Network data are increasingly common in the social sciences and infectious disease epidemiology. Analyses often link network structure to node-level covariates, but existing methods falter with sparse networks and high-dimensional node features. We propose a joint latent space modeling framework for sparse networks with high-dimensional binary node covariates that performs covariate selection while accounting for uncertainty in estimated latent positions. Building on joint latent space models that couple edges and node variables through shared latent positions, we introduce a group lasso screening step and incorporate a measurement-error-aware stabilization term to mitigate bias from using estimated latent positions as predictors. We establish prediction error rates for the covariate component both when latent positions are treated as observed and when they are estimated with bounded error; under uniform control across $q$ covariates and $n$ nodes, the rate is of order $O(\log q / n)$ up to an additional term due to latent position estimation error. Our method addresses three challenges: (1) incorporating information from isolated nodes, which are common in sparse networks but often ignored; (2) selecting relevant covariates from high-dimensional spaces; and (3) accounting for uncertainty in estimated latent positions. Simulations show predictive performance remains stable as covariate sparsity grows, while naive approaches degrade. We illustrate how the method can support efficient study design using household social networks from 75 Indian villages, where an emulated pilot study screens a large covariate battery and substantially reduces required subsequent data collection without sacrificing network predictive accuracy.
An integration of decision trees into latent class modeling with covariates
National Institute for Research in Digital Science and Technology (Inria)（数字科学与技术国家研究院）；Department of Methodology and Statistics, Tilburg University（蒂尔堡大学方法论与统计系）
A key challenge in modern data analysis is understanding connections between complex and differing modalities of data. For example, two of the main approaches to the study of breast cancer are histopathology (analyzing visual characteristics of tumors) and genetics. While histopathology is the gold standard for diagnostics and there have been many recent breakthroughs in genetics, there is little overlap between these two fields. We aim to bridge this gap by developing methods based on Angle-based Joint and Individual Variation Explained (AJIVE) to directly explore similarities and differences…
Propensity score analysis with latent covariates: Measurement error bias correction using the covariate's posterior mean, aka the inclusive factor score
Johns Hopkins Bloomberg School of Public Health（约翰斯·霍普金斯大学彭博公共卫生学院）
The study of network data in the social and health sciences frequently concentrates on two distinct tasks (1) detecting community structures among nodes and (2) associating covariate information to edge formation. In much of this data, it is likely that the effects of covariates on edge formation differ between communities (e.g. age might play a different role in friendship formation in communities across a city). In this work, we introduce a latent space network model where coefficients associated with certain covariates can depend on latent community membership of the nodes. We show that ign…
We develop a nested EM routine for latent class models with covariates which allows maximization of the full-model log-likelihood and, differently from current methods, guarantees monotone log-likelihood sequences along with improved convergence rates.
Usually in Latent Class Analysis (LCA), external predictors are taken to be cluster conditional probability predictors (LC models with covariates), and/or score conditional probability predictors (LC regression models). In such cases, their distribution is not of interest. Class specific distribution is of interest in the distal outcome model, when the distribution of the external variable(s) is assumed to dependent on LC membership. In this paper, we consider a more general formulation, typical in cluster-weighted models, which embeds both the latent class regression and the distal outcome mo…
Reductions in natural habitats urge that we better understand species' interconnection and how biological communities respond to environmental changes. However, ecological studies of species' interactions are limited by their geographic and taxonomic focus which can distort our understanding of interaction dynamics. We focus on bird-plant interactions that refer to situations of potential fruit consumption and seed dispersal. We develop an approach for predicting species' interactions that accounts for errors in the recorded interaction networks, addresses the geographic and taxonomic biases o…
In this paper, we propose a semiparametric, tree based joint latent class modeling approach (JLCT) to model the joint behavior of longitudinal and time-to-event data. Existing joint latent class modeling approaches are parametric and can suffer from high computational cost. The most common parametric approach, the joint latent class model (JLCM), further restricts analysis to using time-invariant covariates in modeling survival risks and latent class memberships. Instead, the proposed JLCT is fast to fit, and can use time-varying covariates in all of its modeling components. We demonstrate the…
In the attention-deficit hyperactivity disorder (ADHD) study, children are prescribed different stimulant medications. The height measurements are recorded longitudinally along with the medication time. Differences among the patients are captured by the parameters suggested the Superimposition by Translation and Rotation (SITAR) model using three subject-specific parameters to estimate their deviation from the mean growth curve. In this paper, we generalize the SITAR model in a Bayesian way with time-invariant covariates. The time-invariant model allows us to predict latent growth factors. Sin…
