Stats最新文献

{"title":"Benchmarking Statistical Methods for Environmental Chemical Mixtures: Prediction, Interaction Detection, and an Applied Analysis of Metals, Essential Elements and Diabetes.","authors":"Aderonke Gbemi Adetunji, Emmanuel Obeng-Gyasi","doi":"10.3390/stats9050096","DOIUrl":"10.3390/stats9050096","url":null,"abstract":"<p><strong>Background: </strong>Human populations are exposed to complex chemical mixtures, making interaction detection a central challenge in environmental epidemiology. We benchmarked methods for prediction and recovery of interaction structure.</p><p><strong>Methods: </strong>Eight approaches-main-effects Lasso (glmnet_main), interaction Lasso (glmnet_int), hierNet, Random Forests, Bayesian Kernel Machine Regression (BKMR), quantile g-computation (qgcomp), weighted quantile sum regression (gWQS) and SuperLearner-were evaluated across eight linear/nonlinear, additive/interaction, continuous/binary data-generating processes (500 replicates each). Every method completed in all 500 replicates of all eight scenarios. Prediction was assessed on held-out test data using observed-outcome and oracle-referenced metrics; interaction detection was assessed against three known pairwise interactions among 45 candidate pairs, using both hard selection and a threshold-free ranking criterion. BKMR was evaluated at 2000 versus 25,000 MCMC iterations with multi-chain convergence diagnostics. Sensitivity analyses varied sample size, exposure correlation, signal strength, and interaction form. BKMR was also applied illustratively to six metals and prevalent diabetes in NHANES.</p><p><strong>Results: </strong>In additive settings, observed-outcome prediction was similar across methods, but oracle-referenced continuous-outcome error differed by up to six-fold. With interactions, interaction-aware methods clearly outperformed additive-only approaches on the continuous oracle-referenced metrics: in LMI, the oracle MSE was 1.57 for hierNet and 1.87 for glmnet_int against 3.80 for glmnet_main and 4.94 for qgcomp. glmnet_int and hierNet showed comparable sensitivity; hierNet had a modestly lower mean per-replicate false discovery proportion in paired comparisons, while pooled false discovery favored hierNet in the continuous scenarios and glmnet_int in the binary ones; pooled false discovery rates were 0.79 to 0.82 in every interaction scenario, so roughly four in five selected pairs were false. In the scenarios without true interactions, the pooled false discovery rate was exactly 1. Under threshold-free ranking, BKMR was competitive with the penalized methods (pair-ranking AUC: 0.758 to 0.781 across the four interaction scenarios). BKMR's apparent instability at 2000 iterations reflected inadequate sampling: 93% of monitored parameters had a Gelman-Rubin statistic above 1.1 and the minimum effective sample size was 7.5, whereas at 25,000 iterations the median statistic was 1.02 and the oracle MSE in LMI fell from 6.38 to 2.08. In NHANES, lead, manganese, and iron had the highest posterior inclusion probabilities, with predominantly nonlinear exposure-response functions.</p><p><strong>Conclusions: </strong>Method choice matters most when interactions are present. Interaction-aware methods are preferable when joint effects are relevant, selected interactions require rep","PeriodicalId":93142,"journal":{"name":"Stats","volume":"9 5","pages":"96"},"PeriodicalIF":1.1,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13580283/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148993049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Practical Framework for Incorporating Complex Survey Design in Bayesian Kernel Machine Regression.","authors":"Doreen Jehu-Appiah, Emmanuel Obeng-Gyasi","doi":"10.3390/stats9030046","DOIUrl":"10.3390/stats9030046","url":null,"abstract":"<p><p>Large-scale population datasets are rarely generated via simple random sampling; instead, they reflect complex designs involving stratification, clustering, and unequal inclusion probabilities. While survey weights are provided to recover population-representative estimates, standard Bayesian Kernel Machine Regression (BKMR), a flexible nonlinear model for high-dimensional exposure mixtures, does not explicitly accommodate these design features. We present a simulation-based framework that evaluates performance under complex sampling by comparing two analytic strategies applied to identical survey-like data: (i) a naïve, unweighted BKMR implementation and (ii) a design-aware workflow that can be executed using existing software without modifying the BKMR algorithm itself. Finite populations are generated with correlated exposures and a known nonlinear data-generating function. Stratified two-stage cluster samples are then drawn under both non-informative and exposure-dependent (informative) selection mechanisms, with controlled intra-class correlation (ICC). The design-aware approach incorporates sampling weights through resampling of the dataset while preserving primary sampling unit structure, followed by standard BKMR fitting. Methods are evaluated using bias, interval width, and empirical 95% coverage relative to the known truth. Across simulation scenarios, naïve BKMR exhibits bias and systematic under-coverage under informative sampling, with empirical 95% coverage often dropping to approximately 0-40%, whereas the design-aware workflow improves coverage to approximately 40-60%, moving results closer to nominal levels. These findings provide a practical, implementation-ready strategy for integrating survey design considerations into BKMR analyses and delineate conditions under which accounting for sampling design affects inference. While the proposed approach improves inferential performance relative to naïve BKMR, it does not fully achieve nominal coverage, indicating that further methodological development is required for fully valid uncertainty quantification under complex survey designs.