SVM and N-best algorithm classify microbial marker clades from genome sequences.
problem Classifying microbial clades from genome sequences, especially new species.
method Support vector machine (SVM) with N-best algorithm, time series feature extraction, random fragment generation, k-mer size selection.
result Recognition accuracy rates above 28% in top-1 candidate, above 91% in top-10 candidate.
Method improves microbial biomass yield estimation from noisy data.
problem Estimating microbial biomass yields from noisy cell counts and substrate measurements.
method Probabilistic macrochemical modeling to relax cell weight assumptions and improve robustness.
result Model provides accurate uncertainty estimates of key parameters.
Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms o…
AMP0 predicts antimicrobial peptides targeting specific microbes.
problem Low-throughput screening of antimicrobial peptides.
method Zero-shot and few-shot machine learning.
result AMP0 can predict antimicrobial activity against specific microbes.
Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets,…
GraphKKE learns fixed-length feature vectors from time-evolving graphs of human microbiome data.
problem Understanding dynamic changes in human microbiome graphs over time.
method Spectral analysis of transfer operators and graph kernels.
result GraphKKE captures temporal changes in human microbiome graphs.
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs," which are communities of bacteria administered to patients for specific therapeuti…
AI enhances microbiology and microbiome research through machine learning.
problem Understanding microbial life and its impact on health and the environment.
method AI-driven approaches including machine learning and deep learning.
result Transformative role in enhancing microbial life understanding.
New model identifies microbial subcommunities robustly, accounting for cross-sample heterogeneity.
problem Inference in LDA is sensitive to the number of subcommunities and often creates artificial ones.
method Incorporates logistic-tree normal (LTN) model into LDA to account for cross-sample heterogeneity.
result Restores robustness of inference and identifies meaningful subcommunities.
The present study provides a comparative assessment of non-invasive sensors as means of estimating the microbial contamination and time-on-shelf (i.e. storage time) of leafy green vegetables, using a novel unified spectra analysis workflow. Two fresh ready-to-eat green salads were used in the context of this study for …
A new method avoids overfitting in network reconstruction by using the minimum description length principle.
problem Determining the optimal model complexity in network reconstruction to prevent overfitting.
method Hierarchical Bayesian inference and weight quantization based on the minimum description length principle.
result The method yields increased accuracy in reconstructing both artificial and empirical networks.
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital compon…
New method learns from non-uniform data and partial physical knowledge.
problem Identifying dynamical systems from non-uniformly sampled data.
method Physics-informed neural networks integrating numerical integration methods.
result Learning unknown kinetic rates and estimating parameters from non-uniform data.
Model accurately gates ocean microbes from high-frequency flow cytometry data.
problem Gating of high-frequency flow cytometry data for ocean microbes is challenging.
method Trend filtered mixture of experts with smooth parameter variation.
result Model accurately matches human-annotated gating and corrects errors.
CARE method estimates precision matrix for compositional data, achieving optimality in high dimensions.
problem Challenges in inferring conditional dependence relationships in high-dimensional compositional data.
method Composition adaptive regularized estimation (CARE) method for sparse basis precision matrix.
result CARE estimator achieves minimax optimality in high dimensions, performing as well as if the basis were observed.
Many complex ecosystems, such as those formed by multiple microbial taxa, involve intricate interactions amongst various sub-communities. The most basic relationships are frequently modeled as co-occurrence networks in which the nodes represent the various players in the community and the weighted edges encode levels o…
New algorithm predicts geolocation of fungi samples with high accuracy.
problem Identifying the origin of biological material at crime scenes.
method Ensemble of deep neural network classifiers trained on Voronoi partitions.
result More than half of geolocation errors under 100 kilometers for continental analysis and nearly 90% accuracy for global analysis.
Pipeline integrates cross-sectional and longitudinal multi-omics data for IBD research.
problem Integrating diverse data types from the same individuals for disease understanding.
method Statistical and deep learning methods for variable selection, feature extraction, and joint integration.
result Identified microbial pathways, metabolites, and genes discriminating IBD status.
Unified method for discovering biclusters and triclusters in longitudinal data.
problem High-dimensional, sparsely sampled, irregularly observed longitudinal data.
method Tri-SfSVD, a unified sparse functional Singular Value Decomposition framework.
result Identified localized structures at the subject, subject-feature, and subject-feature-time levels.
Machine learning predicts plant phenotypes from soil microbiome data.
problem Predicting plant phenotypes from soil microbiome data.
method Two models (random forest and Bayesian neural network) were used to predict plant phenotypes from soil properties and microbial population density.
result Human decisions and normalization strategies significantly impact model performance.
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
Study uses machine learning to identify IBD biomarkers from gut microbiota.
problem Identifying biomarkers for Inflammatory Bowel Disease (IBD) from gut microbiota.
method Ensemble feature selection methods (CMIM, FCBF, mRMR, XGBoost) applied to IBD-associated metagenomics dataset.
result XGBoost minimizes microbiota used for IBD diagnosis, improving classification accuracy.