We consider joint selection of fixed and random effects in general mixed-effects models. The interpretation of estimated mixed-effects models is challenging since changing the structure of one set of effects can lead to different choices of important covariates in the model. We propose a stepwise selection algorithm to perform simultaneous selection of the fixed and random effects. It is based on BIC-type criteria whose penalties are adapted to mixed-effects models. The proposed procedure performs model selection in both linear and nonlinear models. It should be used in the low-dimension setti…
Randomized block factorial experiments are widely used in industrial engineering, clinical trials, and social science. Researchers often use a linear model and analysis of covariance to analyze experimental results; however, limited studies have addressed the validity and robustness of the resulting inferences because assumptions for a linear model might not be justified by randomization in randomized block factorial experiments. In this paper, we establish a new finite population joint central limit theorem for usual (unadjusted) factorial effect estimators in randomized block $2^K$ factorial…
Latent space models are effective tools for statistical modeling and exploration of network data. These models can effectively model real world network characteristics such as degree heterogeneity, transitivity, homophily, etc. Due to their close connection to generalized linear models, it is also natural to incorporate covariate information in them. The current paper presents two universal fitting algorithms for networks with edge covariates: one based on nuclear norm penalization and the other based on projected gradient descent. Both algorithms are motivated by maximizing likelihood for a s…
On a penalised likelihood approach for joint modelling of longitudinal covariates and partly interval-censored data -- an application to the Anti-PD1 brain collaboration trial
Robust Community Detection for Noisy Networks with Covariates: Application to Functional Brain Networks
University of Connecticut（康涅狄格大学）；University of Pennsylvania（宾夕法尼亚大学）；University of Texas MD Anderson Cancer Center（德克萨斯大学安德森癌症中心）；Yale University（耶鲁大学）
Products manufactured from the same batch or utilized in the same region often exhibit correlated lifetime observations due to the latent heterogeneity caused by the influence of shared but unobserved covariates. The unavailable group-shared covariates involve multiple different types (e.g., discrete, continuous, or mixed-type) and induce different structures of indispensable group-shared latent heterogeneity. Without carefully capturing such latent heterogeneity, the lifetime modeling accuracy will be significantly undermined. In this work, we propose a generic Bayesian lifetime modeling appr…
The paper describes a new class of capture-recapture models for closed populations when individual covariates are available. The novelty consists in combining a latent class model for the distribution of the capture history, where the class weights and the conditional distributions given the latent may depend on covariates, with a model for the marginal distribution of the available covariates as in \cite{Liu2017}. In addition, any general form of serial dependence is allowed when modeling capture histories conditionally on the latent and covariates. A Fisher-scoring algorithm for maximum like…
An important phenomenon in high dimensional biological data is the presence of unobserved covariates that can have a significant impact on the measured response. When these factors are also correlated with the covariate(s) of interest (i.e. disease status), ignoring them can lead to increased type I error and spurious false discovery rate estimates. We show that depending on the strength of this correlation and the informativeness of the observed data for the latent factors, previously proposed estimators for the effect of the covariate of interest that attempt to account for unobserved covari…
Researchers are usually interested in examining the impact of covariates when separating heterogeneous samples into latent classes that are more homogeneous. The majority of theoretical and empirical studies with such aims have focused on identifying covariates as predictors of class membership in the structural equation modeling framework. In other words, the covariates only indirectly affect the sample heterogeneity. However, the covariates' influence on between-individual differences can also be direct. This article presents a mixture model that investigates covariates to explain within-clu…
The current research has two aims. First, to demonstrate the utility conditional nonparametric multilevel latent class analysis (NP-MLCA) for multi-site program evaluation using an empirical dataset. Second, to investigate how classification accuracy and parameter estimation of a conditional NP-MLCA are affected by six study factors: the quality of latent class indicators, the number of latent class indicators, level-1 covariate effects, cross-level covariate effects, the number of level-2 units, and the size of level-2 units. A total of 96 conditions was examined using a simulation study. The…
Examination of Nonlinear Longitudinal Processes with Latent Variables, Latent Processes, Latent Changes, and Latent Classes in the Structural Equation Modeling Framework: The R package nlpsem
