NoLimits.jl: Flexible and Composable Nonlinear Mixed-Effects Modeling in Julia
problem Flexible and composable nonlinear mixed-effects modeling
method Macro-based modeling language and unified interface
result Substantially expand the range of nonlinear mixed-effects models
A new method combines machine learning with mixed-effects models for better repeated measurement analysis.
problem Inference of linear coefficients in partially linear mixed-effects models with complex interactions and high-dimensional variables.
method Double machine learning approach to estimate nonparametrically nonlinear variables, then use standard linear mixed-effects techniques to estimate the linear coefficient.
result The estimated fixed effects coefficient converges at the parametric rate and is semiparametrically efficient.
A scalable Bayesian inference method for mixed-effects models in systems biology.
problem Scalable Bayesian inference for complex hierarchical mixed-effects models in systems biology.
method Constructing amortized approximations of likelihood and posterior distributions, refined for each individual dataset.
result Our method is both fast and competitive in statistical accuracy compared to exact pseudomarginal Bayesian inference.
Study compares neural and statistical models for Parkinson's disease progression from voice data.
problem Difficult statistical analysis of longitudinal voice biomarkers due to subject correlation, small cohorts, and varied disease trajectories.
method Evaluated Neural Mixed Effects (NME), Generalized Neural Network Mixed Models (GNMMs), and semi-parametric Generalized Additive Mixed Models (GAMMs).
result GAMMs achieve stronger predictive performance and retain interpretable smooth effects and subject-level structure.
Neural models improve GLMMs for complex data.
problem Nonlinear relationships in grouped data.
method Replaced linear function with neural networks.
result Improved performance on synthetic and real-world data.
ARMED models improve deep learning interpretability and generalize better on clustered data.
problem Clustered data leads to spurious associations and poor model fitting.
method Adversarial regularization and mixed effects subnetworks.
result ARMED models outperform conventional methods in accuracy and generalization.
metabeta uses neural networks to speed up Bayesian mixed-effects regression.
problem Bayesian mixed-effects regression is computationally expensive.
method metabeta is a neural network model that pre-trains to estimate posterior distributions.
result metabeta achieves comparable performance to MCMC at a fraction of the time.
Mixed effects (ME) models inform a vast array of problems in the physical and social sciences, and are pervasive in meta-analysis. We consider ME models where the random effects component is linear. We then develop an efficient approach for a broad problem class that allows nonlinear measurements, priors, and constrain…
RoME optimizes mobile health interventions by modeling user and time-specific effects.
problem Challenges in optimizing mobile health interventions due to participant heterogeneity, nonstationarity, and nonlinear relationships.
method RoME uses a Robust Mixed-Effects contextual bandit algorithm with random effects, network cohesion penalties, and debiased machine learning.
result RoME achieves robust regret bounds even with complex baseline rewards, demonstrating superior performance in simulations and studies.
Deep-SITAR uses autoencoders to predict growth patterns.
problem Predicting individual growth trajectories from population data.
method Deep learning framework integrating autoencoders and B-spline models.
result Deep-SITAR predicts individual growth without full model re-estimation.
New Krylov subspace methods speed up mixed-effects models with crossed random effects.
problem Slow computations for high-dimensional crossed random effects in mixed-effects models.
method Krylov subspace-based methods for generalized mixed-effects models with cross effects.
result Speedups by factors of up to 10,000 in computations for mixed-effects models.
We link disjoint longitudinal data for rare disease patients using latent representations and mixed-effects regression.
problem Analyzing treatment switches in rare diseases with limited data and changing measurement instruments.
method We embed item values into a shared latent space using variational autoencoders and apply mixed-effects regression to quantify treatment effects.
result Our approach allows for statistical inference and quantifies the impact of treatment switches in spinal muscular atrophy.
MC-GMENN improves neural networks for clustered data using Monte Carlo methods.
problem Improving neural network performance on clustered data with correlations.
method MC-GMENN employs Monte Carlo methods to train generalized mixed effects neural networks.
result MC-GMENN outperforms existing models in generalization and quantifying inter-cluster variance.
Graph neural networks (GNNs) have emerged as a powerful tool for nonlinear processing of graph signals, exhibiting success in recommender systems, power outage prediction, and motion planning, among others. GNNs consists of a cascade of layers, each of which applies a graph convolution, followed by a pointwise nonlinea…
Proposes meTS for efficient exploration in correlated bandits.
problem Efficiently explore in bandits with correlated actions.
method Mixed-effect model with Thompson Sampling.
result Bound on Bayes regret with two terms.
