Publications

A curated bibliography of Ruoqing Zhu’s research.

Research in statistical learning, sequential decisions, and biomedical applications.

Showing 68 publications

Preprints

2026

Rectified Fisher-Bingham Model for Compositional Data with Zeros

Han, E., Perez-Tamayo, M., Holscher, H. D., Zhu, R.

Preprint2026

Method & Theory Nutrition Science

Vector-Valued Distributional Reinforcement Learning Policy Evaluation: A Hilbert Space Embedding Approach

Mohammadi, M., Zheng, Q., Zhu, R.

arXiv preprint arXiv:2601.189522026

Method & Theory Reinforcement Learning

2024

Consistent Order Determination of Markov Decision Process

Ye, C., Zhu, L., Zhu, R.

Preprint2024

Method & Theory Reinforcement Learning

2023

Distributional Shift-Aware Off-Policy Interval Estimation: A Unified Error Quantification Framework

Zhou, W., Li, Y., Zhu, R., Qu, A.

Preprint2023

Method & Theory Reinforcement Learning

2022

Confidence Band Estimation for Survival Random Forests

Formentini, S. E., Liang, W., Zhu, R.

Preprint2022

Method & Theory Random Forests Survival Analysis

Published work

2026

From Problem to Method: Designing Multiview Sequential Canonical Covariance Analysis for Online Word-of-Mouth Dynamics

Cao, X., Folta, T., Li, H., Zhu, R.

In SAGE Research Methods: Doing Research Online2026

Collaborative Others

Interpretability of an FDA-authorized AI/ML sepsis diagnostic tool improved by SHAP values

Watson, G. L., Staples, G., Carver, R., Bhargava, A., López-Espina, C., Schmalz, L., Ali, F., Antkowiak, P. S., Azad, S., Berghea, R., Chawla, L., Crisp, M., Dagan, A., Davila, F., Davila, H., DeMarco, C., Doodlesack, A., Espinosa, A., Evans, N. S., Ezekiel, C., Friederich, A., Gosai, F., Halalau, A., Iyer, K., Kravitz, M. S., Kurtzman, N., Lee, J. H., Maddens, N., Malkani, R., Mayer, S., Oke, V., Palagiri, A. V., Patel, R., Raghavakurup, L., Raouf, S., Reseland, E., Sadaka, F., Sarma, D., Smith, S., Shvilkina, T., Sims, M. D., Singh, S., Stenson, B. A., Syed, A., Tafa, M., Thomas, K., Zhao, S. D., Zhu, R., Bashir, R., Reddy Jr., B., Shapiro, N. I.

JAMIA Open 9(1), ooag0202026

Collaborative Sepsis

Kernel Mean Embedding Deviation Subspace for Unsupervised Learning with Heterogeneous Data

Yu, L., Zhu, L., Zhu, R., Zhu, X.

Journal of Machine Learning Research 27(97), 1-522026

Method & Theory Dimension Reduction

Machine Learning and Artificial Intelligence in Nutrition Research: Analytical Methods, Applications, and Key Considerations

Southey, N. L., Zhu, R., Holscher, H. D.

The Journal of Nutrition 1015282026

Collaborative Nutrition Science

Reinforcement Learning with Continuous Actions Under Unmeasured Confounding

Li, Y., Han, E., Hu, Y., Zhou, W., Qi, Z., Cui, Y., Zhu, R.

Journal of the American Statistical Association 121(553), 209-2222026

Method & Theory Reinforcement Learning

The Sepsis ImmunoScore Predicts Sepsis, Mortality, and Deterioration Better than Clinical Scores and Widely Available Biomarkers

Watson, G. L., Updike, L. C., López-Espina, C. G., Bhargava, A., Schmalz, L. A., Khan, S., Urdiales, D. S., Sims, M. D., Palagiri, A. V., Haimovich, A. D., Dagan, A., Davis, B. P., White, K. C., Gurbel, P. A., Mayer, S. M., Syed, A., Zhao, S. D., Zhu, R., Bashir, R., Shapiro, N. I., Reddy Jr., B.

Diagnostics 16(13), 19622026

Collaborative Sepsis

2025

Detecting Gender Stereotype Biases Against Women Entrepreneurs in Large Language Models

Cao, X., Li, H., Xu, Q., Zhu, R.