Univariate or multivariate ordinal responses are often assumed to arise from a latent continuous parametric distribution, with covariate effects which enter linearly. We introduce a Bayesian nonparametric modeling approach for univariate and multivariate ordinal regression, which is based on mixture modeling for the joint distribution of latent responses and covariates. The modeling framework enables highly flexible inference for ordinal regression relationships, avoiding assumptions of linearity or additivity in the covariate effects. In standard parametric ordinal regression models, computat…
Logistic regression is a common classification method in supervised learning. Surprisingly, there are very few solutions for performing logistic regression with missing values in the covariates. We suggest a complete approach based on a stochastic approximation version of the EM algorithm to do statistical inference with missing values including the estimation of the parameters and their variance, derivation of confidence intervals and a model selection procedure. We also tackle the problem of prediction for new observations (on a test set) with missing covariate data. The methodology is compu…
In this paper we recast the problem of missing values in the covariates of a regression model as a latent Gaussian Markov random field (GMRF) model in a fully Bayesian framework. Our proposed approach is based on the definition of the covariate imputation sub-model as a latent effect with a GMRF structure. We show how this formulation works for continuous covariates and provide some insight on how this could be extended to categorical covariates. The resulting Bayesian hierarchical model naturally fits within the integrated nested Laplace approximation (INLA) framework, which we use for model …
Researchers continue to be interested in exploring the effects that covariates have on the heterogeneity in trajectories. The inclusion of covariates associated with latent classes allows for a more clear understanding of individual differences and a more meaningful interpretation of latent class membership. Many theoretical and empirical studies have focused on investigating heterogeneity in change patterns of a univariate repeated outcome and examining the effects on baseline covariates that inform the cluster formation. However, developmental processes rarely unfold in isolation; therefore,…
We extend conformal prediction methodology beyond the case of exchangeable data. In particular, we show that a weighted version of conformal prediction can be used to compute distribution-free prediction intervals for problems in which the test and training covariate distributions differ, but the likelihood ratio between these two distributions is known---or, in practice, can be estimated accurately with access to a large set of unlabeled data (test covariate points). Our weighted extension of conformal prediction also applies more generally, to settings in which the data satisfies a certain w…
Many high dimensional and high-throughput biological datasets have complex sample correlation structures, which include longitudinal and multiple tissue data, as well as data with multiple treatment conditions or related individuals. These data, as well as nearly all high-throughput `omic' data, are influenced by technical and biological factors unknown to the researcher, which, if unaccounted for, can severely obfuscate estimation and inference on effects due to the known covariate of interest. We therefore developed CBCV and CorrConf: provably accurate and computationally efficient methods t…
Flexibly modeling how an entire density changes with covariates is an important but challenging generalization of mean and quantile regression. While existing methods for density regression primarily consist of covariate-dependent discrete mixture models, we consider a continuous latent variable model in general covariate spaces, which we call DR-BART. The prior mapping the latent variable to the observed data is constructed via a novel application of Bayesian Additive Regression Trees (BART). We prove that the posterior induced by our model concentrates quickly around true generative function…
There is an increasing recognition of the role of brain networks as neuroimaging biomarkers in mental health and psychiatric studies. Our focus is posttraumatic stress disorder (PTSD), where the brain network interacts with environmental exposures in complex ways to drive the disease progression. Existing linear models seeking to characterize the relation between the clinical phenotype and the entire edge set in the brain network may be overly simplistic and often involve inflated number of parameters leading to computational burden and inaccurate estimation. In one of the first such efforts, …
Multivariate compositional count data arise in many applications including ecology, microbiology, genetics, and paleoclimate. A frequent question in the analysis of multivariate compositional count data is what values of a covariate(s) give rise to the observed composition. Learning the relationship between covariates and the compositional count allows for inverse prediction of unobserved covariates given compositional count observations. Gaussian processes provide a flexible framework for modeling functional responses with respect to a covariate without assuming a functional form. Many scient…
The analysis of high dimensional survival data is challenging, primarily due to the problem of overfitting which occurs when spurious relationships are inferred from data that subsequently fail to exist in test data. Here we propose a novel method of extracting a low dimensional representation of covariates in survival data by combining the popular Gaussian Process Latent Variable Model (GPLVM) with a Weibull Proportional Hazards Model (WPHM). The combined model offers a flexible non-linear probabilistic method of detecting and extracting any intrinsic low dimensional structure from high dimen…
