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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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 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 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 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.
A tutorial on various methods for clustering longitudinal data.
problem Identifying groups with different trends in longitudinal data.
method Group-based trajectory modeling, growth mixture modeling, longitudinal k-means.
result Strengths, limitations, and model extensions of the methods are discussed.
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.
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…
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.
LPCI provides valid prediction intervals for longitudinal data.
problem Current conformal prediction methods for time series data lack cross-sectional coverage when applied to longitudinal datasets.
method Modeling residual data as a quantile fixed-effects regression problem, constructing prediction intervals with a trained quantile regressor.
result LPCI achieves valid cross-sectional coverage and outperforms existing benchmarks in terms of longitudinal coverage rates.
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.
GANs improve longitudinal data imputation but face challenges in missing data and class imbalance.
problem Missing data and class imbalance in longitudinal data.
method GANs applied to longitudinal data imputation (LDI).
result GANs show potential but need more versatile approaches.
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.
New method models longitudinal data using variational inference and normalizing flows.
problem Handling high-dimensional longitudinal data with time dependency.
method Variational inference with normalizing flows for latent variables.
result The method achieves better likelihood estimates and more reliable missing data imputation.
Deep neural networks are a family of computational models that have led to a dramatical improvement of the state of the art in several domains such as image, voice or text analysis. These methods provide a framework to model complex, non-linear interactions in large datasets, and are naturally suited to the analysis of…
latrend simplifies longitudinal clustering for numeric measurements.
problem Clustering of longitudinal data to identify common trends over time.
method Unified framework for applying various clustering methods.
result Facilitates comparison and rapid prototyping of new methods.
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
HL-VAE extends VAE for heterogeneous temporal and longitudinal data.
problem Handling heterogeneous data in temporal and longitudinal datasets.
method Proposes HL-VAE, an extension of existing VAEs for temporal and longitudinal data, incorporating likelihood models for various data types.
result HL-VAE achieves competitive performance in missing value imputation and predictive accuracy.
Automates kernel discovery for longitudinal data analysis.
problem Handling irregularly sampled, sparse longitudinal data with multilevel correlation.
method Combines deep neural networks and non-parametric kernel methods to discover complex multilevel correlation structure.
result Significantly outperforms state-of-the-art methods on benchmark data sets.
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.
Develops new algorithms for QRF to handle mixed-frequency and longitudinal data.
problem Handling mixed-frequency and longitudinal data in quantile regression.
method Mixed-Frequency Quantile Regression Forest (MIDAS-QRF) and Finite Mixture Quantile Regression Forest (FM-QRF).
result Valid and flexible models for complex empirical settings in financial risk management and climate-change impact evaluation.
A scalable model for high-dimensional longitudinal data.
problem Modeling high-dimensional, non-linear, time-varying longitudinal data.
method LMM-VAE, combining linear mixed models and amortized variational inference.
result Competitive performance across simulated and real-world datasets.
New method calibrates asynchronous, error-prone covariates for longitudinal data.
problem Estimation biases and slow convergence in analyzing time-varying covariates with measurement error.
method Functional calibration approach based on functional principal component analysis.
result Asymptotically unbiased and consistent estimators for time-invariant coefficients; optimal convergence rate for time-varying coefficients.
Finite mixture models have become a popular tool for clustering. Amongst other uses, they have been applied for clustering longitudinal data and clustering high-dimensional data. In the latter case, a latent Gaussian mixture model is sometimes used. Although there has been much work on clustering using latent variables…
CausalLongPFN predicts counterfactual outcomes from time-series data.
problem Predicting future outcomes under varying treatments in time-series data with confounding and heterogeneity.
method Prior-fitted network pretrained on synthetic episodes of temporal structural causal models.
result CausalLongPFN outperforms domain-trained models on factual and counterfactual prediction tasks.
Develops algorithm to find subgroups with different treatment effects in HIV patients.
problem Estimating treatment effects in EHR data with challenges like time-varying confounding.
method SDLD algorithm combining generalized interaction tree and longitudinal targeted maximum likelihood estimation.
result Identifies subgroups of HIV patients at higher risk of weight gain with dolutegravir-containing ARTs.
This paper reviews random forest methods for analyzing longitudinal data in precision medicine.
problem Analyzing longitudinal data for precision medicine.
method Extensions of random forest for longitudinal data analysis.
result Categorization of random forest methods for different data structures and repeated measurements.
We study regularized estimation in high-dimensional longitudinal classification problems, using the lasso and fused lasso regularizers. The constructed coefficient estimates are piecewise constant across the time dimension in the longitudinal problem, with adaptively selected change points (break points). We present an…
VTD uses deep embeddings to estimate treatment effects from longitudinal data without unconfoundedness assumption.
problem Challenges in estimating individualized treatment effects from longitudinal observational data due to confounding bias.
method Leverages deep variational embeddings and observed proxies to learn hidden confounders.
result Effective in estimating treatment effects when hidden confounding is the leading bias.
While studying response trajectory, often the population of interest may be diverse enough to exist distinct subgroups within it and the longitudinal change in response may not be uniform in these subgroups. That is, the timeslope and/or influence of covariates in longitudinal profile may vary among these different sub…
TransformerLSR models longitudinal, recurrent, and survival data jointly.
problem Joint modeling of longitudinal measurements, recurrent events, and survival data with dependencies.
method Transformer-based deep learning framework integrating deep temporal point processes and latent structure representation.
result TransformerLSR effectively models all three components simultaneously, demonstrating necessity and effectiveness through simulations and real-world data.
CDM models counterfactual outcomes in longitudinal data with improved accuracy.
problem Predicting counterfactual outcomes in longitudinal data with complex time-dependent confounding.
method Causal Diffusion Model (CDM) using denoising diffusion architecture with relational self-attention.
result CDM outperforms state-of-the-art methods in generating full probabilistic distributions of counterfactual outcomes.
TraCeR uses transformers to analyze survival data with longitudinal covariates.
problem Handling longitudinal covariates and assessing model calibration in survival analysis.
method Transformer-based survival analysis framework with factorized self-attention architecture.
result TraCeR achieves significant performance improvements over state-of-the-art methods.
DEBIAS learns causal effects from psychiatric longitudinal data by optimizing outcome weights.
problem Causal inference challenges in psychiatric longitudinal data due to symptom heterogeneity and latent confounding.
method DEBIAS algorithm that optimizes outcome weights to maximize durable treatment effects and minimize confounding.
result DEBIAS consistently outperforms state-of-the-art methods in recovering causal effects for clinically interpretable composite outcomes.
Model uses smartphone data to assess MS trajectories.
problem Personalized longitudinal MS assessment.
method Imputation, generalized estimation equation, ensemble learning, fine-tuning.
result Promising model for predicting MS over time.
Proposes L-VAE for longitudinal data analysis.
problem Analyse high-dimensional longitudinal data with missing values.
method Uses a multi-output additive Gaussian process (GP) prior to extend VAE's capability.
result Achieves highly accurate predictive performance.
We consider the problem of learning predictive models from longitudinal data, consisting of irregularly repeated, sparse observations from a set of individuals over time. Such data often exhibit {\em longitudinal correlation} (LC) (correlations among observations for each individual over time), {\em cluster correlation…