Journal of Business Ethics2025

Collaborative Others

Integrating Prior Knowledge From Genome-Scale Metabolic Model With Metabolomics for Diet Assessment

Sarker, K., Zhu, R., Holscher, H. D., Zhai, C.

IEEE Transactions on Computational Biology and Bioinformatics 22(4), 1347-13572025

Collaborative Nutrition Science

Multiplexed cytokine profiling identifies diagnostic signatures for latent tuberculosis and reactivation risk stratification

Meserve, K., Chapman, C. A., Xu, M., Zhou, H., Laniado-Laborin, R., Zhu, R., Escalante, P., Bailey, R. C.

PloS one 20(4), e03166482025

Collaborative Disease Diagnostics and Treatment

Nasal and systemic immune responses correlate with viral shedding after influenza challenge in people with complex preexisting immunity

Walters, K.-A., Blatti, C. A., Zhu, R., Banbury, B., Giurgea, L. T., Bean, R., Han, E., Li, Y., Scherler, K., Sherry, J., Formentini, S., Zhou, W., Cervantes-Medina, A., Gouzoulis, M., Rosas, L. A., Han, A., Gatzke, L., Bushell, C., Sherry, N., Taubenberger, J. K., Memoli, M. J., Kash, J. C.

Science Translational Medicine 17(810), eadt14522025

Collaborative Influenza

Predicting Cognitive Outcome Through Nutrition and Health Markers Using Supervised Machine Learning

Verma, S., Holthaus, T. A., Martell, S., Holscher, H. D., Zhu, R., Khan, N. A.

The Journal of Nutrition 155(7), 2144-21532025

Collaborative Nutrition Science

Probabilistic exponential family inverse regression and its applications

Pang, D., Zhu, R., Zhao, H., Wang, T.

Biometrics 81(2), ujaf0652025

Method & Theory Dimension Reduction

Unraveling the molecular complexity of myxomatous mitral valve degeneration: integrating transcriptomic and miRNA profiling using random forests with Boruta feature selection

Hagler, M. A., Thalji, N., Russell, N. T., Welge, M. E., Zhu, R., Bushell, C., Miller, J. D.

Journal of the Heart Valve Society 2(2), 137-1532025

Collaborative Random Forests

2024

Analyzing the online word of mouth dynamics: A novel approach

Cao, X., Folta, T. B., Li, H., Zhu, R.

Decision Support Systems 1143062024

Collaborative Others

Dietary patterns among US food insecure cancer survivors and the risk of mortality: NHANES 1999 2018

Maino Vieytes, C. A., Zhu, R., Gany, F., Koester, B. D., Arthur, A. E.

Cancer Causes & Control 1-142024

Collaborative Nutrition Science Survival Analysis

Estimating Optimal Infinite Horizon Dynamic Treatment Regimes via pT-Learning

Zhou, W., Zhu, R., Qu, A.

Journal of the American Statistical Association 119(545), 625-6382024

Method & Theory Personalized Medicine Reinforcement Learning

FDA-Authorized AI/ML Tool for Sepsis Prediction: Development and Validation

Bhargava, A., Lopez-Espina, C., Schmalz, L., Khan, S., Watson, G. L., Urdiales, D., Zhao, S. D., Zhu, R., Bashir, B., Reddy Jr., B., Shapiro, N. I.

NEJM AI 1(12), AIoa24008672024

Collaborative Sepsis

Fecal metagenomics to identify biomarkers of food intake in healthy adults: Findings from randomized, controlled, nutrition trials

Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., Holscher, H. D.

The Journal of Nutrition 154(1), 271-2832024

Collaborative Nutrition Science

On Variance Estimation of Random Forests with Infinite-Order U-statistics

Xu, T., Zhu, R., Shao, X.

Electronic Journal of Statistics 18(1), 2135-22072024

Method & Theory Random Forests

Policy learning for individualized treatment regimes on infinite time horizon

Zhou, W., Li, Y., Zhu, R.

In Statistics in Precision Health: Theory, Methods and Applications (pp. 65-100). Cham: Springer International Publishing. Editor: Yichuan Zhao2024

Method & Theory Personalized Medicine Reinforcement Learning

Prevalence, Management, and Comorbidities of Adults With Atrial Fibrillation in the United States, 2019 to 2023

Oltman, C. G., Kim, T. P., Lee, J. W., Lupu, J. D., Zhu, R., Moussa, I. D.

