ERIC D

ERIC D. MJOLSNESS

AppleMark

emj@uci.edu

EDUCATION

Ph.D., Physics and Computer Science. September 1985. California Institute of Technology. Thesis title: Neural Networks, Pattern Recognition, and Fingerprint Hallucination. Thesis advisor: John J. Hopfield.
A.B., Physics and Mathematics. May 1980. Washington University in St. Louis. Graduated magna cum laude.

EXPERIENCE

Associate Professor, Department of Information and Computer Science, University of California, Irvine. July 2002-Present.
Visiting Associate in Biology, California Institute of Technology. July 2002 - present.
Group leader, Systems Biology, Institute for Genomics and Bioinformatics, University of California, Irvine, October 2003 – present.
Group Supervisor, Principal, Jet Propulsion Laboratory, California Institute of Technology. April 2000 - Spring 2002.
Faculty Associate in Biology, California Institute of Technology. February 2000 - July 2002.
Computer Scientist - Principal, Jet Propulsion Laboratory, California Institute of Technology. September 1998 - April 2000 ; Spring 2002 - present.
Computer Scientist - Senior, Jet Propulsion Laboratory, California Institute of Technology. June 1997 - August 1998.
Research Scientist, Department of Computer Science and Engineering, University of California, San Diego. January 1995 to May 1998.
Faculty member of the Institute for Neural Computation, University of California, San Diego, October 1994 to May 1998.
Visiting Scholar, September to December 1994, Department of Computer Science and Engineering, University of California, San Diego.
Associate Professor. July, 1990 to December 1994. Department of Computer Science, Yale University, New Haven.
Project Director for Artificial Neural Networks, at the Yale Center for Theoretical and Applied Neuroscience, August 1991 to December 1994.
Co-Director (with Gunter Wagner), Center for Computational Ecology of the Yale Institute for Biospheric Studies, August 1992-December 1994.
Faculty member of the Yale Program in Neuroscience, July 1990 to December 1994.
Collaborator, Los Alamos National Laboratory. July, 1983 to 1993.
Consultant to the Federal Bureau of Investigation on automated fingerprint identification, summer 1991 and summer 1992.
Assistant Professor. September, 1985 to June, 1990. Yale University, New Haven.
Visiting Scientist, Institute for Theoretical Physics, Santa Barbara. November - December 1986.
Graduate Research Assistant. August, 1980 to June, 1985. California Institute of Technology, Pasadena.
Teaching Assistant. October 1981 to May, 1985. California Institute of Technology, Pasadena.
PhD thesis advisor for: Christopher Hart, “Inferring Genetic Regulatory Network Structure: Integrative Analysis of Genome-Scale Data”, jointly supervised with Barbara Wold, from California Institute of Technology March 2005; Steven Gold, Matching and Learning Structural and Spatial Representations with Neural Networks; Chien-Ping Lu: Online Pose Estimation and Model Matching; both graduated May 1996 from Yale University. Dimitris Tsioutsias, Multiscale Attention as a Globally Convergent Framework for Large-Scale Nonlinear Optimization; Georgios Marnellos, Gene Network Models Applied Development and Evolution; both graduated May 1997 from Yale University.

HONORS

Senior Member of Sigma Xi, May 1999.
NASA Summer Faculty Fellowship in Aeronautics and Space Research, at the Jet Propulsion Laboratory, 1996.
Senior Faculty Fellowship, Yale University, 1991-92.
Phi Beta Kappa, 1980.
Arthur Holly Compton Fellowship, Washington University in St. Louis, 1976-1980.