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"9 3","pages":""},"PeriodicalIF":1.1,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13220982/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148145770","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ordering and Quantifying Textual Cohesion via Semantic, Geometric and Statistical Structure","authors":"Stelios Arvanitis","doi":"10.3390/stats9020025","DOIUrl":"https://doi.org/10.3390/stats9020025","url":null,"abstract":"We propose a semantic, geometric, and statistical framework for quantifying and ordering textual cohesion in long-form discourse. Sentences are embedded into a semantic similarity graph and Ollivier–Ricci curvature is used to extract sentence- and document-level structural profiles, represented as step functions on a normalized rhetorical-time axis. On this functional space we define the Weighted Utopia Index (wUI), a corpus-relative measure of weighted shortfall from an upper-envelope profile under a dominance-type ordering. The rhetorical-time weighting function is learned self-supervised: we generate controlled sentence-order perturbations with known ordinal coherence degradation and estimate the weight parameters via an ordered probit model on a training split. We evaluate ordering recovery on held-out State of the Union speeches using rank correlations, pairwise and adjacent ordering accuracy, and violation-localization diagnostics with bootstrap uncertainty. Across these criteria, wUI systematically outperforms embedding-only adjacent-similarity baselines, while a Nash-type aggregation provides an interpretable semantic–structural trade-off score. An application to later-period speeches illustrates how the method yields interpretable cohesion rankings and curvature-profile diagnostics without requiring external annotations.","PeriodicalId":93142,"journal":{"name":"Stats","volume":"9 2","pages":"25-25"},"PeriodicalIF":0.0,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.mdpi.com/2571-905X/9/2/25/pdf?version=1772529532","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147905601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bidirectional f-Divergence-Based Deep Generative Method for Imputing Missing Values in Time-Series Data.","authors":"Wen-Shan Liu, Tong Si, Aldas Kriauciunas, Marcus Snell, Haijun Gong","doi":"10.3390/stats8010007","DOIUrl":"10.3390/stats8010007","url":null,"abstract":"<p><p>Imputing missing values in high-dimensional time-series data remains a significant challenge in statistics and machine learning. Although various methods have been proposed in recent years, many struggle with limitations and reduced accuracy, particularly when the missing rate is high. In this work, we present a novel f-divergence-based bidirectional generative adversarial imputation network, tf-BiGAIN, designed to address these challenges in time-series data imputation. Unlike traditional imputation methods, tf-BiGAIN employs a generative model to synthesize missing values without relying on distributional assumptions. The imputation process is achieved by training two neural networks, implemented using bidirectional modified gated recurrent units, with f-divergence serving as the objective function to guide optimization. Compared to existing deep learning-based methods, tf-BiGAIN introduces two key innovations. First, the use of f-divergence provides a flexible and adaptable framework for optimizing the model across diverse imputation tasks, enhancing its versatility. Second, the use of bidirectional gated recurrent units allows the model to leverage both forward and backward temporal information. This bidirectional approach enables the model to effectively capture dependencies from both past and future observations, enhancing its imputation accuracy and robustness. We applied tf-BiGAIN to analyze two real-world time-series datasets, demonstrating its superior performance in imputing missing values and outperforming existing methods in terms of accuracy and robustness.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"8 1","pages":""},"PeriodicalIF":0.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11793919/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143257500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exact Inference for Random Effects Meta-Analyses for Small, Sparse Data.","authors":"Jessica Gronsbell, Zachary R McCaw, Timothy Regis, Lu Tian","doi":"10.3390/stats8010005","DOIUrl":"10.3390/stats8010005","url":null,"abstract":"<p><p>Meta-analysis aggregates information across related studies to provide more reliable statistical inference and has been a vital tool for assessing the safety and efficacy of many high-profile pharmaceutical products. A key challenge in conducting a meta-analysis is that the number of related studies is typically small. Applying classical methods that are asymptotic in the number of studies can compromise the validity of inference, particularly when heterogeneity across studies is present. Moreover, serious adverse events are often rare and can result in one or more studies with no events in at least one study arm. Practitioners remove studies in which no events have occurred in one or both arms or apply arbitrary continuity corrections (e.g., adding one event to arms with zero events) to stabilize or define effect estimates in such settings, which can further invalidate subsequent inference. To address these significant practical issues, we introduce an exact inference method for random effects meta-analysis of a treatment effect in the two-sample setting with rare events, which we coin \"XRRmeta\". In contrast to existing methods, XRRmeta provides valid inference for meta-analysis in the presence of between-study heterogeneity and when the event rates, number of studies, and/or the within-study sample sizes are small. Extensive numerical studies indicate that XRRmeta does not yield overly conservative inference. We apply our proposed method to two real-data examples using our open-source R package.