PhD Theses

Prof. Mjolsness has supervised the following PhD theses (except his own at the end):

  • (2024) Eric Medwedeff, “Approximate Simulations of Dynamical Graph Grammars using the Dynamical Graph Grammar Modeling Library”. PhD thesis, UC Irvine and San Diego State University Joint Degree Program in Computational Science, July 2024. [Thesis web site.]
  • (2021) Oliver Ernst, PhD thesis, “Modeling Reaction-Diffusion Systems with Dynamic Boltzmann Distributions”. Jointly supervised with Prof.  Terrence Sejnowski, UC San Diego, June 2021. [Thesis web site.]
  • (2021) Cory Scott, “Diffusion Distance: Efficient Computation and Applications”. PhD thesis, UC Irvine, May 2021. [Thesis web site. Diffusion distance software.]
  • (2012) David Orendorff, “Exact and Hierarchical Reaction Leaping: Asymptotic Improvements to the Stochastic Simulation Algorithm”. PhD thesis, UC Irvine, June 2012. [ Thesis web site. Links to software: ERleap, hierleap.]
  • (2012)  Behnam Compani-Tabrizi, “Schematic Representation and Database Population Strategies for Sigmoid, a Biochemical Network Modeling System”. PhD thesis, UC Irvine, May 2012. [Thesis web site.]
  • (2012) Gary Todd Johnson, “Dependency Diagrams and Graph-Constrained Correlation Dynamics: New Systems for Probabilistic Graphical Modeling”, UC Irvine, March 2012. [Thesis web site . Links to thesis and to software: dependency diagrams and graph-constrained correlation dynamics.]
  • (2009) Guy Yosiphon, “Stochastic Parameterized Grammars: Formalization, Inference, and Modeling Applications”, June 2009. [ Guy Yosiphon |  Thesis web site ]
  • (2008)  Li Zhang, “Dynamic Biological Signal Pathway Modeling and Parameter Estimation through Optimization, June 2008.
  • (2005)  Tarek Najdi, “Biological Analysis and Mathematical Modeling of Glucose Metabolism and the Aspartate and Pyruvate Family Amino Acid Biosyntheses in Escherichia coli K12”, jointly supervised with Prof. Wesley Hatfield, UC Irvine, March 2008.
  • (2005)  Christopher Hart, “Inferring genetic regulatory network structure: Integrative analysis of genome-scale data”, jointly supervised with Prof. Barbara Wold, California Institute of Technology, March 2005.
  • (1997)  Dimitris Tsioutsias, “Multiscale attention as a globally convergent framework for large-scale nonlinear optimization”, Yale University, May 1997. [Tsioutsias thesis in .zip format – large]
  • (1997)  Georgios Marnellos, “Gene network models applied development and evolution”, Yale University, May 1997.
  • (1996)  Steven Gold, “Matching and learning structural and spatial representations with neural networks”, Yale University, May 1996 .
  • (1996)  Chien-Ping Lu, “Online pose estimation and model matching, Yale University, May 1996.
  • (1985)  Eric Mjolsness, “Neural Networks, Pattern Recognition, and Fingerprint Hallucination”. Thesis advisor: John J. Hopfield, September 1985. [Mjolsness Thesis]