SERVICE

Action Editor, Neural Computation, January 1995 to present.
Co-organized (with Przemyslaw Prusinkiewicz) symposium “Modeling plant development: From genes to phenotypes”, at the International Botanical Congress, Vienna 2005.
University of California, Irvine representative for the executive committee of the UC Information Technology for Life Sciences program, May 2005- present.
International Program Committee, Bioinformatics of Genome Regulation and Structure 2004, Novosibirsk Russia
Associate Editor, IEEE Transactions on Neural Networks, January-December 1998, June 1991 to December 1992.
Board Member, Neural Information Processing Systems Foundation, April 1995 to present. Treasurer 1995- 1998.
Program committee, KDD-97 Knowledge Discovery and Datamining, Newport Beach CA 1997.
Program committee, AAAI-96 The Thirteenth National Conference on Artificial Intelligence. Also on program committee, International Conference on Neural Information Processing (ICONIP'96), Hong Kong, 1996.
Board of Advisors, Neural Computing Surveys, July 1996 to present.
Co-organized, with Gunter Wagner, the Center for Computational Ecology of the Yale Institute for Biospheric Studies. Fall 1991-December 1994.
Member of the Executive Committee of the Yale Program in Neuroscience, July 1990 to June 1993.
Contributed to the founding proposal and establishment of Yale's Center for Theoretical and Applied Neuroscience (subsequently Neuroengineering and Neuroscience Center). Summer 1990.
Organized a workshop at the Neural Information Processing Systems conference, in 1993 and 1995.
Referee reports for Neural Computation, IEEE Transactions on Neural Networks, Bioinformatics Journal, Neural Networks, Journal of the Optical Society of America, SIAM Journal on Scientific and Statistical Computing, Journal of the Association for Computing Machinery, Biological Cybernetics, the International Parallel Processing Symposium, SIGGRAPH, Cambridge University Press, Kluwer Academic Publishers.

AFFILIATIONS

Association for Computing Machinery
American Mathematical Society
Society for Industrial and Applied Mathematics
American Association for the Advancement of Science
International Society for Computational Biology

JOURNAL PUBLICATIONS

J31 “Modeling the Organization of the WUSCHEL Expression Domain in the Shoot Apical Meristem”, Henrik Jönsson, Marcus Heisler, G. Venugopala Reddy, Vikas Agrawal, Victoria Gor, Bruce E. Shapiro, Eric Mjolsness, Elliot M. Meyerowitz. Bioinformatics 21(Suppl. 1):i232-i240 June 2005.

J30 “A mathematical and computational framework for quantitative comparison and integration of large scale gene expression data.” Hart CE, Sharenbroich L, Bornstein BJ, Trout D. King B., Mjolsness E., and Wold BJ. Nucleic Acids Research, May 10;33(8):2580-94, 2005.

J29 “Sigmoid: Towards an Intelligent, Scalable, Software Infrastructure for Pathway Bioinformatics and Systems Biology”, Jianlin Cheng, Lucas Scharenbroich, Pierre Baldi, Eric Mjolsness, IEEE Intelligent Systems, May/June 2005.

J28 “A Mathematical Model for the Branched Chain Amino Acid Biosynthetic Pathways of Escherichia coli K12”, Chin-Ran Yang, Bruce E. Shapiro, She-pin Hung, Eric D. Mjolsness, and G. Wesley Hatfield, Journal of Biological Chemistry, 2005 Mar 25;280(12):11224-32 .

J27 “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.

J26 “Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.” Bruce E. Shapiro, Andre Levchenko, Elliot M. Meyerowitz, Barbara J. Wold and Eric D. Mjolsness. Bioinformatics, 19(5):677-678, 2003.

J25 “The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models”, M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano , A. P. Arkin , B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J.-H. Hofmey, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Nov` ere, L. M. Loew, D. Lucio , P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, Bioinformatics Vol 19, no 4, pp 524-531, 2003.

J24 “Clustering Analysis of Microarray Gene Expression Data by Splitting Algorithm”, Ruye Wang, Lucas Scharenbroich, Christopher Hart, Barbara Wold, and Eric Mjolsness. Journal of Parallel and Distributed Computing. Volume 63, Numbers 7-8, pp. 692-706, July-August 2003.

J23 “Machine Learning for Science: State of the Art and Future Prospects”, Eric Mjolsness and Dennis DeCoste, Science 293, 2051-2055, September 14, 2001.

J22 "Strategies for autonomous rovers and Mars", Martha S. Gilmore, Rebecca Castaño, Tobias Mann, Robert C. Anderson, Eric D. Mjolsness, Roberto Manduchi, and R. Stephen Saunders, Journal of Geophysical Research - Planets, December 25 2000.

J21 "Fast and Globally Convergent Pose Estimation from Video Images", C.-P. Lu, G. D. Hager and E. Mjolsness, IEEE Pattern Analysis and Machine Intelligence 22(6), 610-622, 2000.

J20 "The Synergy of Biology, Intelligent Systems, and Space Exploration", E. Mjolsness and A. Tavormina, IEEE Expert Systems April-May 2000.