JACC: Advances 3(11), 1013302024

Collaborative Disease Diagnostics and Treatment

Prior-guided longitudinal metabolomic analysis

Sarker, K., Zhu, R., Holscher, H. D., Zhai, C.

In 2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 351-356). IEEE2024

Collaborative Nutrition Science

Random forest weighted local Frechet regression with random objects

Qiu, R., Yu, Z., Zhu, R.

Journal of Machine Learning Research 25(107), 1-692024

Method & Theory Random Forests Survival Analysis

Stage-aware learning for dynamic treatments

Ye, H., Zhou, W., Zhu, R., Qu, A.

Journal of Machine Learning Research 25(408), 1-512024

Method & Theory Reinforcement Learning

2023

Augmenting nutritional metabolomics with a genome-scale metabolic model for assessment of diet intake

Sarker, K., Zhu, R., Holscher, H. D., Zhai, C.

In Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (pp. 1-10)2023

Collaborative Nutrition Science

Estimating heterogeneous treatment effects with right-censored data via causal survival forests

Cui, Y., Kosorok, M. R., Sverdrup, E., Wager, S., Zhu, R.

Journal of the Royal Statistical Society: Series B 85(2): 179-2112023

Method & Theory Personalized Medicine Random Forests Survival Analysis

Quasi-optimal Reinforcement Learning with Continuous Treatments

Li, Y., Zhou, W., Zhu, R.

ICLR 20232023

Method & Theory Reinforcement Learning

Random Forests for Survival Analysis and High-Dimensional Data

Formentini, S. E., Cui, Y., Zhu, R.

In Springer Handbook of Engineering Statistics (pp. 831-847). London: Springer London. Editor: Hoang Pham2023

Method & Theory Random Forests Survival Analysis

2022

Calibrate and Debias Layer-wise Sampling for Graph Convolutional Networks. TMLR

Chen, Y., Xu, T., Hakkani-Tur, D., Jin, D., Yang, Y., Zhu, R.

Journal2022

Method & Theory Others

Consistency of survival forest and tree models: splitting bias and correction

Cui, Y., Zhu, R., Zhou, M., Kosorok, M.

Statistica Sinica 32(3), 1245-12672022

Method & Theory Random Forests Survival Analysis

Dermoscopic Image Classification with Neural Style Transfer

Li, Y., Zhu, R., Qu, A., Yeh, M.

Journal of Computational and Graphical Statistics 31(4), 1318-13312022

Method & Theory Disease Diagnostics and Treatment

Dimension Reduction Forests: Local Variable Importance using Structured Random Forests

Loyal, J., Zhu, R., Cui, Y., Xin, Z.

Journal of Computational and Graphical Statistics 31(4): 1104-1113. GitHub2022

Method & Theory Random Forests Dimension Reduction

Efficient gradient boosting for prognostic biomarker discovery

Li, K., Yao, S., Zhang, Z., Cao, B., Wilson, C. M., Kalos, D., Kuan, P. F., Zhu, R., Wang, X.

Bioinformatics 38(6), 1631-16382022

Method & Theory Disease Diagnostics and Treatment

Empirical Dietary Patterns Associated with Food Insecurity in US Cancer Survivors: NHANES 1999 2018

Maino Vieytes, C. A., Zhu, R., Gany, F., Burton-Obanla, A., Arthur, A. E.

International journal of environmental research and public health 19(21), 140622022

Collaborative Nutrition Science

Fecal Metabolites as Biomarkers for Predicting Food Intake By Healthy Adults

Shinn, L. M., Mansharamani, A., Baer, D. J., Novotny, J. A., Charron, C. S., Khan, N. A., Zhu, R., Holscher, H. D.

The Journal of Nutrition 152 (12), 2956-29652022

Collaborative Nutrition Science

Optimizing Health Coaching for Patients With Type 2 Diabetes Using Machine Learning: Model Development and Validation Study

Di, S., Petch, J., Gerstein, H. C., Zhu, R., Sherifali, D.

