Modeling Frameworks Papers

  • (2023) Eric Medwedeff and Eric Mjolsness, “Approximate Simulation of Cortical Microtubule Models using Dynamical Graph Grammars”,  Physical Biology, v 20 no. 5, 7 July 2023.
  • (2022) Eric Mjolsness, “Explicit Calculation of Structural Commutation Relations for Stochastic and Dynamical Graph Grammar Rule Operators in Biological Morphodynamics”. Frontiers in Systems Biology, 09 September 2022. https://doi.org/10.3389/fsysb.2022.898858 . Also a book chapter in https://www.frontiersin.org/research-topics/30021/pattern-formation-in-biology (—>epub).
  • (2021) C.B. Scott and Eric Mjolsness, “Graph diffusion distance: Properties and efficient computation”. PLoS One, https://doi.org/10.1371/journal.pone.0249624  April 27, 2021.
  • (2019) Eric Mjolsness, “Prospects for Declarative Mathematical Modeling of Complex Biological Systems”. Bulletin of Mathematical Biology, first online 7 June 2019. https://doi.org/10.1007/s11538-019-00628-7. Also preprint http://arxiv.org/abs/1804.11044 in a different format.
  • (2015) Todd Johnson, Thomas Bartol, Terrence Sejnowski, and Eric Mjolsness. “Model Reduction for Stochastic CaMKII Reaction Kinetics in Synapses by Graph-Constrained Correlation Dynamics”. Physical Biology 12:4, July 2015.
  • (2013) Eric Mjolsness. Time-ordered product expansions for computational stochastic systems biology. Physical Biology 10 035009, 2013. [Author’s version, Journal paper, open access.]
  • (2010) Eric Mjolsness. Towards Measurable Types for Dynamical Process Modeling Languages , Electronic Notes in Theoretical Computer Science (ENTCS), vol. 265, pp. 123-144, 6 Sept. 2010, Elsevier. Also Proceedings of the 26th Conference on Mathematical Foundations of Programming Semantics (MFPS 2010). [ Author’s technical report version, PDF ]
  • (2006) Eric Mjolsness and Guy Yosiphon. Stochastic Process Semantics for Dynamical Grammars, Annals of Mathematics and Artificial Intelligence, 47(3-4) August 2006. [Authors’ Version (Technical Report) | View Paper at Publisher’s Web Site ]
  • (2005) Eric Mjolsness. Stochastic Process Semantics for Dynamical Grammer Syntax: An Overview. For 9th International Symposium on Artificial Intelligence and Mathematics, presented Jan 2006. Written versions November 2005: [ Preprint from arXiv.org |Technical Report ]
  • (2005) An enzyme mechanism language for the mathematical modeling of metabolic pathways . Yang, C-R., Shapiro, B.E., Mjolsness, E.D., and Hatfield, G.W..Bioinformatics, vol. 21 no. 6, pages 774-780, March 2005. [ Authors’ version | View Paper at Publisher’s Web Site ].
  • (2005)  Static and Dynamic Models of Biological Networks. Ashish Bhan and Eric Mjolsness, UCI ICS TR# 05-15. December 2005. [ Technical Report ]
  • (2005)  Variable-structure systems from graphs and grammars. Eric Mjolsness, UCI ICS TR# 05-09. July 2005. [Technical Report]  [old link to Technical Report ]
  • (2004)  Labeled graph notations for graphical models: Extended Report. Eric Mjolsness, UCI ICS TR# 04-03. March 2004. [ Technical Report ]
  • (1998)  A Lagrangian formulation of neural networks I: Theory and analog dynamics. , Eric Mjolsness and Willard L. Miranker, Neural, Parallel and Scientific Computations vol 6 no. 3, pp. 297-336, 1998. [ Scanned PDF | Journal ]
  • (1998)  A Lagrangian formulation of neural networks II: Clocked objective functions and applications. Willard L. Miranker and Eric Mjolsness, Neural, Parallel and Scientific Computations, vol 6 no. 3, pp. 337-372, 1998. [ Scanned PDF | Journal ]
  • (1993)  Multiscale models of developmental processes David H. Sharp, John Reinitz, and Eric Mjolsness, Open Systems and Information Dynamics, vol 2 no 1, pp. 1-10, Nicholas Copernicus University Press, Torun, Poland, 1993. [ Scanned PDF | Journal ] /
  • (1993)  Animation of plant development Przemyslaw Prusinkiewicz, Mark S. Hammel, and Eric Mjolsness, SIGGRAPH ’93 Conference Proceedings, ACM 1993. [ Preprint ]
  • (1992)  Visual grammars and their neural nets Eric Mjolsness, Advances in Neural Information Processing Systems 4, editors Moody, Hanson and Lippmann, pp. 428-435, Morgan-Kaufman 1992. [ Paper ]
  • (1991)  A Lagrangian Approach to Fixed Points. Eric Mjolsness and Willard L. Miranker,Advances in Neural Information Processing Systems 3, editors Lippmann, Moody and Touretsky, Morgan-Kaufman 1991. [ Paper ]
  • (1991)  Multiscale optimization in neural networks, Eric Mjolsness, Charles Garrett, and Willard Miranker, IEEE Transactions on Neural Networks , vol 2 no 2, March 1991. [Paper ]
  • (1991)  A connectionist model of development. Mjolsness E, Sharp DH, Reinitz J.Journal of Theoretical Biology 152: 429-453. [ Abstract | Paper ]
  • (1990)  Bayesian inference on visual grammars by neural nets that optimize. Eric Mjolsness, Report YALEU/DCS/TR- 854, May 1990. [ Technical Report ]