J19 "Convergence Properties of the Softassign Quadratic Assignment Algorithm", Anand Rangarajan, Alan Yuille, and Eric Mjolsness, Neural Computation 11(6), 1455-1474 1999.

J18 "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.

J17 "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.

J16 "New Algorithms for 2D and 3D Point Matching: Pose Estimation and Correspondence", Steven Gold, Chien- Ping Lu, Anand Rangarajan, Suguna Pappu, and Eric Mjolsness, Pattern Recognition vol. 31 no. 8, pp. 1019-1031 August 1998.

J15 "A Robust Point Matching Algorithm for Autoradiograph Alignment", Anand Rangarajan, Haili Chui, Eric Mjolsness, Suguna Pappu, Lila Davachi, Patricia S. Goldman-Rakic, and James S. Duncan, Medical Image Analysis, vol 1 no 4, 1997.

J14 "Lagrangian Relaxation Network for Graph Matching", Anand Rangarajan and Eric Mjolsness, IEEE Transactions on Neural Networks, vol 7 no 6, November 1996.

J13 "A Novel Optimizing Network Architecture with Applications", Anand Rangarajan, Steven Gold, and Eric Mjolsness, Neural Computation, vol 8 no 5, July 1996.

J12 "Learning with Preknowledge: Clustering with Point and Graph Matching Distance Measures", Steven Gold, Anand Rangarajan, and Eric Mjolsness, Neural Computation, vol 8 no 4, May 15 1996. Reprinted in "Unsupervised Learning: Foundations of Neural Computation", eds. G. Hinton and T. J. Sejnowski, MIT Press 1999.

J11 "Online Computation of Exterior Orientation with Application to Hand-Eye Calibration", Chien-Ping Lu, Eric Mjolsness, and Gregory D. Hager, Mathematical and Computer Modelling Journal, vol. 24 no. 5-6, pp. 121-43, September 1996.

J10 "Model for Cooperative Control of Positional Information in Drosophila by bcd and Maternal hb", John Reinitz, Eric Mjolsness and David H. Sharp, Journal of Experimental Zoology 271:47-56, 1995.

J9 "Optimization Dynamics for Partitioned Neural Networks", Dimitris I. Tsioutsias and Eric Mjolsness. International Journal of Neural Systems, December 1994.

J8 "Accelerating Neural Net Dynamics by Boundary Layer Methods", Willard L. Miranker and Eric Mjolsness, Applied Mathematics Letters, vol 6, no 3, pp. 85-89, 1993.

J7 "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.

J6 "A Center-of-Mass Computation Describes the Precision of Random Dot Displacement Discrimination", by Joy Hirsch and Eric Mjolsness,Vision Research, vol 32 no 2, pp 335-346, February 1992.

J5 "A Connectionist Model of Development", Eric Mjolsness, David H. Sharp, and John Reinitz, Journal of Theoretical Biology, vol 152 no 4, pp 429-454, 1991.

J4 "Multiscale Optimization in Neural Networks", by Eric Mjolsness, Charles Garrett, and Willard Miranker, IEEE Transactions on Neural Networks, vol 2 no 2, March 1991.

J3 "Algebraic Transformations of Objective Functions", Eric Mjolsness and Charles Garrett, Neural Networks, vol 3, no 6, pp 651-669, 1990.

J2 "Optimization in Model Matching and Perceptual Organization", Eric Mjolsness, Gene Gindi, and P. Anandan. Neural Computation, vol 1 no 2, Summer 1989.

J1 "Scaling, Machine Learning, and Genetic Neural Nets", Eric Mjolsness, David H. Sharp, and Bradley K. Alpert. Advances in Applied Mathematics, June 1989.

BOOK CHAPTERS

B13 “A Software Architecture for Developmental Modeling in Plants: The Computable Plant Project”, Victoria Gor, Bruce E. Shapiro, Henrik Jönsson, Marcus Heisler, G. Venugopola Reddy, Elliot M. Meyerowitz and Eric Mjolsness. In: Bioinformatics of Genome Regulation and Structure II, (Eds. N.Kolchanov and R. Hofestaedt) Springer Science+Business Media, Inc. 2005, pp. 345-354 (in press).

