arXiv subjects

Peter X. -K. Song

Publications and source records attributed to Peter X. -K. Song.

17 recordsLinked to original sources

arXiv2025

Quantification and cross-fitting inference of asymmetric relations under generative exposure mapping models

Learning directionality between variables is crucial yet challenging, especially for mechanistic relationships without a priori ordering assumptions. We propose a coefficient of asymmetry to quantify directional asymmetry using Shannon's entropy within a generative exposure mapping (GEM) framework. GEMs arise from experiments where a generative function $g$ maps exposure $X$ to outcome $Y$ through $Y = g(X)$, extended to noise-perturbed GEMs as $Y = g(X) + ε$. Our approach considers a rich class of generative functions while providing statistical inference for uncertainty quantification - a gap in existing bivariate causal discovery techniques. We establish large-sample theoretical guarantees through data-splitting and cross-fitting techniques, implementing fast Fourier transformation-based density estimation to avoid parameter tuning. The methodology accommodates contamination in outcome measurements. Extensive simulations demonstrate superior performance compared to competing causal discovery methods. Applied to epigenetic data examining DNA methylation and blood pressure relationships, our method unveils novel pathways for cardiovascular disease genes \emph{FGF5} and \emph{HSD11B2}. This framework serves as a discovery tool for improving scientific research rigor, with GEM-induced asymmetry representing a low-dimensional imprint of underlying causality

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arXiv2025

Copula Structural Equation Models for Mediation Pathway Analysis

Structural equation models (SEMs) are fundamental to causal mediation pathway discovery. However, traditional SEM approaches often rely on \emph{ad hoc} model specifications when handling complex data structures such as mixed data types or non-normal data in which Gaussian assumptions for errors are rather restrictive. The invocation of copula dependence modeling methods to extend the classical linear SEMs mitigates several of key technical limitations, offering greater modeling flexibility to analyze non-Gaussian data. This paper presents a selective review of major developments in this area, highlighting recent advancements and their methodological implications.

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arXiv2025

A Framework for Covariate-Adjusted Bivariate Causal Discovery

Ascertaining causal direction from observational data is a fundamental challenge in scientific inquiry. Of particular interest is the problem of covariate-adjusted bivariate causal discovery, i.e., determining the causal direction between X and Y in the presence of Z. While unadjusted bivariate causal discovery has seen significant advances (Hoyer et al., 2008; Ni, 2022), there is a lack of methodology dealing with real-world bivariate relationships, which are often modulated by a set of covariate(s), Z. Building on previous work in Purkayastha and Song (2025), we introduce a novel, nonparametric framework for the covariate-adjusted bivariate causal discovery problem and propose a conditional asymmetry coefficient to track said direction of causation. We develop a robust estimation procedure using kernel-based conditional density estimation with cross-fitting and also provide rigorous uncertainty quantification using a nonparametric kernel smoothing technique, addressing a key limitation of many existing algorithms. As a key application, we demonstrate how this framework can be applied to the problem of collider detection, a persistent challenge in causal structure learning. Simulation studies show our method's superior performance in identifying causal structures. We apply our approach to an epigenetic study (Perng et al., 2019), investigating the role of blood pressure in regulating the effects of DNA methylation. In summary, our work offers methodological advancement by providing a robust, inferential toolkit for dissecting complex, moderated bivariate causal relationships in observational data.

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arXiv2024

Quantile Mediation Analytics

Mediation analytics help examine if and how an intermediate variable mediates the influence of an exposure variable on an outcome of interest. Quantiles, rather than the mean, of an outcome are scientifically relevant to the comparison among specific subgroups in practical studies. Albeit some empirical studies available in the literature, there lacks a thorough theoretical investigation of quantile-based mediation analysis, which hinders practitioners from using such methods to answer important scientific questions. To address this significant technical gap, in this paper, we develop a quantile mediation analysis methodology to facilitate the identification, estimation, and testing of quantile mediation effects under a hypothesized directed acyclic graph. We establish two key estimands, quantile natural direct effect (qNDE) and quantile natural indirect effect (qNIE), in the counterfactual framework, both of which have closed-form expressions. To overcome the issue that the null hypothesis of no mediation effect is composite, we establish a powerful adaptive bootstrap method that is shown theoretically and numerically to achieve a proper type I error control. We illustrate the proposed quantile mediation analysis methodology through both extensive simulation experiments and a real-world dataset in that we investigate the mediation effect of lipidomic biomarkers for the influence of exposure to phthalates on early childhood obesity clinically diagnosed by 95\% percentile of body mass index.

