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README.md
README.md
 
 
compute_performance_per_sample_test_set.ipynb
compute_performance_per_sample_test_set.ipynb
 
 
model_aggregated_3domainFeatures_class.ipynb
model_aggregated_3domainFeatures_class.ipynb
 
 
model_aggregated_3domainFeatures_family.ipynb
model_aggregated_3domainFeatures_family.ipynb
 
 
model_aggregated_3domainFeatures_genus.ipynb
model_aggregated_3domainFeatures_genus.ipynb
 
 
model_aggregated_3domainFeatures_order.ipynb
model_aggregated_3domainFeatures_order.ipynb
 
 
model_aggregated_3domainFeatures_phylum.ipynb
model_aggregated_3domainFeatures_phylum.ipynb
 
 
model_reference_1domainFeatures_age.ipynb
model_reference_1domainFeatures_age.ipynb
 
 
model_reference_1domainFeatures_inbreds.ipynb
model_reference_1domainFeatures_inbreds.ipynb
 
 
model_reference_1domainFeatures_maizeLine.ipynb
model_reference_1domainFeatures_maizeLine.ipynb
 
 
model_reference_1domainFeatures_rain.ipynb
model_reference_1domainFeatures_rain.ipynb
 
 
model_reference_1domainFeatures_temperature.ipynb
model_reference_1domainFeatures_temperature.ipynb
 
 
model_reference_2domainFeatures_age-rain.ipynb
model_reference_2domainFeatures_age-rain.ipynb
 
 
model_reference_2domainFeatures_age-temperature.ipynb
model_reference_2domainFeatures_age-temperature.ipynb
 
 
model_reference_2domainFeatures_temperature-rain.ipynb
model_reference_2domainFeatures_temperature-rain.ipynb
 
 
model_reference_3domainFeatures.ipynb
model_reference_3domainFeatures.ipynb
 
 
model_reference_3domainFeatures_MLPcopyingCombinedAE.ipynb
model_reference_3domainFeatures_MLPcopyingCombinedAE.ipynb
 
 
model_reference_3domainFeatures_MLPcopyingCombinedAE_withNotes.ipynb
model_reference_3domainFeatures_MLPcopyingCombinedAE_withNotes.ipynb
 
 
model_reference_allDomainFeatures.ipynb
model_reference_allDomainFeatures.ipynb
 
 
model_transferLearningMaarastawi2018_phylum.ipynb
model_transferLearningMaarastawi2018_phylum.ipynb
 
 
model_transferLearningWaltersSubset_2domainFeatures.ipynb
model_transferLearningWaltersSubset_2domainFeatures.ipynb
 
 
model_transferLearningWaltersSubset_3domainFeatures.ipynb
model_transferLearningWaltersSubset_3domainFeatures.ipynb
 
 
model_transferLearningWaltersSubset_allDomainFeatures.ipynb
model_transferLearningWaltersSubset_allDomainFeatures.ipynb
 
 
reference_model_novel_predictions.ipynb
reference_model_novel_predictions.ipynb
 
 

README.md

The auxiliary notebooks are divided into:

  • model_aggregated_*: microbiome prediction at different taxonomic levels (class, family, genus, order, phylum)

  • model_reference_*domainFeatures*: relevant feature analysis (1, 2, 3 or all domain features)

  • model_transferLearning*: transfer learning analysis. In a 100 samples subset from Walters et al., 2018 with 2, 3 or all features; or in Maarastawi et al. dataset with differente features.

  • compute_performance_per_sample_test_set: computation for supplementary figure.

  • reference_model_novel_predictions: base notebook for the not-installation user-friendly interface https://tinyurl.com/DeepLatentMicrobiome-Maize