B12 “AGNS—A Database on expression of Arabidopsis Genes”. Nadezhda Omelyanchuk, Viktoria Mironova, Aleksander Poplavsky, Nikolay Podkoldny, Nikolay Kolchanov, Eric Mjolsness, Elliot Meyerowitz. In Bioinformatics of Genome Regulation and Structure, Second Biennial Volume”, Nikolay Kolchanov, editor. Kluwer, in press, 2005.

B11 “Gene Network Models and Neural Development,” George Marnellos and Eric D. Mjolsness. In Modeling Neural Development, edited by Arjen van Ooyen. The MIT Press, Cambridge, Massachusetts, 2003.

B10 “Signaling in Multicellular Models of Plant Development.” H. Jönsson, B. E. Shapiro, E. M. Meyerowitz and E. Mjolsness (2003). In S. Kumar and P.J. Bentley (Eds.) "On Growth, Form, and Computers", Academic Press, London, UK, pages 156-161, 2003.

B9 “Modeling plant development with gene regulation networks including signaling and cell division.” Mjolsness E, Jönnson H, Shapiro BE, Meyerowitz EM (2003) in Bioinformatics of Genome Regulation and Structure, eds R. Hofestaedt and N. Kolchanov, Kluwer Publications (in press 2003).

B8 "Automatic model generation for signal transduction with applications to MAP-kinase pathways", B. E. Shapiro, A. Levchenko, E. Mjolsness. In Foundations of Systems Biology, ed. H. Kitano, MIT Press 2001.

B7 “Gene Regulation Networks for Modeling Drosophila Development”, Eric Mjolsness, in Computational Methods in Molecular Biology, eds. J. M. Bower and H. Bolouri, MIT Press 2001.

B6 “Modeling the Activity of Single Genes”, Michael Gibson and Eric Mjolsness, in Computational Methods in Molecular Biology, eds. J. M. Bower and H. Bolouri, MIT Press 2001.

B5 “Symbolic Neural Networks Derived from Stochastic Grammar Domain Models”, Eric Mjolsness, in Connectionist Symbolic Integration, eds. R. Sun and F. Alexandre, Lawrence Erlbaum Associates, 1997.

B4 “Modeling the Connection between Development and Evolution: Preliminary Report”, Eric Mjolsness, Charles D. Garrett, John Reinitz, and David H. Sharp, in Evolution and Biocomputation: Computational Models of Evolution eds. Wolfgang Banzhaf and Frank H. Eeckman, Lecture Notes in Computer Science, Springer, Berlin, 1995.

B3 "Connectionist Grammars for High-Level Vision", Eric Mjolsness, in Artificial Intelligence and Neural Networks: Steps Toward Principled Integration, eds. Vasant Honavar and Leonard Uhr, Academic Press, 1994.

B2 “A Connectionist Model of the Drosophila Blastoderm”, J. Reinitz, E. Mjolsness, and D. H. Sharp, in The Principles of Organization in Organisms, eds. Jay E. Mittenthal and Arthur B. Baskin, Santa Fe Institute Studies in the Sciences of Complexity, Addison-Wesley 1992.

B1 “Neural Networks for Model-Based Recognition”, Gene Gindi, Eric Mjolsness, and P. Anandan, in Neural Networks: Concepts, Applications, and Implementations, Volume III, eds. P. Antognetti and V. Milutinovic, pp 144-173, Prentice Hall 1991.

RECENT TALKS AND PRESENTATIONS

RTP05.10 “Computational modeling and image processing approaches to understanding the dynamics of the Arabidopsis thaliana shoot apical meristem”, E. Mjolsness, T. Bacarian, P. Baldi, V. Gor, M. Heisler, H. Jonsson, V. Reddy, A. Sadovsky, B. Shapiro, E. Meyerowitz. Symposium “Modeling plant development: From genes to phenotypes”, in International Botanical Congress, Vienna 2005.

RTP05.9 “The Sigmoid Biological Pathway Modeling System”. The Seventh Annual BioPathways Meeting, Special Interest Group at the Intelligent Systems in Molecular Biology conference, Detroit, June 24, 2005.

RTP05.8 “Physics-inspired models of regulatory networks for cellular and developmental biology”. Invited seminar Center for Theoretical Biological Physics (CTBP) in San Diego, a joint effort between research groups at UCSD, the Salk Institute, the Scripps Research Institute and the San Diego Supercomputer Center.

http://ctbp.ucsd.edu/seminars.html . May 20, 2005.

