arXiv subjects

Jeanine Houwing-Duistermaat

Publications and source records attributed to Jeanine Houwing-Duistermaat.

9 recordsLinked to original sources

arXiv2025

Functional principal component analysis for functional data with detection limits

When measurements fall below or above a detection threshold, the resulting data are missing not at random (MNAR), posing challenges for statistical analysis. For example, in longitudinal biomarker studies, observations may be subject to detection limits. Functional principal component analysis (FPCA) is commonly used method for dimension reduction of dense and sparse data measured along a continuum, but standard approaches typically ignore MNAR mechanisms by imputing detection limit values, leading to biased estimates of principal components and scores. Building on recent work by Liu and Houwing-Duistermaat (2022, 2023), who proposed estimators for the mean and covariance functions under detection limits, we extend FPCA to accommodate functional data affected by such limits. We derive the asymptotic properties of the resulting estimators and assess their performance through simulations, comparing them to standard methods. Finally, we illustrate our approach using longitudinal biomarker data subject to detection limits. Our method yields more accurate estimates of functional principal components and scores, enhancing the reliability of functional data analysis in the presence of detection limits.

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arXiv2022

Joint Modeling of An Outcome Variable and Integrated Omic Datasets Using GLM-PO2PLS

In many studies of human diseases, multiple omic datasets are measured. Typically, these omic datasets are studied one by one with the disease, thus the relationship between omics are overlooked. Modeling the joint part of multiple omics and its association to the outcome disease will provide insights into the complex molecular base of the disease. In this article, we extend dimension reduction methods which model the joint part of omics to a novel method that jointly models an outcome variable with omics. We establish the model identifiability and develop EM algorithms to obtain maximum likelihood estimators of the parameters for normally and Bernoulli distributed outcomes. Test statistics are proposed to infer the association between the outcome and omics, and their asymptotic distributions are derived. Extensive simulation studies are conducted to evaluate the proposed model. The model is illustrated by a Down syndrome study where Down syndrome and two omics - methylation and glycomics - are jointly modeled.

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arXiv2021

Statistical Integration of Heterogeneous Data with PO2PLS

The availability of multi-omics data has revolutionized the life sciences by creating avenues for integrated system-level approaches. Data integration links the information across datasets to better understand the underlying biological processes. However, high-dimensionality, correlations and heterogeneity pose statistical and computational challenges. We propose a general framework, probabilistic two-way partial least squares (PO2PLS), which addresses these challenges. PO2PLS models the relationship between two datasets using joint and data-specific latent variables. For maximum likelihood estimation of the parameters, we implement a fast EM algorithm and show that the estimator is asymptotically normally distributed. A global test for testing the relationship between two datasets is proposed, and its asymptotic distribution is derived. Notably, several existing omics integration methods are special cases of PO2PLS. Via extensive simulations, we show that PO2PLS performs better than alternatives in feature selection and prediction performance. In addition, the asymptotic distribution appears to hold when the sample size is sufficiently large. We illustrate PO2PLS with two examples from commonly used study designs: a large population cohort and a small case-control study. Besides recovering known relationships, PO2PLS also identified novel findings. The methods are implemented in our R-package PO2PLS. Supplementary materials for this article are available online.

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arXiv2019

On estimation of the effect lag of predictors and prediction in functional linear model

We propose a functional linear model to predict a response using multiple functional and longitudinal predictors and to estimate the effect lags of predictors. The coefficient functions are written as the expansion of a basis system (e.g. functional principal components, splines), and the coefficients of the fixed basis functions are estimated via optimizing a penalization criterion. Then time lags are determined by simultaneously searching on a prior grid mesh based on minimization of prediction error criterion. Moreover, mathematical properties of the estimated parameters and predicted responses are studied and performance of the method is evaluated by extensive simulations.

