Article

Deep Learning Enables Design of Multifunctional Synthetic Human Gut Microbiome Dynamics

2021-09-28

Abstract excerpt

Predicting the dynamics and functions of microbiomes constructed from the bottom-up is a key challenge in exploiting them to our benefit. Current ordinary differential equation-based models fail to capture complex behaviors that fall outside of a predetermined ecological theory and do not scale well with increasing community complexity and in considering multiple functions. We develop and apply a long short-term m...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: e5148987-4cde-502e-8b69-160f7862c01f
DOI: 10.1101/2021.09.27.461983

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Deep Learning Enables Design of Multifunctional Synthetic Human Gut Microbiome DynamicsDOI 10.1101/2021.09.27.461983Read

Predicting microbiome compositions from species assemblages through deep learningSemantic proximity Read

System Biology Modeling with Compositional Microbiome Data Reveals Personalized Gut Microbial Dynamics and Keystone SpeciesSemantic proximity Read

Learning functional groups in complex microbiomesSemantic proximity Read

Perturbation-Aware Neural ODE (pNODE) Learns Microbiome Dynamics from Clinical Data and Predicts Gut-Borne Bloodstream Infections in Patients Receiving Cancer TreatmentSemantic proximity Read

Predicting metabolomic profiles from microbial composition through neural ordinary differential equationsSemantic proximity Read

MGM as a large-scale pretrained foundation model for microbiome analyses in diverse contextsSemantic proximity Read

DeepBioSim: Efficient and Versatile Methods for Microbiome Data Simulation with Minimal Statistical AssumptionsSemantic proximity Read

Bayesian inference captures metabolite-bacteria interactions in a microbial communitySemantic proximity Read

MDITRE: scalable and interpretable machine learning for predicting host status from temporal microbiome dynamicsSemantic proximity Read

Microbial dynamics inference at ecosystem-scaleSemantic proximity Read

BiomeGPT: A foundation model for the human gut microbiomeSemantic proximity Read

mbDriver: identifying driver microbes in microbial communities based on time-series microbiome dataSemantic proximity Read