Projects per year
Abstract
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 (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning.
Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.
Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.
Original language | English |
---|---|
Publisher | arXiv |
Publication status | Published - 2022 |
Fingerprint
Dive into the research topics of 'Graph Neural Networks for Microbial Genome Recovery'. Together they form a unique fingerprint.Projects
- 2 Finished
-
Data Science meets Microbial Dark Matter
Albertsen, M. (PI), Hose, K. (PI), Nielsen, T. D. (PI), Lamurias, A. (Project Participant) & Mølvang Dall, S. (Project Participant)
Villum Foundation, Danish E-infrastructure Cooperation
01/01/2021 → 31/12/2023
Project: Research
-
Poul Due Jensen Professorate in Big Data and Artificial Intelligence
Hose, K. (PI), Jendal, T. E. (Project Participant) & Hansen, E. R. (Project Participant)
01/11/2019 → 31/10/2024
Project: Research