Related papers: Graph Neural Networks for Microbial Genome Recover…

Graph Nerual Networks (GNNs) are effective models in graph embedding. It extracts shallow features and neighborhood information by aggregating neighbor information to learn the embedding representation of different nodes. However, the local…

A significant advancement in bioinformatics is using genome graph techniques to improve variation discovery across organisms. Traditional approaches, such as bwa mem, rely on linear reference genomes for genomic analyses but may introduce…

Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as…

Graph Convolutional Networks (GCNs) have been shown to be a powerful concept that has been successfully applied to a large variety of tasks across many domains over the past years. In this work we study the theory that paved the way to the…

Deep Convolutional Neural Networks (CNNs) are capable of learning unprecedentedly effective features from images. Some researchers have struggled to enhance the parameters' efficiency using grouped convolution. However, the relation between…

We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…

Graph neural networks (GNNs) have shown prominent performance on attributed network embedding. However, existing efforts mainly focus on exploiting network structures, while the exploitation of node attributes is rather limited as they only…

Graph Neural Networks (GNNs) have been widely applied to various fields due to their powerful representations of graph-structured data. Despite the success of GNNs, most existing GNNs are designed to learn node representations on the fixed…

Semantic segmentation consists in classifying each pixel of an image by assigning it to a specific label chosen from a set of all the available ones. During the last few years, a lot of attention shifted to this kind of task. Many computer…

Multi-view clustering is an important machine learning task for multi-media data, encompassing various domains such as images, videos, and texts. Moreover, with the growing abundance of graph data, the significance of multi-view graph…

Metagenomics research has accelerated the studies of microbial organisms, providing insights into the composition and potential functionality of various microbial communities. Metatranscriptomics (studies of the transcripts from a mixture…

When analyzing communities of microorganisms from their sequenced DNA, an important task is taxonomic profiling: enumerating the presence and relative abundance of all organisms, or merely of all taxa, contained in the sample. This task can…

Employing graph neural networks (GNNs) for graph clustering has shown promising results in deep graph clustering. However, existing methods disregard the reciprocal relationship between representation learning and structure augmentation:…

De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…

Exploiting the wealth of imaging and non-imaging information for disease prediction tasks requires models capable of representing, at the same time, individual features as well as data associations between subjects from potentially large…

Graph neural networks (GNNs) are increasingly used to model biological systems, yet the reliability of post-hoc explanation methods for recovering meaningful molecular mechanisms remains unclear. Here, we systematically evaluate four widely…

Graph Neural Networks (GNNs) show strong expressive power on graph data mining, by aggregating information from neighbors and using the integrated representation in the downstream tasks. The same aggregation methods and parameters for each…

A large number of real-world graphs or networks are inherently heterogeneous, involving a diversity of node types and relation types. Heterogeneous graph embedding is to embed rich structural and semantic information of a heterogeneous…

From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to…

Predicting interspecies interactions is a key challenge in microbial ecology, as these interactions are critical to determining the structure and activity of microbial communities. In this work, we used data on monoculture growth…