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GeNet: Deep Representations for Metagenomics

https://doi.org/10.1101/537795
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1007/s10618-010-0175-9openalex-snapshot
A survey of hierarchical classification across different application domains
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The importance of the label hierarchy in hierarchical multi-label classification
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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle
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Hierarchical multi-label classification using local neural networks
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/ismej.2010.118openalex-snapshot
Dominant and diet-responsive groups of bacteria within the human colonic microbiota
inferredcites →https://doi.org/10.1038/nature06244openalex-snapshot
The Human Microbiome Project
inferredcites →https://doi.org/10.1038/nature18846openalex-snapshot
Diet–microbiota interactions as moderators of human metabolism
inferredcites →https://doi.org/10.1038/s41467-018-07641-9openalex-snapshot
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
inferredcites →https://doi.org/10.1038/s41587-020-00777-4openalex-snapshot
Improved metagenome binning and assembly using deep variational autoencoders
inferredcites →https://doi.org/10.1080/13102818.2018.1521302openalex-snapshot
A hierarchical multi-label classification method based on neural networks for gene function prediction
inferredcites →https://doi.org/10.1093/bioinformatics/bty191openalex-snapshot
Minimap2: pairwise alignment for nucleotide sequences
inferredcites →https://doi.org/10.1093/gigascience/giz043openalex-snapshot
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
inferredcites →https://doi.org/10.1093/nar/gkt1114openalex-snapshot
RefSeq: an update on mammalian reference sequences
inferredcites →https://doi.org/10.1101/353474openalex-snapshot
A deep learning approach to pattern recognition for short DNA sequences
inferredcites →https://doi.org/10.1101/gr.210641.116openalex-snapshot
Centrifuge: rapid and sensitive classification of metagenomic sequences
inferredcites →https://doi.org/10.1109/cvpr.2016.90openalex-snapshot
Deep Residual Learning for Image Recognition
inferredcites →https://doi.org/10.1126/science.1208344openalex-snapshot
Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
inferredcites →https://doi.org/10.1145/1015330.1015427openalex-snapshot
A hierarchical method for multi-class support vector machines
inferredcites →https://doi.org/10.1162/neco_a_00990openalex-snapshot
Deep Convolutional Neural Networks for Image Classification: A Comprehensive Review
inferredcites →https://doi.org/10.1186/1471-2164-13-1openalex-snapshot
Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s13059-016-1103-0openalex-snapshot
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
inferredcites →https://doi.org/10.48550/arxiv.1502.03167openalex-snapshot
Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-032-16808-5_6openalex-snapshot
Taxonomic Classification of Gene Sequences Using Deep Learning
inferred← citeshttps://doi.org/10.1007/s11760-026-05505-0openalex-snapshot
YOLOv11-ShipNet: a remote sensing image ship detection model based on dual-domain attention and focal-MPDIoU loss
inferred← citeshttps://doi.org/10.1038/s42003-022-03498-3openalex-snapshot
AMAISE: a machine learning approach to index-free sequence enrichment
inferred← citeshttps://doi.org/10.1073/pnas.2122636119openalex-snapshot
Taxonomic classification of DNA sequences beyond sequence similarity using deep neural networks
inferred← citeshttps://doi.org/10.1093/nargab/lqaa009openalex-snapshot
DeepMicrobes: taxonomic classification for metagenomics with deep learning
inferred← citeshttps://doi.org/10.1093/nargab/lqad082openalex-snapshot
MetaTransformer: deep metagenomic sequencing read classification using self-attention models
inferred← citeshttps://doi.org/10.1101/2020.10.29.360297openalex-snapshot
Towards end-to-end disease prediction from raw metagenomic data
inferred← citeshttps://doi.org/10.1101/2025.01.27.634943openalex-snapshot
Phylo-HS: A phylogenetic hierarchical softmax for taxonomic classification
inferred← citeshttps://doi.org/10.1109/icdmw53433.2021.00067openalex-snapshot
Metagenome2Vec: Building Contextualized Representations for Scalable Metagenome Analysis
inferred← citeshttps://doi.org/10.1186/s12859-020-03744-7openalex-snapshot
Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life
inferred← citeshttps://doi.org/10.1186/s12859-024-05760-3openalex-snapshot
MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes
inferred← citeshttps://doi.org/10.2174/9789815079005123050011openalex-snapshot
Deep Learning Techniques for Biomedical Research and Significant Gene Identification using Next Generation Sequencing (NGS) Data: - A Review
inferred← citeshttps://doi.org/10.2991/jaims.d.201028.001openalex-snapshot
Application of Deep Learning in Microbiome
inferred← citeshttps://doi.org/10.3390/biom13040585openalex-snapshot
DL-TODA: A Deep Learning Tool for Omics Data Analysis
inferred← citeshttps://doi.org/10.3390/metabo11010055openalex-snapshot
Linking Gut Microbiome and Lipid Metabolism: Moving beyond Associations
inferred← citeshttps://doi.org/10.70675/792af726z4ec2z4c52z868az6d92631761e6openalex-snapshot
End-to-End Deep Learning and Subgroup discovery approaches to learn from metagenomics data
inferred← citeshttps://doi.org/10.70675/bc11fdd1z0c3az45c3z9f9ez65301994b39dopenalex-snapshot
Continuous embeddings for large-scale machine learning with DNA sequences
inferred← citeshttps://doi.org/10.7250/itms-2020-0005openalex-snapshot
An Overview of the Application of Deep Learning in Short-Read Sequence Classification
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