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arXiv2024

Privacy enhanced collaborative inference in the Cox proportional hazards model for distributed data

Data sharing barriers are paramount challenges arising from multicenter clinical studies where multiple data sources are stored in a distributed fashion at different local study sites. Particularly in the case of time-to-event analysis when global risk sets are needed for the Cox proportional hazards model, access to a centralized database is typically necessary. Merging such data sources into a common data storage for a centralized statistical analysis requires a data use agreement, which is often time-consuming. Furthermore, the construction and distribution of risk sets to participating clinical centers for subsequent calculations may pose a risk of revealing individual-level information. We propose a new collaborative Cox model that eliminates the need for accessing the centralized database and constructing global risk sets but needs only the sharing of summary statistics with significantly smaller dimensions than risk sets. Thus, the proposed collaborative inference enjoys maximal protection of data privacy. We show theoretically and numerically that the new distributed proportional hazards model approach has little loss of statistical power when compared to the centralized method that requires merging the entire data. We present a renewable sieve method to establish large-sample properties for the proposed method. We illustrate its performance through simulation experiments and a real-world data example from patients with kidney transplantation in the Organ Procurement and Transplantation Network (OPTN) to understand the factors associated with the 5-year death-censored graft failure (DCGF) for patients who underwent kidney transplants in the US.

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arXiv2023

A Class of Directed Acyclic Graphs with Mixed Data Types in Mediation Analysis

We propose a unified class of generalized structural equation models (GSEMs) with data of mixed types in mediation analysis, including continuous, categorical, and count variables. Such models extend substantially the classical linear structural equation model to accommodate many data types arising from the application of mediation analysis. Invoking the hierarchical modeling approach, we specify GSEMs by a copula joint distribution of outcome variable, mediator and exposure variable, in which marginal distributions are built upon generalized linear models (GLMs) with confounding factors. We discuss the identifiability conditions for the causal mediation effects in the counterfactual paradigm as well as the issue of mediation leakage, and develop an asymptotically efficient profile maximum likelihood estimation and inference for two key mediation estimands, natural direct effect and natural indirect effect, in different scenarios of mixed data types. The proposed new methodology is illustrated by a motivating epidemiological study that aims to investigate whether the tempo of reaching infancy BMI peak (delay or on time), an important early life growth milestone, may mediate the association between prenatal exposure to phthalates and pubertal health outcomes.

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arXiv2022

Collaborative causal inference with a distributed data-sharing management

Data sharing barriers are paramount challenges arising from multicenter clinical trials where multiple data sources are stored in a distributed fashion at different local study sites. Merging such data sources into a common data storage for a centralized statistical analysis requires a data use agreement, which is often time-consuming. Data merging may become more burdensome when causal inference is of primary interest because propensity score modeling involves combining many confounding variables, and systematic incorporation of this additional modeling in meta-analysis has not been thoroughly investigated in the literature. We propose a new causal inference framework that avoids the merging of subject-level raw data from multiple sites but needs only the sharing of summary statistics. The proposed collaborative inference enjoys maximal protection of data privacy and minimal sensitivity to unbalanced data distributions across data sources. We show theoretically and numerically that the new distributed causal inference approach has little loss of statistical power compared to the centralized method that requires merging the entire data. We present large-sample properties and algorithms for the proposed method. We illustrate its performance by simulation experiments and a real-world data example on a multicenter clinical trial of basal insulin treatment for reducing the risk of post-transplantation diabetes among kidney-transplant patients.

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arXiv2022

Supervised Homogeneity Fusion: a Combinatorial Approach

Fusing regression coefficients into homogenous groups can unveil those coefficients that share a common value within each group. Such groupwise homogeneity reduces the intrinsic dimension of the parameter space and unleashes sharper statistical accuracy. We propose and investigate a new combinatorial grouping approach called $L_0$-Fusion that is amenable to mixed integer optimization (MIO). On the statistical aspect, we identify a fundamental quantity called grouping sensitivity that underpins the difficulty of recovering the true groups. We show that $L_0$-Fusion achieves grouping consistency under the weakest possible requirement of the grouping sensitivity: if this requirement is violated, then the minimax risk of group misspecification will fail to converge to zero. Moreover, we show that in the high-dimensional regime, one can apply $L_0$-Fusion coupled with a sure screening set of features without any essential loss of statistical efficiency, while reducing the computational cost substantially. On the algorithmic aspect, we provide a MIO formulation for $L_0$-Fusion along with a warm start strategy. Simulation and real data analysis demonstrate that $L_0$-Fusion exhibits superiority over its competitors in terms of grouping accuracy.

