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Longhai Li

Publications and source records attributed to Longhai Li.

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An Entropy-based Coefficient of Determination with Adjustment of Optimization Bias

Classical likelihood-ratio tests and $\Delta$AIC exacerbate the statistical significance crisis by scaling with sample size, often flagging negligible improvements as highly significant. While causal estimands like the average treatment effect (ATE) quantify practical magnitude, their reliance on the expectation operator ties them to the data's original coordinate scale. Furthermore, existing pseudo-$R^2$ metrics are inadequate: variance-based measures ignore higher-order distributional changes, and current formulations lack invariance to monotone transformations. We resolve these limitations by introducing Entropic Variance (EV) as a rigorous, scale-independent generalization of error variance in ordinary least squares. We define the population EV-based parameter, $\rho^2_V$, which projects unbounded cross-entropy onto a standardized $[0,1]$ scale, and establish that the EV-based $F_\text{V}$ statistic asymptotically follows an $F$-distribution. Building on these distributional properties, we propose two estimators: the empirical population $R^2_{\text{SV}}$ and the out-of-sample predictive $R^2_{\text{SVP}}$. Both are derived by exponentiating per-observation cross-entropy and incorporate a degrees-of-freedom correction for training optimism. Leveraging the $F_\text{V}$-distribution, we derive refined $p$-values and confidence intervals for $\rho^2_V$ without requiring intractable Fisher information matrices. Simulation studies and a Parkinson's disease microbiome application demonstrate the superiority of variable selection via these EV-$R^2$ metrics. Notably, evaluating the $R^2_{\text{SVP}}$ of a LASSO path via data-splitting reduced false discovery rates from 80% to 6% in simulations while fully preserving signal recall.

stat.ME

A Comparison of Parameter Estimation Methods for Shared Frailty Models

This paper compares six different parameter estimation methods for shared frailty models via a series of simulation studies. A shared frailty model is a survival model that incorporates a random effect term, where the frailties are common or shared among individuals within specific groups. Several parameter estimation methods are available for fitting shared frailty models, such as penalized partial likelihood (PPL), expectation-maximization (EM), pseudo full likelihood (PFL), hierarchical likelihood (HL), maximum marginal likelihood (MML), and maximization penalized likelihood (MPL) algorithms. These estimation methods are implemented in various R packages, providing researchers with various options for analyzing clustered survival data using shared frailty models. However, there is a limited amount of research comparing the performance of these parameter estimation methods for fitting shared frailty models. Consequently, it can be challenging for users to determine the most appropriate method for analyzing clustered survival data. To address this gap, this paper aims to conduct a series of simulation studies to compare the performance of different parameter estimation methods implemented in R packages. We will evaluate several key aspects, including parameter estimation, bias and variance of the parameter estimates, rate of convergence, and computational time required by each package. Through this systematic evaluation, our goal is to provide a comprehensive understanding of the advantages and limitations associated with each estimation method.

stat.ME

Cross-validatory Z-Residual for Diagnosing Shared Frailty Models

Residual diagnostic methods play a critical role in assessing model assumptions and detecting outliers in statistical modelling. In the context of survival models with censored observations, Li et al. (2021) introduced the Z-residual, which follows an approximately normal distribution under the true model. This property makes it possible to use Z-residuals for diagnosing survival models in a way similar to how Pearson residuals are used in normal regression. However, computing residuals based on the full dataset can result in a conservative bias that reduces the power of detecting model mis-specification, as the same dataset is used for both model fitting and validation. Although cross-validation is a potential solution to this problem, it has not been commonly used in residual diagnostics due to computational challenges. In this paper, we propose a cross-validation approach for computing Z-residuals in the context of shared frailty models. Specifically, we develop a general function that calculates cross-validatory Z-residuals using the output from the \texttt{coxph} function in the \texttt{survival} package in R.Our simulation studies demonstrate that, for goodness-of-fit tests and outlier detection, cross-validatory Z-residuals are significantly more powerful and more discriminative than Z-residuals without cross-validation. We also compare the performance of Z-residuals with and without cross-validation in identifying outliers in a real application that models the recurrence time of kidney infection patients. Our findings suggest that cross-validatory Z-residuals can identify outliers that are missed by Z-residuals without cross-validation.

