Latent factor regression models for grouped outcomes.
Ontology highlight
ABSTRACT:
SUBMITTER: Woodard DB
PROVIDER: S-EPMC4171058 | biostudies-literature | 2013 Sep
REPOSITORIES: biostudies-literature
Publications
Latent factor regression models for grouped outcomes.
Woodard D B DB Love T M T TM Thurston S W SW Ruppert D D Sathyanarayana S S Swan S H SH
Biometrics 20130711 3
We consider regression models for multiple correlated outcomes, where the outcomes are nested in domains. We show that random effect models for this nested situation fit into a standard factor model framework, which leads us to view the modeling options as a spectrum between parsimonious random effect multiple outcomes models and more general continuous latent factor models. We introduce a set of identifiable models along this spectrum that extend an existing random effect model for multiple out ...[more]
Similar Datasets
Project description:BACKGROUND:The standard lasso penalty and its extensions are commonly used to develop a regularized regression model while selecting candidate predictor variables on a time-to-event outcome in high-dimensional data. However, these selection methods focus on a homogeneous set of variables and do not take into account the case of predictors belonging to functional groups; typically, genomic data can be grouped according to biological pathways or to different types of collected data. Another challenge is that the standard lasso penalisation is known to have a high false discovery rate. RESULTS:We evaluated different penalizations in a Cox model to select grouped variables in order to further penalize variables that, in addition to having a low effect, belong to a group with a low overall effect; and to favor the selection of variables that, in addition to having a large effect, belong to a group with a large overall effect. We considered the case of prespecified and disjoint groups and proposed diverse weights for the adaptive lasso method. In particular we proposed the product Max Single Wald by Single Wald weighting (MSW*SW) which takes into account the information of the group to which it belongs and of this biomarker. Through simulations, we compared the selection and prediction ability of our approach with the standard lasso, the composite Minimax Concave Penalty (cMCP), the group exponential lasso (gel), the Integrative L1-Penalized Regression with Penalty Factors (IPF-Lasso), and the Sparse Group Lasso (SGL) methods. In addition, we illustrated the methods using gene expression data of 614 breast cancer patients. CONCLUSIONS:The adaptive lasso with the MSW*SW weighting method incorporates both the information in the grouping structure and the individual variable. It outperformed the competitors by reducing the false discovery rate without severely increasing the false negative rate.
| S-EPMC7331150 | biostudies-literature
Project description:BackgroundTime- and dose-to-event phenotypes used in basic science and translational studies are commonly measured imprecisely or incompletely due to limitations of the experimental design or data collection schema. For example, drug-induced toxicities are not reported by the actual time or dose triggering the event, but rather are inferred from the cycle or dose to which the event is attributed. This exemplifies a prevalent type of imprecise measurement called grouped failure time, where times or doses are restricted to discrete increments. Failure to appropriately account for the grouped nature of the data, when present, may lead to biased analyses.ResultsWe present groupedSurv, an R package which implements a statistically rigorous and computationally efficient approach for conducting genome-wide analyses based on grouped failure time phenotypes. Our approach accommodates adjustments for baseline covariates, and analysis at the variant or gene level. We illustrate the statistical properties of the approach and computational performance of the package by simulation. We present the results of a reanalysis of a published genome-wide study to identify common germline variants associated with the risk of taxane-induced peripheral neuropathy in breast cancer patients.ConclusionsgroupedSurv enables fast and rigorous genome-wide analysis on the basis of grouped failure time phenotypes at the variant, gene or pathway level. The package is freely available under a public license through the Comprehensive R Archive Network.
| S-EPMC6540566 | biostudies-literature
Project description:In studies involving functional data, it is commonly of interest to model the impact of predictors on the distribution of the curves, allowing flexible effects on not only the mean curve but also the distribution about the mean. Characterizing the curve for each subject as a linear combination of a high-dimensional set of potential basis functions, we place a sparse latent factor regression model on the basis coefficients. We induce basis selection by choosing a shrinkage prior that allows many of the loadings to be close to zero. The number of latent factors is treated as unknown through a highly-efficient, adaptive-blocked Gibbs sampler. Predictors are included on the latent variables level, while allowing different predictors to impact different latent factors. This model induces a framework for functional response regression in which the distribution of the curves is allowed to change flexibly with predictors. The performance is assessed through simulation studies and the methods are applied to data on blood pressure trajectories during pregnancy.
