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 …
microbiomes. Though concealed from the naked eye, microbiomes govern and influence …
[HTML][HTML] Artificial intelligence approaches to human-microbiome protein–protein interactions
Host-microbiome interactions play significant roles in human health and disease. Artificial
intelligence approaches have been developed to better understand and predict the …
intelligence approaches have been developed to better understand and predict the …
Gut microbiome-metabolome interactions predict host condition
Background The effect of microbes on their human host is often mediated through changes
in metabolite concentrations. As such, multiple tools have been proposed to predict …
in metabolite concentrations. As such, multiple tools have been proposed to predict …
phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data
Motivation Research shows that human microbiome is highly dynamic on longitudinal
timescales, changing dynamically with diet, or due to medical interventions. In this article, we …
timescales, changing dynamically with diet, or due to medical interventions. In this article, we …
Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE
Background The human microbiome plays a critical role in maintaining human health. Due
to the recent advances in high-throughput sequencing technologies, the microbiome profiles …
to the recent advances in high-throughput sequencing technologies, the microbiome profiles …
Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy
The human gut microbiome is associated with a large number of disease etiologies. As
such, it is a natural candidate for machine-learning-based biomarker development for …
such, it is a natural candidate for machine-learning-based biomarker development for …
Predicting microbiome compositions from species assemblages through deep learning
Microbes can form complex communities that perform critical functions in maintaining the
integrity of their environment or their hosts' wellbeing. Rationally managing these microbial …
integrity of their environment or their hosts' wellbeing. Rationally managing these microbial …
DeepMicroGen: a generative adversarial network-based method for longitudinal microbiome data imputation
Motivation The human microbiome, which is linked to various diseases by growing
evidence, has a profound impact on human health. Since changes in the composition of the …
evidence, has a profound impact on human health. Since changes in the composition of the …
EnsDeepDP: an ensemble deep learning approach for disease prediction through metagenomics
Y Shen, J Zhu, Z Deng, W Lu… - IEEE/ACM Transactions …, 2022 - ieeexplore.ieee.org
A growing number of studies show that the human microbiome plays a vital role in human
health and can be a crucial factor in predicting certain human diseases. However …
health and can be a crucial factor in predicting certain human diseases. However …
MicroHDF: predicting host phenotypes with metagenomic data using a deep forest-based framework
K Shi, Q Liu, Q Ji, Q He, XM Zhao - Briefings in Bioinformatics, 2024 - academic.oup.com
The gut microbiota plays a vital role in human health, and significant effort has been made to
predict human phenotypes, especially diseases, with the microbiota as a promising indicator …
predict human phenotypes, especially diseases, with the microbiota as a promising indicator …