stat.ME

Z-residual diagnostics for detecting misspecification of the functional form of covariates for shared frailty models

In survival analysis, the hazard function often depends on a set of covariates. Martingale and deviance residual are most widely used for examining the validity of the function form of covariates by checking whether there is a discernible trend in their scatterplot against continuous covariates. However, visual inspection of martingale and deviance residuals is often subjective. In addition, these residuals lack a reference distribution due to censoring. It is therefore challenging to derive numerical statistical tests based on martingale or deviance residuals. In this paper, we extend the idea of randomized survival probability (Li et al. 2021) and develop a residual diagnostic tool that can provide both graphical and numerical tests for checking the covariate functional form in semi-parametric shared frailty models. We develop a general function that calculates Z-residuals for semi-parametric shared frailty models based on the output from the \texttt{coxph} function in the \texttt{survival} package in R. Our extensive simulation studies indicate that the derived numerical test based on Z-residuals has great power for checking the functional form of covariates. In a real data application on modelling the survival time of acute myeloid leukemia patients, the Z-residual diagnosis results show that a model with log-transformation is inappropriate for modelling the survival time, which could not be detected by other diagnostic methods.

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Model diagnostics for censored regression via randomized survival probabilities

Residuals in normal regression are used to assess a model's goodness-of-fit (GOF) and discover directions for improving the model. However, there is a lack of residuals with a characterized reference distribution for censored regression. In this paper, we propose to diagnose censored regression with normalized randomized survival probabilities (RSP). The key idea of RSP is to replace the survival probability of a censored failure time with a uniform random number between 0 and the survival probability of the censored time. We prove that RSPs always have the uniform distribution on $(0,1)$ under the true model with the true generating parameters. Therefore, we can transform RSPs into normally-distributed residuals with the normal quantile function. We call such residuals by normalized RSP (NRSP residuals). We conduct simulation studies to investigate the sizes and powers of statistical tests based on NRSP residuals in detecting the incorrect choice of distribution family and non-linear effect in covariates. Our simulation studies show that, although the GOF tests with NRSP residuals are not as powerful as a traditional GOF test method, a non-linear test based on NRSP residuals has significantly higher power in detecting non-linearity. We also compared these model diagnostics methods with a breast-cancer recurrent-free time dataset. The results show that the NRSP residual diagnostics successfully captures a subtle non-linear relationship in the dataset, which is not detected by the graphical diagnostics with CS residuals and existing GOF tests.

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Randomized Predictive P-values: A Versatile Model Diagnostic Tool with Unified Reference Distribution

Examining residuals such as Pearson and deviance residuals, is a standard tool for assessing normal regression. However, for discrete response, these residuals cluster on lines corresponding to distinct response values. Their distributions are far from normality; graphical and quantitative inspection of these residuals provides little information for model diagnosis. Marshall and Spiegelhalter (2003) defined a cross-validatory predictive p-value for identifying outliers. Predictive p-values are uniformly distributed for continuous response but not for discrete response. We propose to use randomized predictive p-values (RPP) for diagnosing models with discrete responses. RPPs can be transformed to "residuals" with normal distribution, called NRPPs by us. NRPPs can be used to diagnose all regression models with scalar response using the same way for diagnosing normal regression. The NRPPs are nearly the same as the randomized quantile residuals (RQR), which are previously proposed by Dunn and Smyth (1996) but remain little known by statisticians. This paper provides an exposition of RQR using the RPP perspective. The contributions of this exposition include: (1) we give a rigorous proof of uniformity of RPP and illustrative examples to explain the uniformity under the true model; (2) we conduct extensive simulation studies to demonstrate the normality of NRPPs under the true model; (3) our simulation studies also show that the NRPP method is a versatile diagnostic tool for detecting many kinds of model inadequacies due to lack of complexity. The effectiveness of NRPP is further demonstrated with a health utilization dataset.

stat.ME

High-dimensional Feature Selection Using Hierarchical Bayesian Logistic Regression with Heavy-tailed Priors