JMIR formative research 6(9), e378382022

Collaborative Disease Diagnostics and Treatment

Population analysis of mortality risk: Predictive models from passive monitors using motion sensors for 100,000 UK Biobank participants

Zhou, H., Zhu, R., Ung, A., Schatz, B.

PLOS Digital Health 1(10), e00000452022

Collaborative Survival Analysis

2021

A Parsimonious Personalized Dose Finding Model via Dimension Reduction

Zhou, W., Zhu, R., Zeng, D.

Biometrika 108(3), 643-6592021

Method & Theory Personalized Medicine Dimension Reduction

Diagnostic and prognostic capabilities of a biomarker and EMR based machine learning algorithm for sepsis

Taneja, I., Damhorst, G. L., Lopez-Espina, C., Zhao, S. D., Zhu, R., Khan, S., Bashir, R.

Clinical and Translational Science2021

Collaborative Sepsis

Estimating Heterogeneous Treatment Effect on Multivariate Responses using Random Forests

Guo, B., Holscher, H. D., Auvil, L. S., Welge, M. E., Bushell, C. B., Novotny, J. A., Baer, D. J., Burd, N. A., Khan, N. A., Zhu, R.

Statistics in Biosciences2021

Method & Theory Personalized Medicine Random Forests

Lung epithelial and endothelial damage, loss of tissue repair, inhibition of fibrinolysis, and cellular senescence in fatal COVID-19

Agnillo, F., Walters, K. A., Xiao, Y., Sheng, Z. M., Scherler, K., Park, J., Gygli, S., Rosas, L. A., Sadtler, K., Kalish, H., Blatti III, C. A., Zhu, R., Kash, J. C., Taubenberger, J. K.

Science Translational Medicine 13(620), p.eabj77902021

Collaborative Others

Risk assessment of latent tuberculosis infection through a multiplexed cytokine biosensor assay and machine learning feature selection

Robison, H. M., Chapman, C. A., Zhou, H., Erskine, C. L., Theel, E., Peikert, T., Lindestam Arlehamn, C. S., Sette, A., Bushell, C., Welge, M., Zhu, R., Bailey, R. C., Escalante, P.

Scientific Reports 11(1), 1-102021

Collaborative Disease Diagnostics and Treatment

Topic Modeling on Triage Notes With Semiorthogonal Nonnegative Matrix Factorization

Li, J. Y., Zhu, R., Qu, A., Ye, H., Sun, Z.

Journal of the American Statistical Association, A&C 116(536): 1609-16242021

Method & Theory Disease Diagnostics and Treatment

2020

Assessment of peritoneal microbial features and tumor marker levels as potential diagnostic tools for ovarian cancer

Miao, R., Badger, T. C., Groesch, K., Diaz-Sylvester, P. L., Wilson, T., Ghareeb, A., Martin, J. A., Cregger, M., Welge, M., Bushell, C., Auvil, L., Zhu, R., Braundmeier-Fleming, A.

PLoS ONE 15(1), e02277072020

Collaborative Disease Diagnostics and Treatment

Constructing Dynamic Treatment Regimes with Shared Parameters for Censored Data

Zhao, Y. Q., Zhu, R., Chen, G., Zheng, Y.

Statistics In Medicine 39 (9), 1250-12632020

Method & Theory Survival Analysis

Fecal bacteria as biomarkers for predicting food intake in healthy adults

Shinn, L., Li, Y., Mansharamani, A., Auvil, L. S., Welge, M. E., Bushell, C., Khan, N. A., Charron, C. S., Novotny, J. A., Baer, D. J., Zhu, R., Holscher, H. D.

The Journal of Nutrition 151(2), 423-4332020

Collaborative Nutrition Science

2019

Bagging and Deep Learning in Optimal Individualized Treatment Rules

Mi, X., Zhu, R., Zou, F.

Biometrics 75(2):674-684. R packages: [dnnet and ITRlearn] Example R File2019

Method & Theory Personalized Medicine

Counting Process Based Dimension Reduction Method for Censored Outcomes

Sun, Q., Zhu, R., Wang, T., Zeng, D.