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"8 1","pages":""},"PeriodicalIF":1.1,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12456449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating Risk Factors for Racial Disparity in E-Cigarette Use with PATH Study.","authors":"Amy Liu, Kennedy Dorsey, Almetra Granger, Ty-Runet Bryant, Tung-Sung Tseng, Michael Celestin, Qingzhao Yu","doi":"10.3390/stats7030037","DOIUrl":"10.3390/stats7030037","url":null,"abstract":"<p><strong>Background: </strong>Previous research has identified differences in e-cigarette use and socioeconomic factors between different racial groups However, there is little research examining specific risk factors contributing to the racial differences.</p><p><strong>Objective: </strong>This study sought to identify racial disparities in e-cigarette use and to determine risk factors that help explain these differences.</p><p><strong>Methods: </strong>We used Wave 5 (2018-2019) of the Adult Population Assessment of Tobacco and Health (PATH) Study. First, we conducted descriptive statistics of e-smoking across our risk factor variables. Next, we used multiple logistic regression to check the risk effects by adjusting all covariates. Finally, we conducted a mediation analysis to determine whether identified factors showed evidence of influencing the association between race and e-cigarette use. All analyses were performed in R or SAS. The R package mma was used for the mediation analysis.</p><p><strong>Results: </strong>Between Hispanic and non-Hispanic White populations, our potential risk factors collectively explain 17.5% of the racial difference, former cigarette smoking explains 7.6%, receiving e-cigarette advertising 2.6%, and perception of e-cigarette harm explains 27.8% of the racial difference. Between non-Hispanic Black and non-Hispanic White populations, former cigarette smoking, receiving e-cigarette advertising, and perception of e-cigarette harm explain 5.2%, 1.8%, and 6.8% of the racial difference, respectively. E-cigarette use is most prevalent in the non-Hispanic White population compared to non-Hispanic Black and Hispanic populations, which may be explained by former cigarette smoking, exposure to e-cigarette advertising, and e-cigarette harm perception.</p><p><strong>Conclusions: </strong>These findings suggest that racial differences in e-cigarette use may be reduced by increasing knowledge of the dangers associated with e-cigarette use and reducing exposure to e-cigarette advertisements. This comprehensive analysis of risk factors can be used to significantly guide smoking cessation efforts and address potential health burden disparities arising from differences in e-cigarette usage.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"7 3","pages":"613-626"},"PeriodicalIF":0.9,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756910/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Doubly Robust Estimation and Semiparametric Efficiency in Generalized Partially Linear Models with Missing Outcomes.","authors":"Lu Wang, Zhongzhe Ouyang, Xihong Lin","doi":"10.3390/stats7030056","DOIUrl":"10.3390/stats7030056","url":null,"abstract":"<p><p>We investigate a semiparametric generalized partially linear regression model that accommodates missing outcomes, with some covariates modeled parametrically and others nonparametrically. We propose a class of augmented inverse probability weighted (AIPW) kernel-profile estimating equations. The nonparametric component is estimated using AIPW kernel estimating equations, while parametric regression coefficients are estimated using AIPW profile estimating equations. We demonstrate the doubly robust nature of the AIPW estimators for both nonparametric and parametric components. Specifically, these estimators remain consistent if either the assumed model for the probability of missing data or that for the conditional mean of the outcome, given covariates and auxiliary variables, is correctly specified, though not necessarily both simultaneously. Additionally, the AIPW profile estimator for parametric regression coefficients is consistent and asymptotically normal under the semiparametric model defined by the generalized partially linear model on complete data, assuming that the missing data mechanism is missing at random. When both working models are correctly specified, this estimator achieves semiparametric efficiency, with its asymptotic variance reaching the efficiency bound. We validate our approach through simulations to assess the finite sample performance of the proposed estimators and apply the method to a study that investigates risk factors associated with myocardial ischemia.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"7 3","pages":"924-943"},"PeriodicalIF":1.