent years, on various ways of enhancing heuristic search for combinatorial optimization problems with machine learning algorithms. In this study, we investigate the use of predictions from…

Graph Neural Networks (GNNs) face two fundamental challenges when scaled to deep architectures: oversmoothing, where node representations converge to indistinguishable vectors, and oversquashing, where information from distant nodes fails…

Graph neural networks (GNNs) have gained significant interest for applications such as citation network analysis and drug discovery due to their ability to apply machine learning techniques on graph-structured data. GNNs typically employ a…

We apply matrix completion methods for haplotype assembly from NGS reads to develop the new HapSVT, HapNuc, and HapOPT algorithms. This is performed by applying a mathematical model to convert the reads to an incomplete matrix and…

The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating…

Graph neural networks (GNNs) are designed to process data associated with graphs. They are finding an increasing range of applications; however, as with other modern machine learning techniques, their theoretical understanding is limited.…

The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…

Given a large-scale graph with millions of nodes and edges, how to reveal macro patterns of interest, like cliques, bi-partite cores, stars, and chains? Furthermore, how to visualize such patterns altogether getting insights from the graph…

The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…

Graph matching has important applications in pattern recognition and beyond. Current approaches predominantly adopt supervised learning, demanding extensive labeled data which can be limited or costly. Meanwhile, self-supervised learning…

In graph neural networks (GNNs), message passing iteratively aggregates nodes' information from their direct neighbors while neglecting the sequential nature of multi-hop node connections. Such sequential node connections e.g., metapaths,…

With the ubiquitous graph-structured data in various applications, models that can learn compact but expressive vector representations of nodes have become highly desirable. Recently, bearing the message passing paradigm, graph neural…