RTP05.7 “Image understanding and modeling for biological development: the case of a plant shoot meristem”, Eighth Workshop on Mining Scientific and Engineering Datasets, in conjunction with the Fifth SIAM International Conference on Data Mining (SDM 2005), http://www-aig. jpl.nasa.gov /public/MSD05/. Newport Beach, CA. Saturday. Invited keynote. Apr 23, 2005.

RTP05.6 “Variable-structure systems from dependency diagrams and dynamical grammars” E. Mjolsness. The Learning Workshop, http://snowbird.djvuzone.org/ . Snowbird, Utah, April 5-8 2005.

RTP05.5 “Modeling and image understanding for biological development: the case of a plant shoot meristem”, Eric Mjolsness. Computer Modeling in Biology group, Cambridge University, http://www.anat. cam.ac. uk/~comp-cell/CMBGroup /previous.htm. March 29 2005.

RTP05.4 “Some Mathematical Problems in Computational Systems Biology”, Eric Mjolsness. UC Irvine Applied Mathematics seminar. Invited talk. March 14, 2005.

RTP05.3 “Biology and Modeling in the Computable Plant Project”, Eric Mjolsness. Caltech Beckman Institute proposal review. March 10, 2005.

RTP05.2 “Variable-Structure Probabilistic Models”, Eric Mjolsness, IPAM workshop on "Probabilistic Models of Cognition: The Mathematics of Mind", http://www. ipam. ucla.edu /programs/cog2005/. A. Yuille and J. Tenenbaum, organizers. Invited talk. January 2005.

RTP05.1 “Measuring and modeling the growth of a plant shoot apical meristem”, Eric Mjolsness. Dynamics Days, 24^th Annual International Conference. http://www. physics. uci. edu/dynamicsdays2005/. Long Beach CA, January 8, 2005.

RTP04.5 “The Computable Plant: Software and Science”, Eric Mjolsness, dual poster presentation at the Caltech Biology Division Annual Retreat, Redondo Beach CA, October 16 2004.

RTP04.4 “Scientific Applications of Image Pattern Recognition”, Eric Mjolsness, invited presentation at the Round-Table on Scientific Imaging, Institute for Cytology and Genetics, Novosibirsk, Russia July 27 2004.

RTP04.3 “The Computable Plant: A Software Architecture for Developmental Modeling in Plants” by Victoria Gor, Bruce Shapiro, H. Jonsson, M. Heisler, GV.Reddy, E Meyerowitz and Eric Mjolsness. Fourth International Conference on Bioinformatics of Genome Regulation and Structure. http://www.bionet. nsc.ru/meeting/ bgrs2004/ . July 2004.

RTP04.2 “Network Dynamics for Systems Biology”, Eric Mjolsness. International Conference on Complex Systems, Boston MA. http://necsi.org/ events/iccs/ iccscover.html . May 2004.

RTP04.1 Mjolsness E, Shapiro B, Heisler V., and Meyerowitz EM. The Computable Plant: A Software Architecture for Developmental Modeling in Plants. Poster presentation at Pacific Symposium for Biocomputing, Kona Coast, Hawaii, January 2004.

PATENT

PT2 “Cellerator”, Bruce E. Shapiro, Eric D. Mjolsness, and Andre Levchenko, Provisional Patent, November 2000

PT1 "Analysis of Ultrasound Images in the Presence of Contrast Agent", Howard C. Dittrich, Harold Levene, and Eric Mjolsness. United States Patent 5,776,063, July 7, 1998.

REFEREED CONFERENCES (major conferences)

C42 “The Generalized Monod, Wyman, Changeux Model for Mathematical Modeling of Metabolic Enzymes with Allosteric Regulation” Tarek S. Najdi, Chin-Rang Yang, Bruce E. Shapiro, G. Wesley Hatfield and Eric D. Mjolsness. IEEE Computational Systems Bioinformatics Conference, Stanford University, August 8-12 2005.

C41 “Tracking Cell Signals in Fluorescent Images”, Victoria Gor, Tigran Bacarian, Michael Elowitz, Eric Mjolsness. Accepted for the Computer Vision Methods for Bioinformatics (CVMB) workshop at Computer Vision and Pattern Recognition (CVPR). June 2005.