| S-EPMC3530663 | biostudies-literature
Project description:Background and purposePrevious data suggest patient demographics and clinical presentation are primary predictors of motor recovery poststroke, with minimal contributions of physical interventions. Other studies indicate consistent associations between the amount and intensity of stepping practice with locomotor outcomes. The goal of this study was to determine the relative contributions of these combined variables to locomotor outcomes poststroke across a range of patient demographics and baseline function.MethodsData were pooled from 3 separate trials evaluating the efficacy of high-intensity training, low-intensity training, and conventional interventions. Demographics, clinical characteristics, and training activities from 144 participants >1-month poststroke were included in stepwise regression analyses to determine their relative contributions to locomotor outcomes. Subsequent latent profile analyses evaluated differences in classes of participants based on their responses to interventions.ResultsStepwise regressions indicate primary contributions of stepping activity on locomotor outcomes, with additional influences of age, duration poststroke, and baseline function. Latent profile analyses revealed 2 main classes of outcomes, with the largest gains in those who received high-intensity training and achieved the greatest amounts of stepping practice. Regression and latent profile analyses of only high-intensity training participants indicated age, baseline function, and training activities were primary determinants of locomotor gains. Participants with the smallest gains were older (≈60 years), presented with slower gait speeds (<0.40 m/s), and performed 600 to 1000 less steps/session.ConclusionsRegression and cluster analyses reveal primary contributions of training interventions on mobility outcomes in patients >1-month poststroke. Age, duration poststroke, and baseline impairments were secondary predictors. Registration: URL: https://www.clinicaltrials.gov. Unique identifier: NCT02507466 and NCT01789853.
| S-EPMC7530096 | biostudies-literature
Project description:Student Growth Percentiles (SGPs) increasingly are being used in the United States for inferences about student achievement growth and educator effectiveness. Emerging research has indicated that SGPs estimated from observed test scores have large measurement errors. As such, little is known about "true" SGPs, which are defined in terms of nonlinear functions of latent achievement attributes for individual students and their distributions across students. We develop a novel framework using latent regression multidimensional item response theory models to study distributional properties of true SGPs. We apply these methods to several cohorts of longitudinal item response data from more than 330,000 students in a large urban metropolitan area to provide new empirical information about true SGPs. We find that true SGPs are correlated 0.3 to 0.5 across mathematics and English language arts, and that they have nontrivial relationships with individual student characteristics, particularly student race/ethnicity and absenteeism. We evaluate the potential of using these relationships to improve the accuracy of SGPs estimated from observed test scores, finding that accuracy gains even under optimal circumstances are modest. We also consider the properties of SGPs averaged to the teacher level, widely used for teacher evaluations. We find that average true SGPs for individual teachers vary substantially as a function of the characteristics of the students they teach. We discuss implications of our findings for the estimation and interpretation of SGPs at both the individual and aggregate levels.
| S-EPMC5965647 | biostudies-literature
Project description:Simple multilinear methods, such as partial least squares regression (PLSR), are effective at interrelating dynamic, multivariate datasets of cell-molecular biology through high-dimensional arrays. However, data collected in vivo are more difficult, because animal-to-animal variability is often high, and each time-point measured is usually a terminal endpoint for that animal. Observations are further complicated by the nesting of cells within tissues or tissue sections, which themselves are nested within animals. Here, we introduce principled resampling strategies that preserve the tissue-animal hierarchy of individual replicates and compute the uncertainty of multidimensional decompositions applied to global averages. Using molecular-phenotypic data from the mouse aorta and colon, we find that interpretation of decomposed latent variables (LVs) changes when PLSR models are resampled. Lagging LVs, which statistically improve global-average models, are unstable in resampled iterations that preserve nesting relationships, arguing that these LVs should not be mined for biological insight. Interestingly, resampling is less discriminatory for multidimensional regressions of in vitro data, where replicate-to-replicate variance is sufficiently low. Our work illustrates the challenges and opportunities in translating systems-biology approaches from cultured cells to living organisms. Nested resampling adds a straightforward quality-control step for interpreting the robustness of in vivo regression models.
