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.
We model microbiome interactions as graphs to interpret complex dynamics.
problem Understanding the differences in microbiome profiles between healthy and ill individuals.
method Developed a method to learn low-dimensional graph representations of time-evolving microbiome interactions.
result Extracted graph features that highlight microbes and interactions strongly correlated with clinical diseases.
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.
Develops a method for estimating networks and covariate associations in compositional data.
problem Estimating network interactions and covariate associations for compositional data.
method Hierarchical Bayesian model with spike-and-slab priors for edge and covariate selection, variational EM for inference.
result The proposed method outperforms existing methods in network recovery accuracy.
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…
Proposes a multivariate regression model for better analysis of multiple datasets.
problem Insufficient performance of single-dataset analysis in integrative studies.
method Sparse estimation for variable and group selection, alternating direction method of multipliers algorithm.
result Demonstrated improved performance through simulations and real data analysis.
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.
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.
The paper introduces a method to control false splits in tree-based data aggregation.
problem Identifying the correct subgroups to treat as a single entity in tree-based data.
method Introduces the 'false split rate' and proposes a multiple hypothesis testing algorithm for tree-based aggregation.
result The proposed algorithm controls the false split rate, demonstrating its effectiveness on stock volatility and taxi fare data.
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.
Intelligence emerges from stabilizing invariant cycles in memory.
problem Understanding the nature of intelligence and its emergence.
method Structural-dynamical account rooted in a topological closure law: \(\partial^2=0\).
result Memory-amortized inference (MAI) mechanism that implements SbS \(
ightarrow\) CCUP.