C40 “Modeling the Organization of the WUSCHEL Expression Domain in the Shoot Apical Meristem”, Henrik Jönsson, Marcus Heisler, G. Venugopala Reddy, Vikas Agrawal, Victoria Gor, Bruce E. Shapiro, Eric Mjolsness, Elliot M. Meyerowitz. Intelligent Systems in Molecular Biology 2005.

C39 “A Multicellular Model of a Feedback Network Regulating Spatial Gene Expression Domains in the Shoot Apical Meristem”, Henrik Jönsson, Bruce E. Shapiro, Victoria Gor, Marcus Heisler, G. Venugopala Reddy, Elliot M. Meyerowitz, and Eric Mjolsness, ICSB 2004.

C38 “Gene Expression Clustering with Functional Mixture Models”, Padhraic Smyth, Darya Chudova, Christopher Hart, Eric Mjolsness, Advances in Neural Information Processing Systems 2003.

C37 “Translation-Invariant Mixture Models for Curve Clustering”, Darya Chudova, Scott Gaffney, Eric Mjolsness, Padhraic Smyth. Knowledge Discovery and Data Mining Conference 2003.

C36 "Automating Operational and Science Analysis Processes With the Autonomous Sciencecraft Constellation (ASC)", A. G. Davies, R. Greeley, V. Baker, K. K. Williams, J. Dohm, R. Castaño, E. Mjolsness, J. Roden, T. Stough, S. Chien, R. Sherwood, P. Zetocha, and the ASC-Techsat 21 Team, Lunar and Planetary Science Conference, Houston TX, March 2002.

C35 "Can tectonic and fluvial structures be used to date a planetary surface?", Tatiana Vinogradova, R. C. Anderson, and Eric Mjolsness, Lunar and Planetary Science Conference, Houston TX, March 2002.

C34 "Observing active volcanism on Earth and beyond with an autonomous science investigation capability. Ashley Gerard Davies, Wolfgang Fink, Rebecca Castaño,Anthony Barrett, Eric Mjolsness, Michael Burl. American Geophysical Union, San Francisco CA, December 2001.

C33 1/3 “Developmental Simulations with Cellerator”, B. E. Shapiro, E. Mjolsness. Paper presented at the Second International Conference on Systems Biology, Pasadena, CA, November 2001.

C33 "Systematic evaluation of automated geological feature detection methods for impact craters", Tatiana Vinogradova, Michael Burl, Eric Mjolsness, American Geophysical Union, San Francisco CA, December 2001.

C32 "Automatic model generation for signal transduction with applications to MAP-kinase pathways", B. E. Shapiro, A. Levchenko, E. Mjolsness. First International Conference on Systems Biology, Tokyo Japan November 2000.

C31 "Using Scaled Visual Texture for Autonomous Rock Clustering", R. C. Anderson, R. Castaño, T. Stough, V. Gor, and E. Mjolsness, Abstract 2103, Lunar and Planetary Science Conference 2001.

C30 "Autonomous Rover-Based Scientific Investigations Using Invertible Mathematical Models", E. Mjolsness, A. G. Davies, R. Castaño, W. Fink, and J. Z. Lou, American Geophysical Union Fall Meeting December 2000 (poster).

C29 "Autonomous Rock Identification Using Visual Texture", Robert C. Anderson, Rebecca Castaño, Eric Mjolsness, Ashley Davies, Justin Fox, Tim Stough, and Martha Gilmore, abstract 52768, Geological Society of America, Reno NV November 2000.

C28 "Applications of Artificial Intelligence for Spacecraft Autonomy and Enhanced Science Data Return", David J. Atkinson, Steve A. Chien, Eric D. Mjolsness, American Institute of Aeronautics and Astronautics Space 2000, September 2000.

C27 "Software Platform for Systems Biology". Adam Arkin, Hamid Bolouri, Mark T. Borisuk, John Doyle, Koji, M. Kyoda, Eric Mjolsness, Mineo Morohashi, Hiroaki Kitano, RECOMB 2000 : The Fourth Annual International Conference on Computational Molecular Biology , Tokyo, Japan , April 8 - 11, 2000 (poster).

C26 "Reverse Engineering in Systems Biology: Towards Inference of a Gene Regulatory Network", Mineo Morohashi, Koji M. Kyoda, Shuichi Onami, Eric Mjolsness, Hiroaki Kitano, RECOMB 2000 : The Fourth Annual International Conference on Computational Molecular Biology, Tokyo, Japan , April 8 - 11, 2000 (poster).