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arXiv2018

Prediction and forecasting models based on patient's history and biomarkers with application to Scleroderma disease

This paper aims at predicting lung function values based on patients historical lung function values and serum biomarkers in Scleroderma patients. The progression of disease is measured by three lung function indexes (FVC, TLC, DLCO). Values of four biomarkers (TIMP1, P3NP, HA, NT-proBNP) are available. The data are sparse (6 months intervals) and irregular (many visits are missed). We consider two modeling approaches to achieve our goal, namely, the mixed effects model which is the standard approach in epidemiological studies and the functional principal component analysis model which is typically used for dense temporal datasets. We find that functional data methodology was able to recover the trajectories of three lung function indexes and to predict the future values very well.

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arXiv2018

Probabilistic partial least squares model: Identifiability, estimation and application

With a rapid increase in volume and complexity of data sets, there is a need for methods that can extract useful information, for example the relationship between two data sets measured for the same persons. The Partial Least Squares (PLS) method can be used for this dimension reduction task. Within life sciences, results across studies are compared and combined. Therefore, parameters need to be identifiable, which is not the case for PLS. In addition, PLS is an algorithm, while epidemiological study designs are often outcome-dependent and methods to analyze such data require a probabilistic formulation. Moreover, a probabilistic model provides a statistical framework for inference. To address these issues, we develop Probabilistic PLS (PPLS). We derive maximum likelihood estimators that satisfy the identifiability conditions by using an EM algorithm with a constrained optimization in the M step. We show that the PPLS parameters are identifiable up to sign. A simulation study is conducted to study the performance of PPLS compared to existing methods. The PPLS estimates performed well in various scenarios, even in high dimensions. Most notably, the estimates seem to be robust against departures from normality. To illustrate our method, we applied it to IgG glycan data from two cohorts. Our PPLS model provided insight as well as interpretable results across the two cohorts.

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arXiv2018

On trend and its derivatives estimation in repeated time series with subordinated long-range dependent errors

For temporal regularly spaced datasets, a lot of methods are available and the properties of these methods are extensively investigated. Less research has been performed on irregular temporal datasets subject to measurement error with complex dependence structures, while this type of datasets is widely available. In this paper, the performance of kernel smoother for trend and its derivatives is considered under dependent measurement errors and irregularly spaced sampling scheme. The error processes are assumed to be subordinated Gaussian long memory processes and have varying marginal distributions. The functional central limit theorem for the estimators of trend and its derivatives are derived and bandwidth selection problem is addressed.

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arXiv2016

Sequential double cross-validation for assessment of added predictive ability in high-dimensional omic applications

Enriching existing predictive models with new biomolecular markers is an important task in the new multi-omic era. Clinical studies increasingly include new sets of omic measurements which may prove their added value in terms of predictive performance. We introduce a two-step approach for the assessment of the added predictive ability of omic predictors, based on sequential double cross-validation and regularized regression models. We propose several performance indices to summarize the two-stage prediction procedure and a permutation test to formally assess the added predictive value of a second omic set of predictors over a primary omic source. The performance of the test is investigated through simulations. We illustrate the new method through the systematic assessment and comparison of the performance of transcriptomics and metabolomics sources in the prediction of body mass index (BMI) using longitudinal data from the Dietary, Lifestyle, and Genetic determinants of Obesity and Metabolic syndrome (DILGOM) study, a population-based cohort from Finland.

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arXiv2016

On the combination of omics data for prediction of binary outcomes

Enrichment of predictive models with new biomolecular markers is an important task in high-dimensional omic applications. Increasingly, clinical studies include several sets of such omics markers available for each patient, measuring different levels of biological variation. As a result, one of the main challenges in predictive research is the integration of different sources of omic biomarkers for the prediction of health traits. We review several approaches for the combination of omic markers in the context of binary outcome prediction, all based on double cross-validation and regularized regression models. We evaluate their performance in terms of calibration and discrimination and we compare their performance with respect to single-omic source predictions. We illustrate the methods through the analysis of two real datasets. On the one hand, we consider the combination of two fractions of proteomic mass spectrometry for the calibration of a diagnostic rule for the detection of early-stage breast cancer. On the other hand, we consider transcriptomics and metabolomics as predictors of obesity using data from the Dietary, Lifestyle, and Genetic determinants of Obesity and Metabolic syndrome (DILGOM) study, a population-based cohort, from Finland.

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