Dataset Information

Gaussian Process Panel Modeling-Machine Learning Inspired Analysis of Longitudinal Panel Data.

ABSTRACT: In this article, we extend the Bayesian nonparametric regression method Gaussian Process Regression to the analysis of longitudinal panel data. We call this new approach Gaussian Process Panel Modeling (GPPM). GPPM provides great flexibility because of the large number of models it can represent. It allows classical statistical inference as well as machine learning inspired predictive modeling. GPPM offers frequentist and Bayesian inference without the need to resort to Markov chain Monte Carlo-based approximations, which makes the approach exact and fast. GPPMs are defined using the kernel-language, which can express many traditional modeling approaches for longitudinal data, such as linear structural equation models, multilevel models, or state-space models but also various commonly used machine learning approaches. As a result, GPPM is uniquely able to represent hybrid models combining traditional parametric longitudinal models and nonparametric machine learning models. In the present paper, we introduce GPPM and illustrate its utility through theoretical arguments as well as simulated and empirical data.

SUBMITTER: Karch JD

PROVIDER: S-EPMC7096578 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Gaussian Process Panel Modeling-Machine Learning Inspired Analysis of Longitudinal Panel Data.

Karch Julian D JD Brandmaier Andreas M AM Voelkle Manuel C MC

Frontiers in psychology 20200319

In this article, we extend the Bayesian nonparametric regression method <i>Gaussian Process Regression</i> to the analysis of longitudinal panel data. We call this new approach <i>Gaussian Process Panel Modeling (GPPM)</i>. GPPM provides great flexibility because of the large number of models it can represent. It allows classical statistical inference as well as machine learning inspired predictive modeling. GPPM offers frequentist and Bayesian inference without the need to resort to Markov chai ...[more]

PMID: 32265770

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Project description:Temporal multi-omics data can provide information about the dynamics of disease development and therapeutic response. However, statistical analysis of high-dimensional time-series data is challenging. Here we develop a novel approach to model temporal metabolomic and transcriptomic data by combining machine learning with metabolic models. ADAPT (Analysis of Dynamic Adaptations in Parameter Trajectories) performs metabolic trajectory modeling by introducing time-dependent parameters in differential equation models of metabolic systems. ADAPT translates structural uncertainty in the model, such as missing information about regulation, into a parameter estimation problem that is solved by iterative learning. We have now extended ADAPT to include both metabolic and transcriptomic time-series data by introducing a regularization function in the learning algorithm. The ADAPT learning algorithm was (re)formulated as a multi-objective optimization problem in which the estimation of trajectories of metabolic parameters is constrained by the metabolite data and refined by gene expression data. ADAPT was applied to a model of hepatic lipid and plasma lipoprotein metabolism to predict metabolic adaptations that are induced upon pharmacological treatment of mice by a Liver X receptor (LXR) agonist. We investigated the excessive accumulation of triglycerides (TG) in the liver resulting in the development of hepatic steatosis. ADAPT predicted that hepatic TG accumulation after LXR activation originates for 80% from an increased influx of free fatty acids. The model also correctly estimated that TG was stored in the cytosol rather than transferred to nascent very-low density lipoproteins. Through model-based integration of temporal metabolic and gene expression data we discovered that increased free fatty acid influx instead of de novo lipogenesis is the main driver of LXR-induced hepatic steatosis. This study illustrates how ADAPT provides estimates for biomedically important parameters that cannot be measured directly, explaining (side-)effects of pharmacological treatment with LXR agonists.

Dataset Information

Gaussian Process Panel Modeling-Machine Learning Inspired Analysis of Longitudinal Panel Data.

Publications

Gaussian Process Panel Modeling-Machine Learning Inspired Analysis of Longitudinal Panel Data.

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