| S-EPMC6928252 | biostudies-literature
Project description:Machine learning algorithms are becoming increasingly popular for decoding psychological constructs based on neural data. However, as a step towards bridging the gap between theory-driven cognitive neuroscience and data-driven decoding approaches, there is a need for methods that allow to interpret trained decoding models. The present study demonstrates grouped model reliance as a model-agnostic permutation-based approach to this problem. Grouped model reliance indicates the extent to which a trained model relies on conceptually related groups of variables, such as frequency bands or regions of interest in electroencephalographic (EEG) data. As a case study to demonstrate the method, random forest and support vector machine models were trained on within-participant single-trial EEG data from a Sternberg working memory task. Participants were asked to memorize a sequence of digits (0-9), varying randomly in length between one, four and seven digits, where EEG recordings for working memory load estimation were taken from a 3-second retention interval. The present results confirm previous findings insofar as both random forest and support vector machine models relied on alpha-band activity in most subjects. However, as revealed by further analyses, patterns in frequency and topography varied considerably between individuals, pointing to more pronounced inter-individual differences than previously reported.
| S-EPMC6964974 | biostudies-literature
Project description:Using genotype data to perform accurate genetic prediction of complex traits can facilitate genomic selection in animal and plant breeding programs, and can aid in the development of personalized medicine in humans. Because most complex traits have a polygenic architecture, accurate genetic prediction often requires modeling all genetic variants together via polygenic methods. Here, we develop such a polygenic method, which we refer to as the latent Dirichlet process regression model. Dirichlet process regression is non-parametric in nature, relies on the Dirichlet process to flexibly and adaptively model the effect size distribution, and thus enjoys robust prediction performance across a broad spectrum of genetic architectures. We compare Dirichlet process regression with several commonly used prediction methods with simulations. We further apply Dirichlet process regression to predict gene expressions, to conduct PrediXcan based gene set test, to perform genomic selection of four traits in two species, and to predict eight complex traits in a human cohort.Genetic prediction of complex traits with polygenic architecture has wide application from animal breeding to disease prevention. Here, Zeng and Zhou develop a non-parametric genetic prediction method based on latent Dirichlet Process regression models.
| S-EPMC5587666 | biostudies-literature
Project description:Now over 20 years old, functional MRI (fMRI) has a large and growing literature that is best synthesised with meta-analytic tools. As most authors do not share image data, only the peak activation coordinates (foci) reported in the article are available for Coordinate-Based Meta-Analysis (CBMA). Neuroimaging meta-analysis is used to (i) identify areas of consistent activation; and (ii) build a predictive model of task type or cognitive process for new studies (reverse inference). To simultaneously address these aims, we propose a Bayesian point process hierarchical model for CBMA. We model the foci from each study as a doubly stochastic Poisson process, where the study-specific log intensity function is characterized as a linear combination of a high-dimensional basis set. A sparse representation of the intensities is guaranteed through latent factor modeling of the basis coefficients. Within our framework, it is also possible to account for the effect of study-level covariates (meta-regression), significantly expanding the capabilities of the current neuroimaging meta-analysis methods available. We apply our methodology to synthetic data and neuroimaging meta-analysis datasets.
| S-EPMC5682245 | biostudies-literature
Project description:In spite of the success of genome-wide association studies in finding many common variants associated with disease, these variants seem to explain only a small proportion of the estimated heritability. Data collection has turned toward exome and whole genome sequencing, but it is well known that single marker methods frequently used for common variants have low power to detect rare variants associated with disease, even with very large sample sizes. In response, a variety of methods have been developed that attempt to cluster rare variants so that they may gather strength from one another under the premise that there may be multiple causal variants within a gene. Most of these methods group variants by gene or proximity, and test one gene or marker window at a time. We propose a penalized regression method (PeRC) that analyzes all genes at once, allowing grouping of all (rare and common) variants within a gene, along with subgrouping of the rare variants, thus borrowing strength from both rare and common variants within the same gene. The method can incorporate either a burden-based weighting of the rare variants or one in which the weights are data driven. In simulations, our method performs favorably when compared to many previously proposed approaches, including its predecessor, the sparse group lasso [Friedman et al., 2010].
| S-EPMC3842118 | biostudies-other