Biometrika 06(1):181-1962019

Method & Theory Survival Analysis Dimension Reduction

Differential effects of influenza virus NA, HA head, and HA stalk antibodies on peripheral blood leukocyte gene expression during human infection

Walters, K.-A., Zhu, R., Welge, M., Scherler, K., Park, J.-K., Rahil, Z., Wang, H., Auvil, L., Bushell, C., Lee, M. Y., Baxter, D., Bristol, T., Rosas, L. A., Cervantes-Medina, A., Czajkowski, L., Han, A., Memoli, M. J., Taubenberger, J. K., Kash, J. C.

mBio 10(3), e00760-192019

Collaborative Influenza

Nonparametric variable selection and its application to additive models

Feng, Z., Lin, L., Zhu, R., Zhu, L.

Annals of the Institute of Statistical Mathematics 1-282019

Method & Theory Others

orthoDr: Semiparametric Dimension Reduction via Orthogonality Constrained Optimization

Zhu, R., Zhang, J., Zhao, R., Xu, P., Zhou, W., Zhang, X.

The R Journal 11(2), 24-372019

Method & Theory Survival Analysis Dimension Reduction

2018

GradientScanSurv An exhaustive association test method for gene expression data with censored survival outcome

Yi, M., Zhu, R., Stephens, R. M.

PloS one 13(12), p.e02075902018

Collaborative Survival Analysis

Multivariate computational analysis of biosensor data for improved CD64 quantification for sepsis diagnosis

Hassan, U., Zhu, R., Bashir, R.

Lab on a Chip 18(8), 1231-12402018

Collaborative Sepsis

2017

Combining biomarkers with EMR data to improve sepsis identification

Taneja, I., Bobby Reddy Jr, B., Damhorst, G., Zhao, D., Hassan, U., Price, Z., Jensen, T., Ghonge, T., Patel, M., Wachspress, S., Winter, J., Rappleye, M., Smith, G., Healey, R., Ajmal, M., Anwaruddin, S., Khan, M., Patel, J., Rawal, H., Sarwar, R., Soni, S., Davis, B., Kumar, J., White, K., Bashir, R., Zhu, R.

Scientific Reports 7(1), 108002017

Collaborative Sepsis

Greedy Outcome Weighted Tree Learning of Optimal Personalized Treatment Rules

Zhu, R., Zhao, Y., Chen, G., Ma, S., Zhao, H.

Biometrics 73(2), 391 4002017

Method & Theory Personalized Medicine Random Forests

Tree based weighted learning for estimating individualized treatment rules with censored data

Cui, Y., Zhu, R., Kosorok, M.

Electronic Journal of Statistics 11(2), 3927-39532017

Method & Theory Personalized Medicine Survival Analysis

2016

Integrating Multidimensional Omics Data for Cancer Outcome

Zhu, R., Zhao, Q., Zhao, H., Ma, S.

Biostatistics 17(4), 605-182016

Method & Theory Disease Diagnostics and Treatment

2015

Increasing access to state psychiatric hospital beds: Exploring supply-side solutions

La, E. H., Lich, K. H., Wells, R., Ellis, A. R., Swartz, M. S., Zhu, R., Morrissey, J. P.

Psychiatric Services 67(5), 523-5282015

Collaborative Others

Reinforcement Learning Trees

Zhu, R., Zeng, D., Kosorok, M. R.

Journal of the American Statistical Association 110(512), 1770-17842015

Method & Theory Reinforcement Learning

RLT GitHub repository

2014

Identifying Gene-Environment and Gene-Gene Interactions Using a Progressive Penalization Approach

Zhu, R., Zhao, H., Ma, S.

Genetic Epidemiology 38(4), 353-3682014

Method & Theory Disease Diagnostics and Treatment

The Effects of State Psychiatric Hospital Waitlist Policies on Length of Stay and Time to Readmission

La, E. H., Zhu, R., Lich, K. H., Ellis, A. R., Swartz, M. S., Kosorok, M. R., Morrissey, J. P.

Administration and Policy in Mental Health and Mental Health Services Research 42(3), 332-422014

Collaborative Others

2012

Recursively imputed survival trees

Zhu, R., Kosorok, M. R.

Journal of the American Statistical Association 107(497), 331-3402012

Method & Theory Survival Analysis

2008

Diagnostic checking for multivariate regression models

Zhu, L., Zhu, R., Song, S.

Journal of Multivariate Analysis 99(9), 1841-18592008

Method & Theory Others