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12478555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145202384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating Proteomic Analysis and Machine Learning to Predict Prostate Cancer Aggressiveness.","authors":"Sheila M Valle Cortés, Jaileene Pérez Morales, Mariely Nieves Plaza, Darielys Maldonado, Swizel M Tevenal Baez, Marc A Negrón Blas, Cayetana Lazcano Etchebarne, José Feliciano, Gilberto Ruiz Deyá, Juan C Santa Rosario, Pedro Santiago Cardona","doi":"10.3390/stats7030053","DOIUrl":"10.3390/stats7030053","url":null,"abstract":"<p><p>Prostate cancer (PCa) poses a significant challenge because of the difficulty in identifying aggressive tumors, leading to overtreatment and missed personalized therapies. Although only 8% of cases progress beyond the prostate, the accurate prediction of aggressiveness remains crucial. Thus, this study focused on studying retinoblastoma phosphorylated at Serine 249 (Phospho-Rb S249), N-cadherin, β-catenin, and E-cadherin as biomarkers for identifying aggressive PCa using a logistic regression model and a classification and regression tree (CART). Using immunohistochemistry (IHC), we targeted the expression of these biomarkers in PCa tissues and correlated their expression with clinicopathological data of the tumor. The results showed a negative correlation between E-cadherin and β-catenin with aggressive tumor behavior, whereas Phospho-Rb S249 and N-cadherin positively correlated with increased tumor aggressiveness. Furthermore, patients were stratified based on Gleason scores and E-cadherin staining patterns to evaluate their capability for early identification of aggressive PCa. Our findings suggest that the classification tree is the most effective method for measuring the utility of these biomarkers in clinical practice, incorporating β-catenin, tumor grade, and Gleason grade as relevant determinants for identifying patients with Gleason scores ≥ 4 + 3. This study could potentially benefit patients with aggressive PCa by enabling early disease detection and closer monitoring.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"7 3","pages":"875-893"},"PeriodicalIF":1.1,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12494234/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145234320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing Spillover Effects of Medications for Opioid Use Disorder on HIV Risk Behaviors among a Network of People Who Inject Drugs.","authors":"Joseph Puleo, Ashley Buchanan, Natallia Katenka, M Elizabeth Halloran, Samuel R Friedman, Georgios Nikolopoulos","doi":"10.3390/stats7020034","DOIUrl":"10.3390/stats7020034","url":null,"abstract":"<p><p>People who inject drugs (PWID) have an increased risk of HIV infection partly due to injection behaviors often related to opioid use. Medications for opioid use disorder (MOUD) have been shown to reduce HIV infection risk, possibly by reducing injection risk behaviors. MOUD may benefit individuals who do not receive it themselves but are connected through social, sexual, or drug use networks with individuals who are treated. This is known as spillover. Valid estimation of spillover in network studies requires considering the network's community structure. Communities are groups of densely connected individuals with sparse connections to other groups. We analyzed a network of 277 PWID and their contacts from the Transmission Reduction Intervention Project. We assessed the effect of MOUD on reductions in injection risk behaviors and the possible benefit for network contacts of participants treated with MOUD. We identified communities using modularity-based methods and employed inverse probability weighting with community-level propensity scores to adjust for measured confounding. We found that MOUD may have beneficial spillover effects on reducing injection risk behaviors. The magnitudes of estimated effects were sensitive to the community detection method. Careful consideration should be paid to the significance of community structure in network studies evaluating spillover.</p>","PeriodicalId":93142,"journal":{"name":"Stats","volume":"7 2","pages":"549-575"},"PeriodicalIF":1.1,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12165006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144303849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Precise Tensor Product Smoothing via Spectral Splines","authors":"Nathaniel E. Helwig","doi":"10.3390/stats7010003","DOIUrl":"https://doi.org/10.3390/stats7010003","url":null,"abstract":"Tensor product smoothers are frequently used to include interaction effects in multiple nonparametric regression models. Current implementations of tensor product smoothers either require using approximate penalties, such as those typically used in generalized additive models, or costly parameterizations, such as those used in smoothing spline analysis of variance models. In this paper, I propose a computationally efficient and theoretically precise approach for tensor product smoothing. Specifically, I propose a spectral representation of a univariate smoothing spline basis, and I develop an efficient approach for building tensor product smooths from marginal spectral spline representations. The developed theory suggests that current tensor product smoothing methods could be improved by incorporating the proposed tensor product spectral smoothers. Simulation results demonstrate that the proposed approach can outperform popular tensor product smoothing implementations, which supports the theoretical results developed in the paper.","PeriodicalId":93142,"journal":{"name":"Stats","volume":"59 20","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139440934","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}