Study improves maize yield prediction using BNs with mixed-effects models.
problem Limited causal inference in agronomic data models.
method Integrates random effects into Bayesian networks, leveraging hierarchical data structure.
result Significantly reduces maize yield prediction error from 28% to 17%.
Paper develops federated GLMM algorithms for analyzing hierarchical data.
problem Analyzing hierarchical data with non-independent observations in a federated setting.
method Developed two federated GLMM algorithms using Laplace and Gaussian Hermite approximations.
result Federated GLMM can handle hierarchical data and achieve comparable or superior performance.
Many scientific and engineering challenges -- ranging from pharmacokinetic drug dosage allocation and personalized medicine to marketing mix (4Ps) recommendations -- require an understanding of the unobserved heterogeneity in order to develop the best decision making-processes. In this paper, we develop a hypothesis te…
This note is concerned with an accurate and computationally efficient variational bayesian treatment of mixed-effects modelling. We focus on group studies, i.e. empirical studies that report multiple measurements acquired in multiple subjects. When approached from a bayesian perspective, such mixed-effects models typic…
FBMS R package simplifies Bayesian model selection and averaging.
problem Complex regression settings with multi-modal posterior landscapes.
method Efficient MJMCMC and GMJMCMC algorithms for Bayesian model exploration.
result FBMS effectively handles Bayesian generalized linear and nonlinear models.
We develop an HMC algorithm to easily marginalize random effects in LMMs.
problem Bayesian inference in LMMs is challenging, especially marginalizing random effects.
method Developed an HMC algorithm to marginalize random effects in LMMs efficiently.
result Marginalization is always beneficial when applicable and improves various models, especially cognitive science models.
Combines boosting with Gaussian process and mixed effects models.
problem Model misspecifications and independence assumptions in boosting.
method Relaxes zero or linearity assumption in Gaussian process and mixed effects models, and independence assumption in boosting.
result Increased prediction accuracy compared to existing approaches.
Transformers improve Alzheimer's disease progression prediction by accounting for irregular biomarker histories.
problem Difficult prediction of medium-horizon Alzheimer's disease progression due to tied clinical scores and irregular biomarker observations.
method Developed a residual gap-aware transformer that combines statistical reference with transformer-based residual learning.
result The proposed model reduces mean error and improves prediction-observation correlation compared to baseline models.
MOMENT selects and estimates mixed-effects models using moment identities.
problem Selecting and estimating random-effects covariance matrix and fixed-effects coefficients in multiresponse linear mixed-effects models.
method MOMENT is a stage-wise moment-based framework that reduces the random-effects selection problem to a smooth constrained convex optimization problem.
result MOMENT performs competitively and can outperform separate univariate analyses for correlated responses.
We introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of nonlinear mixed-effects (NLME) dynamical systems, the statistical workhorse for ma…
Normative modeling has recently been introduced as a promising approach for modeling variation of neuroimaging measures across individuals in order to derive biomarkers of psychiatric disorders. Current implementations rely on Gaussian process regression, which provides coherent estimates of uncertainty needed for the …
Paper improves Bayesian network learning from related data sets.
problem Learning from heterogeneous data sets with different probabilistic structures.
method Mixed-effects models to pool information across related data sets.
result Mixed-effects models outperform traditional methods in accuracy.
Multi-task learning models using Gaussian processes (GP) have been developed and successfully applied in various applications. The main difficulty with this approach is the computational cost of inference using the union of examples from all tasks. Therefore sparse solutions, that avoid using the entire data directly a…
A new framework models multi-state events and biomarkers.
problem Limited representation of complex multi-state trajectories.
method General multi-state joint modeling framework.
result Accurate parameter recovery and personalized predictions.
Proposes a new model for mortality forecasting considering age groups and cohort effects.
problem Longevity risk due to ageing population.
method Mixed-effects time-series approach with age groups dependency and random cohort effects.
result Remarkable improvements in forecast accuracy compared to the CBD model.
Improved spatial prediction for massive datasets using SME model.
problem Efficiently estimating parameters in massive spatial datasets.
method Spatial Mixed Effects (SME) model with AECM algorithm for flexibility.
result Improved estimation without sacrificing prediction accuracy.
Paper extends LME models to allow sign constraints on coefficients with SDTN random effects.
problem Inference with sign constraints on random effects in LME models.
method Proposes SDTN distribution for random effects and develops likelihood-based approaches for estimation.
result Proposed constrained model improves real-world interpretations and achieves satisfactory performance.