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arXiv2021

Parallel-and-stream accelerator for computationally fast supervised learning

Two dominant distributed computing strategies have emerged to overcome the computational bottleneck of supervised learning with big data: parallel data processing in the MapReduce paradigm and serial data processing in the online streaming paradigm. Despite the two strategies' common divide-and-combine approach, they differ in how they aggregate information, leading to different trade-offs between statistical and computational performance. In this paper, we propose a new hybrid paradigm, termed a Parallel-and-Stream Accelerator (PASA), that uses the strengths of both strategies for computationally fast and statistically efficient supervised learning. PASA's architecture nests online streaming processing into each distributed and parallelized data process in a MapReduce framework. PASA leverages the advantages and mitigates the disadvantages of both the MapReduce and online streaming approaches to deliver a more flexible paradigm satisfying practical computing needs. We study the analytic properties and computational complexity of PASA, and detail its implementation for two key statistical learning tasks. We illustrate its performance through simulations and a large-scale data example building a prediction model for online purchases from advertising data.

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arXiv2021

Real-Time Regression Analysis of Streaming Clustered Data With Possible Abnormal Data Batches

This paper develops an incremental learning algorithm based on quadratic inference function (QIF) to analyze streaming datasets with correlated outcomes such as longitudinal data and clustered data. We propose a renewable QIF (RenewQIF) method within a paradigm of renewable estimation and incremental inference, in which parameter estimates are recursively renewed with current data and summary statistics of historical data, but with no use of any historical subject-level raw data. We compare our renewable estimation method with both offline QIF and offline generalized estimating equations (GEE) approach that process the entire cumulative subject-level data, and show theoretically and numerically that our renewable procedure enjoys statistical and computational efficiency. We also propose an approach to diagnose the homogeneity assumption of regression coefficients via a sequential goodness-of-fit test as a screening procedure on occurrences of abnormal data batches. We implement the proposed methodology by expanding existing Spark's Lambda architecture for the operation of statistical inference and data quality diagnosis. We illustrate the proposed methodology by extensive simulation studies and an analysis of streaming car crash datasets from the National Automotive Sampling System-Crashworthiness Data System (NASS CDS).

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arXiv2020

Joint integrative analysis of multiple data sources with correlated vector outcomes

We propose a distributed quadratic inference function framework to jointly estimate regression parameters from multiple potentially heterogeneous data sources with correlated vector outcomes. The primary goal of this joint integrative analysis is to estimate covariate effects on all outcomes through a marginal regression model in a statistically and computationally efficient way. We develop a data integration procedure for statistical estimation and inference of regression parameters that is implemented in a fully distributed and parallelized computational scheme. To overcome computational and modeling challenges arising from the high-dimensional likelihood of the correlated vector outcomes, we propose to analyze each data source using Qu, Lindsay and Li (2000)'s quadratic inference functions, and then to jointly reestimate parameters from each data source by accounting for correlation between data sources using a combined meta-estimator in a similar spirit to Hansen (1982)'s generalised method of moments. We show both theoretically and numerically that the proposed method yields efficiency improvements and is computationally fast. We illustrate the proposed methodology with the joint integrative analysis of the association between smoking and metabolites in a large multi-cohort study and provide an R package for ease of implementation.

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arXiv2020

Distributed Simultaneous Inference in Generalized Linear Models via Confidence Distribution

We propose a distributed method for simultaneous inference for datasets with sample size much larger than the number of covariates, i.e., N >> p, in the generalized linear models framework. When such datasets are too big to be analyzed entirely by a single centralized computer, or when datasets are already stored in distributed database systems, the strategy of divide-and-combine has been the method of choice for scalability. Due to partition, the sub-dataset sample sizes may be uneven and some possibly close to p, which calls for regularization techniques to improve numerical stability. However, there is a lack of clear theoretical justification and practical guidelines to combine results obtained from separate regularized estimators, especially when the final objective is simultaneous inference for a group of regression parameters. In this paper, we develop a strategy to combine bias-corrected lasso-type estimates by using confidence distributions. We show that the resulting combined estimator achieves the same estimation efficiency as that of the maximum likelihood estimator using the centralized data. As demonstrated by simulated and real data examples, our divide-and-combine method yields nearly identical inference as the centralized benchmark.

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arXiv2020

Doubly Distributed Supervised Learning and Inference with High-Dimensional Correlated Outcomes

This paper presents a unified framework for supervised learning and inference procedures using the divide-and-conquer approach for high-dimensional correlated outcomes. We propose a general class of estimators that can be implemented in a fully distributed and parallelized computational scheme. Modelling, computational and theoretical challenges related to high-dimensional correlated outcomes are overcome by dividing data at both outcome and subject levels, estimating the parameter of interest from blocks of data using a broad class of supervised learning procedures, and combining block estimators in a closed-form meta-estimator asymptotically equivalent to estimates obtained by Hansen (1982)'s generalized method of moments (GMM) that does not require the entire data to be reloaded on a common server. We provide rigorous theoretical justifications for the use of distributed estimators with correlated outcomes by studying the asymptotic behaviour of the combined estimator with fixed and diverging number of data divisions. Simulations illustrate the finite sample performance of the proposed method, and we provide an R package for ease of implementation.