The problem of selecting the most useful features from a great many (eg, thousands) of candidates arises in many areas of modern sciences. An interesting problem from genomic research is that, from thousands of genes that are active (expressed) in certain tissue cells, we want to find the genes that can be used to separate tissues of different classes (eg. cancer and normal). In this paper, we report our empirical experiences of using Bayesian logistic regression based on heavy-tailed priors with moderately small degree freedom (such as 1) and very small scale, and using Hamiltonian Monte Carlo to do computation. We discuss the advantages and limitations of this method, and illustrate the difficulties that remain unsolved. The method is applied to a real microarray data set related to prostate cancer. The method identifies only 3 non-redundant genes out of 6033 candidates but achieves better leave-one-out cross-validated prediction accuracy than many other methods.

stat.AP

Fully Bayesian Logistic Regression with Hyper-Lasso Priors for High-dimensional Feature Selection

High-dimensional feature selection arises in many areas of modern science. For example, in genomic research we want to find the genes that can be used to separate tissues of different classes (e.g. cancer and normal) from tens of thousands of genes that are active (expressed) in certain tissue cells. To this end, we wish to fit regression and classification models with a large number of features (also called variables, predictors). In the past decade, penalized likelihood methods for fitting regression models based on hyper-LASSO penalization have received increasing attention in the literature. However, fully Bayesian methods that use Markov chain Monte Carlo (MCMC) are still in lack of development in the literature. In this paper we introduce an MCMC (fully Bayesian) method for learning severely multi-modal posteriors of logistic regression models based on hyper-LASSO priors (non-convex penalties). Our MCMC algorithm uses Hamiltonian Monte Carlo in a restricted Gibbs sampling framework; we call our method Bayesian logistic regression with hyper-LASSO (BLRHL) priors. We have used simulation studies and real data analysis to demonstrate the superior performance of hyper-LASSO priors, and to investigate the issues of choosing heaviness and scale of hyper-LASSO priors.

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Fully Bayesian Classification with Heavy-tailed Priors for Selection in High-dimensional Features with Grouping Structure

Feature selection is demanded in many modern scientific research problems that use high-dimensional data. A typical example is to find the most useful genes that are related to a certain disease (eg, cancer) from high-dimensional gene expressions. The expressions of genes have grouping structures, for example, a group of co-regulated genes that have similar biological functions tend to have similar expressions. Many statistical methods have been proposed to take the grouping structure into consideration in feature selection, including group LASSO, supervised group LASSO, and regression on group representatives. In this paper, we propose a fully Bayesian Robit regression method with heavy-tailed (sparsity) priors (shortened by FBRHT) for selecting features with grouping structure. The main features of FBRHT include that it discards more aggressively unrelated features than LASSO, and it can make feature selection within groups automatically without a pre-specified grouping structure. In this paper, we use simulated and real datasets to demonstrate that the predictive power of the sparse feature subsets selected by FBRHT are comparable with other much larger feature subsets selected by LASSO, group LASSO, supervised group LASSO, penalized logistic regression and random forest, and that the succinct feature subsets selected by FBRHT have significantly better predictive power than the feature subsets of the same size taken from the top features selected by the aforementioned methods.

stat.ME

Estimating Cross-validatory Predictive P-values with Integrated Importance Sampling for Disease Mapping Models

An important statistical task in disease mapping problems is to identify divergent regions with unusually high or low risk of disease. Leave-one-out cross-validatory (LOOCV) model assessment is the gold standard for estimating predictive p-values that can flag such divergent regions. However, actual LOOCV is time-consuming because one needs to rerun a Markov chain Monte Carlo analysis for each posterior distribution in which an observation is held out as a test case. This paper introduces a new method, called integrated importance sampling (iIS), for estimating LOOCV predictive p-values with only Markov chain samples drawn from the posterior based on a full data set. The key step in iIS is that we integrate away the latent variables associated the test observation with respect to their conditional distribution \textit{without} reference to the actual observation. By following the general theory for importance sampling, the formula used by iIS can be proved to be equivalent to the LOOCV predictive p-value. We compare iIS and other three existing methods in the literature with two disease mapping datasets. Our empirical results show that the predictive p-values estimated with iIS are almost identical to the predictive p-values estimated with actual LOOCV, and outperform those given by the existing three methods, namely, the posterior predictive checking, the ordinary importance sampling, and the ghosting method by Marshall and Spiegelhalter (2003).