As data collections become larger, exploratory regression analysis becomes more important but more challenging. When observations are hierarchically clustered the problem is even more challenging because model selection with mixed effect models can produce misleading results when nonlinear effects are not included into…
Transformers with MLP heads outperform linear baselines in in-context learning.
problem Understanding in-context learning in Transformers with nonlinear MLP heads.
method Analyzing a model with two-layer MLPs trained via gradient steps and fully optimized, under high-dimensional asymptotics.
result Nonlinear MLPs enhance ICL performance, particularly on nonlinear tasks.
The paper analyzes oversmoothing in GNNs and quantifies the effects of mixing and denoising.
problem Oversmoothing in Graph Neural Networks (GNNs).
method Non-asymptotic analysis of graph convolutions and effects of mixing and denoising.
result The number of layers required for oversmoothing to occur is O(logN/log(logN)) for dense graphs. We propose a new data-augmentation strategy for fully Bayesian inference in models with binomial likelihoods. The approach appeals to a new class of Polya-Gamma distributions, which are constructed in detail. A variety of examples are presented to show the versatility of the method, including logistic regression, negat…
Proposes an efficient algorithm for mHealth that makes real-time physical activity suggestions.
problem Training complex models efficiently in real-time mHealth applications.
method Streamlined empirical Bayes procedure for fitting linear mixed effects models.
result Improves accuracy and speed over state-of-the-art approaches in mHealth applications.
OMERF extends random forest for hierarchical data and ordinal responses.
problem Analyzing hierarchical data and ordinal responses using tree-based methods.
method Ordinal Mixed-Effects Random Forest (OMERF) that preserves flexibility and hierarchical structure.
result OMERF identifies discriminating student characteristics and estimates school effects.
The paper introduces a model to measure ASR fairness, addressing key issues.
problem Measuring fairness in ASR systems for different subgroups.
method Mixed-effects Poisson regression to control nuisance factors and handle unobserved heterogeneity.
result The method effectively addresses WER gaps among subgroups and is flexible for practical analyses.
This paper concerns the development of an inferential framework for high-dimensional linear mixed effect models. These are suitable models, for instance, when we have n repeated measurements for M subjects. We consider a scenario where the number of fixed effects p is large (and may be larger than M), but the n…
Develops RF-GLS for binary geospatial data.
problem Challenges in extending RF to binary geospatial data.
method Proposes RF-GLS for binary data, embedding it in generalized mixed effects models.
result Establishes consistency of RF-GP for mean function and covariate effect estimation.
Proposes a method for modeling random objects in metric spaces using random effects.
problem Modeling random objects in non-Euclidean spaces with random effects.
method Nonlinear Fréchet-based algorithm for M-estimation.
result Consistent estimation of prediction target under random-effects formulation.
The Tweedie Compound Poisson-Gamma model is routinely used for modeling non-negative continuous data with a discrete probability mass at zero. Mixed models with random effects account for the covariance structure related to the grouping hierarchy in the data. An important application of Tweedie mixed models is pricing …
GLMM trees identify subgroups with different growth patterns in longitudinal data.
problem Identifying subgroups with distinct growth trajectories in longitudinal studies.
method Extended GLMM trees for longitudinal data.
result Extended GLMM trees outperform other methods in accuracy and speed.
This work relates the framework of model-based clustering for spatial functional data where the data are surfaces. We first introduce a Bayesian spatial spline regression model with mixed-effects (BSSR) for modeling spatial function data. The BSSR model is based on Nodal basis functions for spatial regression and accom…
Proposes incorporating noise sources in machine learning evaluation for more reliable conclusions.
problem Inadequate handling of nondeterminism in machine learning research leads to unreliable results.
method Uses linear mixed effects models (LMEMs) and generalized likelihood ratio tests (GLRT) to analyze performance evaluation scores and assess performance differences.
result Demonstrates how to incorporate various sources of noise and data properties into statistical significance testing and reliability analysis.
This research improves model interpretability and uncertainty estimation for deep learning models on non-iid data.
problem Improving interpretability and uncertainty estimation for deep learning models on non-iid data.
method 4 UQ approaches (BNN, SWAG, MC dropout, ensemble) applied to ARMED MEDL models.
result Ensemble approaches, especially with 90% subsampling, provide best performance in prediction and uncertainty estimation.
Novel approach constructs differential causal networks from EEG data.
problem Difficulty in modeling interactions of thousands of neurons in group comparisons.
method Hierarchical differential dynamic causal nets based on Chen-Fliess expansions.
result Evidence of network functional disruptions in epileptic brains.