We focus on mathematical modeling and machine learning, applied to networked systems in biology and medicine.Current projects include development of algorithms and software for both simulation and inference of discrete stochastic systems, uses of machine learning applied to medical data to improve the care of trauma patients, mathematical modeling of brain processes in migraine, unraveling neural communication in learning, inference of network structure of communities of neurons, and mathematical modeling of the process of cell polarization.

Announcements & News

Congratulations to Yuqing Wang for passing her Proposal Exam in Computer Science on June 8, 2022.
Congratulations to Dengxian (Dara) Yang for successfully passing her Major Area Exam (MAE) in Computer Science on June 6, 2022!
Richard Jiang successfully defended his PhD thesis in Computer Science in October. Richard is now a Data Science Consultant at Accenture. Congratulations, Richard!
On, Monday, August 2, 2021, Bruno successfully defended his thesis in Mechanical Engineering. Bruno is staying local and accepted a job at Carpe Data in Santa Barbara. Congratulations, Bruno!
James successfully defended his thesis on 5/12/2021. James will begin his post-PhD career at the University of Colorado at Boulder. Congratulations, James!

Recent Publications

journal.pcbi_.1009830.pdf Jiang, R., Singh, P., Wrede, F., Hellander, A., & Petzold, L. (2022). Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods. PLoS Comput. Biol. 18(1): e1009830
an_analysis_of_relation_extraction_within_sentences_from_wet_lab_protocols.pdf Yang, X., Zhang, X., Zuo, J., Wilson, S., & Petzold, L. (2021). An Analysis of Relation Extraction within Sentences from Wet Lab Protocols. 2021 IEEE International Conference on Big Data (Big Data) Conference Proceedings.
accepted_preprint.pdf Jacob, B., Drawert, B., Yi, T-M, & Petzold, L. (2021). An arbitrary Lagrangian Eulerian smoothed particle hydrodynamics (ALE-SPH) method with a boundary volume fraction formulation for fluid-structure interaction. Engineering Analysis with Boundary Elements 128, 274-289.
s12859-021-04065-z.pdf Jiang, R. M., Pourzanjani, A. A., Cohen, M. J., & Petzold, L. (2021). Associations of Longitudinal D-Dimer and Factor II on Early Trauma Survival Risk. BMC Bioinformatics 22, 122
20-ba1202.pdf Pourzanjani, A. A., Jiang, R. M., Mitchell, B., Atzberger, P. J., & Petzold, L. R. (2021). Bayesian Inference over the Stiefel Manifold via the Givens Representation. Bayesian Anal. 16(2): 639-666