Improves classification of microbiome data using mixture distributions.
problem Challenges in classifying sparse and heterogeneous microbiome count data.
method Distance-based classification using mixture distributions.
result The method outperforms existing distance-based classifiers and machine learning approaches.
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.
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.
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.
Data augmentation improves microbiome disease prediction.
problem Improving predictive models for microbiome data.
method Defined novel data augmentation strategies for simplex-valued data.
result Set new state-of-the-art for disease prediction tasks.
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.
Unified framework combines dependent microbiome tests.
problem Combining dependent microbiome association tests.
method Generalized meta-analysis framework for dependent tests.
result The vanilla Cauchy combination is a special case.
Develops methods for causal inference in compositional data using instrumental variables.
problem Interpreting summary statistics like diversity indices as causal effects in compositional data.
method Statistical data transformations and regression techniques tailored for compositional data.
result Advantages and limitations of the proposed methods demonstrated on synthetic and real microbiome data.
KernelBiome tackles microbiome research by improving predictive performance and interpretability.
problem Challenges in analyzing high-throughput sequencing data, especially in microbiome research.
method KernelBiome is a kernel-based nonparametric regression and classification framework for compositional data, incorporating prior knowledge and capturing complex signals.
result Improved predictive performance compared to state-of-the-art machine learning methods, with two novel quantities for interpretability.
Bayesian model fuses diverse microbiome data types.
problem Challenges in fusing different types of microbiome data.
method Flexible multinomial-Gaussian generative model with variational EM algorithm.
result Inferred latent variables provide common dimensionality reduction and predictive posterior distribution.
Bayesian method for imputing missing values in tensor data.
problem Missing data in multi-way arrays (tensors) in biomedical studies.
method Flexible Bayesian framework with conjugate priors for CP factorization.
result Accurately captures uncertainty in microbiome profiles at missing timepoints.
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.
PHIBP models complex microbiome data with shared parameters.
problem Complex, sparse count data in microbiome analysis.
method Bayesian nonparametric framework with shared species parameters.
result Flexible multivariate count model with tractable inference.
New models for analyzing microbiome data with interactions.
problem Analyzing compositional data with interactions.
method Exponential family models with generalized score matching.
result Effective estimation methods for compositional data with interactions.
New geometric approach for analyzing compositional data like gut microbiomes.
problem Analyzing non-negative compositional data with relative values only.
method Reinterpret compositional data as quotient topology of a sphere, using spherical harmonics and reflection group actions.
result Construction of Reproducing Kernel Hilbert Space (RKHS) for compositional data.
New method for analyzing compositional data, addressing biases in summary statistics.
problem Inadequate effect measures for compositional data, especially in high-dimensionality and sparsity.
method Perturbation-based effect measures, average perturbation effects.
result Proposed estimators efficiently estimate average perturbation effects, outperforming existing techniques.
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the microbiome level leading to the possibility of personalized medicine whereby tr…
Tree-based variational inference improves PLN model for hierarchical count data.
problem Limited applicability of PLN model in ecosystems due to lack of hierarchical tree structures.
method Introduced PLN-Tree model integrating structured variational inference techniques.
result Enhanced generative improvements and practical interpretability in microbiome modeling.
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.
Generative model identifies temporal count data components with regime-dependent contributions.
problem Modeling temporal count data with regime-dependent dynamics.
method Generative framework combining regime-adaptive dynamics with Poisson log-normal emissions.
result Established identifiability of the model and revealed co-variation patterns and regime shifts.
PolyILR: A Tree-Structured Orthonormal Decomposition of Compositional Data
problem Representing compositional data with hierarchical structure
method PolyILR: A canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology
result PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution
Generative model for tabular data density regression.
problem Estimating conditional distribution of outcomes given covariates.
method Tree-based flow model for efficient sampling and likelihood evaluation.
result Our method achieves comparable or superior performance with reduced training and sampling costs.
The tremendous boost in the next generation sequencing and in the omics technologies makes it possible to characterize human gut microbiome (the collective genomes of the microbial community that reside in our gastrointestinal tract). While some of these microorganisms are considered as essential regulators of our immu…
This paper addresses measurement errors in high-dimensional compositional data using a log-contrast model calibration approach.
problem Measurement errors in high-dimensional regression models involving compositional covariates.
method Calibration approach for the linear log-contrast model under lenient sparsity conditions.
result Established asymptotic normality of the estimator for inference.
Paper tackles multi-source domain adaptation for regression.
problem Predicting HDL cholesterol levels using gut microbiome data.
method Two-step procedure: 1) Extend a flexible single-source DA algorithm for classification to regression. 2) Augment with ensemble learning for multi-source DA.
result Consistent improvement in HDL cholesterol level prediction performance over existing methods.