stat.AP

Approximating Cross-validatory Predictive Evaluation in Bayesian Latent Variables Models with Integrated IS and WAIC

A natural method for approximating out-of-sample predictive evaluation is leave-one-out cross-validation (LOOCV) --- we alternately hold out each case from a full data set and then train a Bayesian model using Markov chain Monte Carlo (MCMC) without the held-out; at last we evaluate the posterior predictive distribution of all cases with their actual observations. However, actual LOOCV is time-consuming. This paper introduces two methods, namely iIS and iWAIC, for approximating LOOCV with only Markov chain samples simulated from a posterior based on a \textit{full} data set. iIS and iWAIC aim at improving the approximations given by importance sampling (IS) and WAIC in Bayesian models with possibly correlated latent variables. In iIS and iWAIC, we first integrate the predictive density over the distribution of the latent variables associated with the held-out without reference to its observation, then apply IS and WAIC approximations to the integrated predictive density. We compare iIS and iWAIC with other approximation methods in three real data examples that respectively use mixture models, models with correlated spatial effects, and a random effect logistic model. Our empirical results show that iIS and iWAIC give substantially better approximates than non-integrated IS and WAIC and other methods.

stat.ME

A Method for Compressing Parameters in Bayesian Models with Application to Logistic Sequence Prediction Models

Bayesian classification and regression with high order interactions is largely infeasible because Markov chain Monte Carlo (MCMC) would need to be applied with a great many parameters, whose number increases rapidly with the order. In this paper we show how to make it feasible by effectively reducing the number of parameters, exploiting the fact that many interactions have the same values for all training cases. Our method uses a single ``compressed'' parameter to represent the sum of all parameters associated with a set of patterns that have the same value for all training cases. Using symmetric stable distributions as the priors of the original parameters, we can easily find the priors of these compressed parameters. We therefore need to deal only with a much smaller number of compressed parameters when training the model with MCMC. The number of compressed parameters may have converged before considering the highest possible order. After training the model, we can split these compressed parameters into the original ones as needed to make predictions for test cases. We show in detail how to compress parameters for logistic sequence prediction models. Experiments on both simulated and real data demonstrate that a huge number of parameters can indeed be reduced by our compression method.

stat.ML

Bayesian Classification and Regression with High Dimensional Features

This thesis responds to the challenges of using a large number, such as thousands, of features in regression and classification problems. There are two situations where such high dimensional features arise. One is when high dimensional measurements are available, for example, gene expression data produced by microarray techniques. For computational or other reasons, people may select only a small subset of features when modelling such data, by looking at how relevant the features are to predicting the response, based on some measure such as correlation with the response in the training data. Although it is used very commonly, this procedure will make the response appear more predictable than it actually is. In Chapter 2, we propose a Bayesian method to avoid this selection bias, with application to naive Bayes models and mixture models. High dimensional features also arise when we consider high-order interactions. The number of parameters will increase exponentially with the order considered. In Chapter 3, we propose a method for compressing a group of parameters into a single one, by exploiting the fact that many predictor variables derived from high-order interactions have the same values for all the training cases. The number of compressed parameters may have converged before considering the highest possible order. We apply this compression method to logistic sequence prediction models and logistic classification models. We use both simulated data and real data to test our methods in both chapters.

stat.ML

A Method for Avoiding Bias from Feature Selection with Application to Naive Bayes Classification Models

For many classification and regression problems, a large number of features are available for possible use - this is typical of DNA microarray data on gene expression, for example. Often, for computational or other reasons, only a small subset of these features are selected for use in a model, based on some simple measure such as correlation with the response variable. This procedure may introduce an optimistic bias, however, in which the response variable appears to be more predictable than it actually is, because the high correlation of the selected features with the response may be partly or wholely due to chance. We show how this bias can be avoided when using a Bayesian model for the joint distribution of features and response. The crucial insight is that even if we forget the exact values of the unselected features, we should retain, and condition on, the knowledge that their correlation with the response was too small for them to be selected. In this paper we describe how this idea can be implemented for ``naive Bayes'' models of binary data. Experiments with simulated data confirm that this method avoids bias due to feature selection. We also apply the naive Bayes model to subsets of data relating gene expression to colon cancer, and find that correcting for bias from feature selection does improve predictive performance.

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