Statistical Signal Processing
This research concerns the development of optimal estimation and control tools for partially-observed Markov decision processes (POMDP). The main goal is to model complex dynamical processes occurring in living tissue, such as system identification of and optimal intervention into biochemical regulatory networks. One of the main tools used in this work is the partially-observed Boolean dynamical system (POBDS) model and its optimal state estimator, the Boolean Kalman Filter and Smoother. Joint estimation of state and parameters is accomplished using maximum-likelihood and Bayesian approaches. State-feedback, point-based, and reinforcement-learning control algorithms are developed for optimal intervention. We are also developing algorithms for the optimal experimental design problem for such systems.
Funding: National Science Foundation, Awards CCF-1320884, CCF-1718924.
Pattern Recognition and Machine Learning
The research goals here concern the solution of significant computational and statistical problems in classifier design and classfication error estimation. The main application is in classification and inference of genomic, proteomic, immunomic, and metagenomic signals based on small samples in high-dimensional spaces. Some of the milestones of this research include the introduction of the Bolstered Error Estimator, the detailed study of the bias and variance of cross-validation methods in small-sample settings and separate sampling schemes, and the analytical study of higher moments and sampling distributions of error estimators for Linear Discriminant Analysis. In addition, we are developing Bayesian classification algorithms for transcriptomic, proteomic, and metagenomic data.
Funding: National Science Foundation, Award CCF-0845407 (CAREER).
Collaborative Applications in Genomics
Our current collaborative work has four main active components: (1) Metagenomics of microbiota-gut epithelial cell interactions. Collaborators: Drs. Xiaoning Qian (Texas A&M Engineering), Ivan Ivanov (Texas A&M Veterinary School), Robert S. Chapkin (Texas A&M AgriLife), Arul Jayaraman (TexasA&M Engineering), and Johanna W. Lampe (Fred Hutchinson Cancer Research Center). (2) Genomics of drought tolerance in Banana cultivars. Collaborator: Dr. Martin Dickman (Texas A&M AgriLife); (3) Study of infectious diseases for discovery of diagnostic/prognostic biomarkers. Collaborator: Ernesto Marques (University of Pittsburgh) and Bartolomeu Accioli (FIOCRUZ, Recife, Brazil). (4) Study of Aging-Related Diseases. Collaborator: Nicolaas Deutz, Texas A&M Center for Translational Research in Aging & Longevity (CTRAL).
- National Science Foundation, Awards CCF-1320884, CCF-1718924,CCF-0845407 (CAREER).
- Texas A&M Engineering Interdisciplinary Seed Grants for Strategic Initiatives.
- Texas A&M Center for Bioinformatics and Genomics Systems Engineering.