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arXiv2020

A Distributed and Integrated Method of Moments for High-Dimensional Correlated Data Analysis

This paper is motivated by a regression analysis of electroencephalography (EEG) neuroimaging data with high-dimensional correlated responses with multi-level nested correlations. We develop a divide-and-conquer procedure implemented in a fully distributed and parallelized computational scheme for statistical estimation and inference of regression parameters. Despite significant efforts in the literature, the computational bottleneck associated with high-dimensional likelihoods prevents the scalability of existing methods. The proposed method addresses this challenge by dividing responses into subvectors to be analyzed separately and in parallel on a distributed platform using pairwise composite likelihood. Theoretical challenges related to combining results from dependent data are overcome in a statistically efficient way using a meta-estimator derived from Hansen's generalized method of moments. We provide a rigorous theoretical framework for efficient estimation, inference, and goodness-of-fit tests. We develop an R package for ease of implementation. We illustrate our method's performance with simulations and the analysis of the EEG data, and find that iron deficiency is significantly associated with two auditory recognition memory related potentials in the left parietal-occipital region of the brain.

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arXiv2019

Method of Contraction-Expansion (MOCE) for Simultaneous Inference in Linear Models

Simultaneous inference after model selection is of critical importance to address scientific hypotheses involving a set of parameters. In this paper, we consider high-dimensional linear regression model in which a regularization procedure such as LASSO is applied to yield a sparse model. To establish a simultaneous post-model selection inference, we propose a method of contraction and expansion (MOCE) along the line of debiasing estimation that enables us to balance the bias-and-variance trade-off so that the super-sparsity assumption may be relaxed. We establish key theoretical results for the proposed MOCE procedure from which the expanded model can be selected with theoretical guarantees and simultaneous confidence regions can be constructed by the joint asymptotic normal distribution. In comparison with existing methods, our proposed method exhibits stable and reliable coverage at a nominal significance level with substantially less computational burden, and thus it is trustworthy for its application in solving real-world problems.

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arXiv2017

Scalable and Efficient Statistical Inference with Estimating Functions in the MapReduce Paradigm for Big Data

The theory of statistical inference along with the strategy of divide-and-conquer for large- scale data analysis has recently attracted considerable interest due to great popularity of the MapReduce programming paradigm in the Apache Hadoop software framework. The central analytic task in the development of statistical inference in the MapReduce paradigm pertains to the method of combining results yielded from separately mapped data batches. One seminal solution based on the confidence distribution has recently been established in the setting of maximum likelihood estimation in the literature. This paper concerns a more general inferential methodology based on estimating functions, termed as the Rao-type confidence distribution, of which the maximum likelihood is a special case. This generalization provides a unified framework of statistical inference that allows regression analyses of massive data sets of important types in a parallel and scalable fashion via a distributed file system, including longitudinal data analysis, survival data analysis, and quantile regression, which cannot be handled using the maximum likelihood method. This paper investigates four important properties of the proposed method: computational scalability, statistical optimality, methodological generality, and operational robustness. In particular, the proposed method is shown to be closely connected to Hansen's generalized method of moments (GMM) and Crowder's optimality. An interesting theoretical finding is that the asymptotic efficiency of the proposed Rao-type confidence distribution estimator is always greater or equal to the estimator obtained by processing the full data once. All these properties of the proposed method are illustrated via numerical examples in both simulation studies and real-world data analyses.

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arXiv2012

Signal extraction and breakpoint identification for array CGH data using robust state space model

Array comparative genomic hybridization(CGH) is a high resolution technique to assess DNA copy number variation. Identifying breakpoints where copy number changes will enhance the understanding of the pathogenesis of human diseases, such as cancers. However, the biological variation and experimental errors contained in array CGH data may lead to false positive identification of breakpoints. We propose a robust state space model for array CGH data analysis. The model consists of two equations: an observation equation and a state equation, in which both the measurement error and evolution error are specified to follow t-distributions with small degrees of freedom. The completely unspecified CGH profiles are estimated by a Markov Chain Monte Carlo(MCMC) algorithm. Breakpoints and outliers are identified by a novel backward selection procedure based on posterior draws of the CGH profiles. Compared to three other popular methods, our method demonstrates several desired features, including false positive rate control, robustness against outliers, and superior power of breakpoint detection. All these properties are illustrated using simulated and real datasets.

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