Machine learning and deep learning applications in microbiome research

R Hernández Medina, S Kutuzova… - ISME …, 2022 - academic.oup.com
The many microbial communities around us form interactive and dynamic ecosystems called
microbiomes. Though concealed from the naked eye, microbiomes govern and influence …

Application of deep learning in plant–microbiota association analysis

Z Deng, J Zhang, J Li, X Zhang - Frontiers in Genetics, 2021 - frontiersin.org
Unraveling the association between microbiome and plant phenotype can illustrate the
effect of microbiome on host and then guide the agriculture management. Adequate …

DeepMicro: deep representation learning for disease prediction based on microbiome data

M Oh, L Zhang - Scientific reports, 2020 - nature.com
Human microbiota plays a key role in human health and growing evidence supports the
potential use of microbiome as a predictor of various diseases. However, the high …

Microbiome-based disease prediction with multimodal variational information bottlenecks

F Grazioli, R Siarheyeu, I Alqassem… - PLOS Computational …, 2022 - journals.plos.org
Scientific research is shedding light on the interaction of the gut microbiome with the human
host and on its role in human health. Existing machine learning methods have shown great …

Developing a new phylogeny-driven Random Forest Model for functional metagenomics

JT Wassan, H Wang, H Zheng - IEEE Transactions on …, 2023 - ieeexplore.ieee.org
Metagenomics is an unobtrusive science linking microbial genes to biological functions or
environmental states. Classifying microbial genes into their functional repertoire is an …

Disease prediction using synthetic image representations of metagenomic data and convolutional neural networks

TH Nguyen, E Prifti, N Sokolovska… - 2019 IEEE-RIVF …, 2019 - ieeexplore.ieee.org
Information from metagenomic data from human microbiome may improve diagnosis and
prognosis for multiple human diseases. However, to achieve a prediction based on bacterial …

Integrating artificial intelligence in exploring multiscale gut microbiota and diet relations for health promotion: A comprehensive review

Z Yang, J Zhu, W Lu, F Tian, H Zhang, W Chen - Food Bioscience, 2024 - Elsevier
The gut microbiome plays a crucial role in human health, particularly its interactions with diet
and specific food components. However, understanding this intricate relationship across …

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

MA Rahman, H Rangwala - Bioinformatics, 2020 - academic.oup.com
Motivation The human body hosts more microbial organisms than human cells. Analysis of
this microbial diversity provides key insight into the role played by these microorganisms on …

A hybrid machine learning approach for the phenotypic classification of metagenomic colon cancer reads based on kmer frequency and biomarker profiling

A Kishk, A Elzizy, D Galal, EA Razek… - 2018 9th Cairo …, 2018 - ieeexplore.ieee.org
Human Microbiome plays a critical role in health and the environment. Colorectal cancer
(CRC) is the most common cause of death in many countries, and hence early diagnosis of …

Clustering-based visualizations for diagnosing diseases on metagenomic data

HT Nguyen, TH Phan, LTT Pham, NH Pham - Signal, Image and Video …, 2024 - Springer
Metagenomic data has recently become crucial for precision or personalized medicine.
However, these data are often complex, challenging to observe and require sophisticated …