kernInt: A kernel framework for integrating supervised and unsupervised analyses in spatio-temporal metagenomic datasets
The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the...
| Autores: | , , , , , |
|---|---|
| Tipo de recurso: | artículo |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/349397 |
| Acceso en línea: | https://hdl.handle.net/2117/349397 https://dx.doi.org/10.3389/fmicb.2021.609048 |
| Access Level: | acceso abierto |
| Palabra clave: | Microbiology Machine learning Microbiome Metagenomics Kernel Supervised Unsupervised Spatio-temporal SVM kPCA Microbiologia Aprenentatge automàtic Àrees temàtiques de la UPC::Informàtica::Intel·ligència artificial::Aprenentatge automàtic Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica |
| Sumario: | The advent of next-generation sequencing technologies allowed relative quantification of microbiome communities and their spatial and temporal variation. In recent years, supervised learning (i.e., prediction of a phenotype of interest) from taxonomic abundances has become increasingly common in the microbiome field. However, a gap exists between supervised and classical unsupervised analyses, based on computing ecological dissimilarities for visualization or clustering. Despite this, both approaches face common challenges, like the compositional nature of next-generation sequencing data or the integration of the spatial and temporal dimensions. Here we propose a kernel framework to place on a common ground the unsupervised and supervised microbiome analyses, including the retrieval of microbial signatures (taxa importances). We define two compositional kernels (Aitchison-RBF and compositional linear) and discuss how to transform non-compositional beta-dissimilarity measures into kernels. Spatial data is integrated with multiple kernel learning, while longitudinal data is evaluated by specific kernels. We illustrate our framework through a single point soil dataset, a human dataset with a spatial component, and a previously unpublished longitudinal dataset concerning pig production. The proposed framework and the case studies are freely available in the kernInt package at https://github.com/elies-ramon/kernInt. |
|---|