New ZIPLN model accounts for zero-inflation in multivariate count data.
problem Zero-inflation in multivariate count data.
method Introduced Zero-Inflated PLN (ZIPLN) model with variational inference.
result ZIPLN significantly improves log-likelihood and reduces dispersion.
Compositional data have two unique characteristics compared to typical multivariate data: the observed values are nonnegative and their summand is exactly one. To reflect these characteristics, a specific regularized regression model with linear constraints is commonly used. However, linear constraints incur additional…
Paper tackles tensor decomposition for unaligned observations using RKHS and novel loss functions.
problem Tackles tensor decomposition for unaligned observations.
method Uses functions in RKHS to represent mode with unaligned observations, introduces versatile loss function, proposes optimization algorithm and stochastic gradient method.
result Demonstrates improved tensor decomposition efficiency and effectiveness with synthetic and real data.
New method corrects correlation bias in feature importance.
problem Correlations between features in high-dimensional data bias statistical and machine learning models.
method Pairwise Permutation Algorithm (PPA)
result PPA corrects correlation bias, identifying biological relevant biomarkers.
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of…
PHIBP predicts infectious disease outbreaks in sparse data regions.
problem Predicting outbreaks in regions with no historical data.
method Poisson Hierarchical Indian Buffet Process (PHIBP) framework.
result PHIBP provides accurate outbreak predictions and meaningful insights in sparse data settings.
Proposes a convex method to estimate GGMs with covariates.
problem Improving conditional independence structure estimation with covariates.
method Convex optimization framework for joint estimation of mean and precision matrix.
result Improved theoretical guarantees and practical utility demonstrated.
A new method approximates deep neural networks using Kalman Filters.
problem Approximating deep neural networks with limited data.
method Matrix Ensemble Kalman Filter-based multi-arm ANN (MEnKF-ANN).
result MEnKF-ANN can adequately approximate LSTM networks and provide uncertainty estimates.
Bayesian model for multi-environment prediction with latent variable changes.
problem Prediction in environments with changing latent variable distributions.
method Bayesian model with empirical Bayes prior and amortized variational algorithm.
result Method outperforms previous approaches in new environments.
Estimates change point in high-dimensional dynamic graphical models.
problem Detecting change points in high-dimensional graphical models.
method Developed an estimator with Op(ψ−2) rate of convergence, established asymptotic distribution under high-dimensional scaling. result Asymptotic distribution characterized under vanishing and non-vanishing jump size regimes.
Despite significant effort in understanding complex systems (CS), we lack a theory for modeling, inference, analysis and efficient control of time-varying complex networks (TVCNs) in uncertain environments. From brain activity dynamics to microbiome, and even chromatin interactions within the genome architecture, many …
We introduce a new method for estimating the support size of an unknown distribution which provably matches the performance bounds of the state-of-the-art techniques in the area and outperforms them in practice. In particular, we present both theoretical and computer simulation results that illustrate the utility and p…
Paper introduces MGLasso for multiscale graph inference in clustering and network analysis.
problem Graphical models in high-dimensional data analysis need to handle clustering and sparsity simultaneously.
method MGLasso combines clustering and graph inference through a convex relaxation of k-means and hierarchical clustering. It uses CONESTA for regularization.
result MGLasso improves network interpretability by estimating graphs at multiple scales.
A new geometry-preserving method for interpreting compositional data.
problem Statistical challenges in high-dimensional compositional data.
method Geometry-preserving framework for dimension reduction of compositional data.
result Identification of a central compositional subspace for compositional predictors.
Proposes a new model to handle noisy data in scientific research.
problem Measurement error in noisy data settings.
method Measurement error BART (meBART) integrates measurement error in Bayesian additive regression trees.
result meBART provides more accurate parameter estimation, robust uncertainty quantification, and superior predictive performance.
Multilayer networks are a useful data structure for simultaneously capturing multiple types of relationships between a set of nodes. In such networks, each relational definition gives rise to a layer. While each layer provides its own set of information, community structure across layers can be collectively utilized to…
A new metric evaluates generative models by comparing real and generated samples.
problem Evaluating the quality of generative models.
method Relative Density Ratio (RDR) function, optimization on variational form of φ-divergence.
result The RDR function provides a clear, interpretable, and numerically stable evaluation metric.
Estimates density ratio for two-sample comparison using tree models.
problem Comparing two distributions given i.i.d. observations.
method Additive tree models with balancing loss for density ratio estimation.
result Bayesian inference provides uncertainty quantification for density ratio.
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…
A new approach to the sparse Canonical Correlation Analysis (sCCA)is proposed with the aim of discovering interpretable associations in very high-dimensional multi-view, i.e.observations of multiple sets of variables on the same subjects, problems. Inspired by the sparse PCA approach of Journee et al. (2010), we also s…
JigSaw discovers high-order interactions from random forests.
problem Identifying complex interactions in biological data.
method Random forest structure analysis to find high-order interactions.
result JigSaw can explain outcomes in heart disease and breast cancer.