Ulisses de Mendonça Braga-Neto, Ph.D.

Academic Website

Research Group

Post-Doctoral Associate:

  • Xingzhuo “Gesa” Chen (TAMIDS)

Ph.D. Students:

  • Luis Aguilar Loo
  • Tripp Cator
  • Steven Chiu

Graduated Ph.D. Students:

  1. Sambandh Dhal
    Committee Co-Chairs: Ulisses M. Braga-Neto and Stavros Kalafatis
    Thesis Title: “Uncertainty-Aware Data-Driven Approaches For Modelling Sparse Agricultural Datasets To Sustain A Society”
    Current Employment: Idaho National Laboratory

  2. Caio Davi (Spring 2019 – Fall 2022)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Novel Architectures and Training Algorithms for Deep Neural Networks”
    Current Employment: Hewlett Packard Enterprise

  3. Parisa Ghane (Fall 2016-Summer 2022)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Novel Approaches in Classification Error Estimation, Predicting Generalization in Deep Learning, and Hybrid Compartmental Models”

  4. Levi McClenny (Fall 2017-Spring 2022)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Convergence, Adaptivity, and Applications of Physics-Informed Machine Learning”
    Current Employment: Post-Doctoral Fellow, Brown University

  5. Yukun Tan (Fall 2017-Spring 2021)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Maximum Likelihood Adaptive Filter Using Metaheuristic Optimization for Stochastic Nonlinear Dynamic Systems”
    Current Employment: Post-Doctoral Fellow, University of Texas MD Anderson Cancer Center, Houston, TX

  6. Shuilian Xie (Summer 2015-Spring 2021)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Edward R. Dougherty
    Thesis Title: “Pattern Recognition for Restricted and Nonstationary Data”

  7. Alireza Karbalayghareh (Fall 2015-Summer 2019)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Edward R. Dougherty
    Thesis Title: “Optimal Bayesian Transfer Learning For Classification And Regression”
    Current Employment: Post-Doctoral Fellow, Sloan Kettering Cancer Center, New York, NY

  8. Mahdi Imani (Fall 2014-Spring 2019)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Estimation, Inference and Learning in Nonlinear State-Space Models”
    Current Employment: Assistant Professor, George Washington University (from Fall 2019)

  9. Emre Arslan (Fall 2014-Fall 2018)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Analyzing High-Dimensional Biological Data Using Novel Bayesian Rank-Based Techniques”
    Current Employment: Research Scientist, MD Anderson Cancer Center

  10. Arghavan Bahadorinejad (Fall 2013-Spring 2017)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Fault Detection and Diagnosis in Gene Regulatory Network and Optimal Bayesian Classification of Metagenomic Data”
    Current Employment: Apple, Inc

  11. Xingde Jiang (Fall 2012-Fall 2016)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Naive Bayes Bolstered Error Estimation, Model Selection and Identification of Stress Induced Pathways in Bananas.”
    Current Employment: Humana, Inc

  12. Esmaeil Atashpaz-Gargari (Fall 2011-Summer 2014)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Edward R. Dougherty
    Thesis Title: “Biomarker Discovery and Validation for Proteomics and Genomics: Modeling and Systematic Analysis.”
    Current Employment: CEO of Online Educational Company FaraDars; Assistant Professor at National University, San Diego, CA

  13. Ting Chen (Fall 2009-Fall 2013)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Estimation and Detection of Multivariate Gene Regulatory Relationships”
    Current Employment: Bioinformatician at Emmes Corporation, Rockville, MD

  14. Youting Sun (Fall 2008-Spring 2011)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Edward R. Dougherty
    Thesis Title: “Model-based Biomarker Detection and Systematic Analysis in Translational  Science”
    Current Employment: Bioinformatician at Sequenom Center for Molecular Medicine, San Diego, CA

  15. Thang Vu (Spring 2007-Spring 2011)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “The Bootstrap in Supervised Learning and Its Applications in Genomics/Proteomics”
    Current Employment: Data Analyst at VinGroup, Vietnam

  16. Amin Zollanvari (Spring 2007-Fall 2010)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Edward R. Dougherty
    Thesis Title: “Analytical Study of Performance of Error Estimators for Linear Discriminant Analysis with Applications in Genomics”
    Current Employment: Assistant Professor at Nazarbayev University, Kazakhstan

Graduated Master’s Students:

  1. Sambandh Dhal (August 2018 – October 2019)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Jorge Alvarado
    Thesis Title: “Development of a Machine Learning Algorithm to Minimize Runoff Through an Automated Smart Irrigation System”
    Current Employment: Texas A&M Ph.D. Student

  2. Kashyap Nagaraja (August 2016 – December 2018)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Bayesian Classification Of Proteomics Biomarkers From Selected Reaction Monitoring Data Using An ABC-MCMC Approach”
    Current Employment: Data Scientist at IBM- Chief analytics, New York.

  3. Ratanond Koonchanok (August 2016 – December 2017)
    Committee Co-Chairs: Ulisses M. Braga-Neto and Ivan Ivanov
    Thesis Title: “Computational Tool For Applications Of Sparse Canonical Correlation Analysis on Biological Data”

  4. Levi McCleney (May 2015 – June 2016)
    Committee Chair: Ulisses M. Braga-Neto
    Thesis Title: “Optimal Estimation of Partially Observed Boolean Dynamical Systems in the Presence of Correlated Observation Noise”
    Current Employment: U.S. Army and Texas A&M University (Ph.D. student)

  5. Upamanyu Banerjee (Mar 2015 – May 2016)
    Advisor: Ulisses M. Braga-Neto (no-thesis option)
    Current Employment: Intel

Former Post-Doc Researchers:

  1. Diego Marcondes (Aug 2023 – Aug 2024, supported by FAPESP)
  2. Ming Zhong (Jul 2021 – Jul 2022, supported by TAMIDS)
  3. Dehao Liu (Sep 2021 – Dec 2021, supported by TAMIDS/MSEN, co-advisor: Raymundo Arroyave)
  4. Ting Chen (Oct 2013 – Apr 2014, supported by NSF award CCF-0845407)

Former Undergraduate Students:

  1. Jonathan Liu (USRG Program Summer 2023)

  2. Tripp Cator (Fall 2020 – Summer 2022)

  3. Zach Williams (Fall 2020)

  4. Alex Arze (NSF REU Summer 2019)

  5. Pranati Chinthapenta (Fall 2017)

  6. Gustavo Estrela (CNPq Internship Summer 2016)

  7. Arthur do Nascimento (CNPq Internship Summer 2016)

  8. Levi McClenny (NSF REU Spring 2015)

  9. Elijah Rockers (NSF REU Spring 2015)