C 25 1/2 “Delta-Notch lateral inhibitory patterning in the emergence of ciliated cells in Xenopus: Experimental observations and a gene network model”, G. Marnellos, G. A. Deblandre, E. Mjolsness, C. Kintner. Pacific Symposium on Biocomputing, pp. 329-40, 2000.

C25 "A new distance measure for non-rigid image matching", Anand Rangarajan, Haili Chui and Eric Mjolsness, Energy Minimization Methods in Computer Vision and Pattern Recognition (EMMCVPR), Edwin Hancock and Marcello Pelillo,editors, pages 237-252, Springer, 1999.

C24 "Robotic Geologists at Mars", M. S. Gilmore, R. Castaño, T. Mann, E. Mjolsness, R. C. Anderson, R. Manduchi, R. S. Saunders, American Geophysical Union Fall Meeting, Dec. 1999.

C23 "From Coexpression to Coregulation: An Approach to Inferring Transcriptional Regulation among Gene Classes from Large-Scale Expression Data", E. Mjolsness, T. Mann, R. Castaño, and B. Wold. Advances in Neural Information Processing Systems 1999.

C22 "An Integrated System for Multi-Rover Scientific Exploration", Tara Estlin, Tobias Mann, Alexander Gray, Gregg Rabideau, Rebecca Castaño, Steve Chien, and Eric Mjolsness, Proceedings of the American Association for Artificial Intelligence conference, July 1999.

C21 "Texture Analysis for Mars Rover Images", R. Castaño, T. Mann and E. Mjolsness, Applications of Digital Image Processing XXII, Proc. SPIE Vol 3808, July 1999.

C20 "An Integrated Architecture for Cooperating Rovers", T. Estlin, S. Hayati, A. Jain, J. Yen, G. Rabideau, R. Castaño, R. Petra, S. Peters, D. Decoste, E. Tunstel, S. Chien, E. Mjolsness, R. Steele, D. Mutz, A. Gray, T. Mann, International Symposium on Artificial Intelligence Robotics and Automation in Space (ISAIRAS), 1999.

C19 "Hypothesis-driven Active Data Analysis of Geological Phenomena Using Semi-autonomous Rovers: Exploring Simulations of Martian Hydrothermal Deposits", A. G. Davies, E. D. Mjolsness, A. G Gray, T. P. Mann, R. Castaño, T. A. Estlin and R. S. Saunders, Amer. Geophys. U. Spring Meeting (abstract) 1999.

C18 "Morphogenesis in Plants: Modeling the Shoot Apical Meristem, and Possible Applications", E. Mjolsness, E. Meyerowitz, V. Gor, and T. Mann. Accepted for Proceedings, 1999 NASA Workshop on Evolvable Hardware.

C17 "Clustering Methods for the Analysis of C. elegans Gene Expression Array Data", E. Mjolsness, R. Castaño, T. Mann, J. Roden, A. Gray, B. Wold, Pacific Symposium on Biocomputing (poster), Mauna Lani, Hawaii, January 1999.

C16 "Spectroscopic Measurements at Silver Lake, CA Testbed for the FIDO Rover", M. S. Gilmore, R. S. Saunders, R. Castaño, T. Mann, E. Mjolsness, and T. L. Roush, American Geophysical Union Fall Meeting (abstract), December 1998.

C15 "Effect of Distance and Azimuth on Spectroscopic Measurements at Silver Lake, CA", M. S. Gilmore, R. Castaño, T. Roush, T. Mann, E. Mjolsness, R. S. Saunders, and E. Guiness, Lunar and Planetary Science Conference (poster), March 1999.

C14 "A Gene Network Model of Resource Allocation to Growth and Reproduction", G. Marnellos and E. Mjolsness, Artificial Life VI, eds. C. Adami, R. K. Belew, H. Kitano, and C. E. Taylor, MIT Press, 1998.

C13 "Probing the Dynamics of Cell Differentiation in a Model of Drosophila Neurogenesis", G. Marnellos and E. Mjolsness, Artificial Life VI, eds. C. Adami, R. K. Belew, H. Kitano, and C. E. Taylor, MIT Press, 1998.

C12 "A Gene Network Approach to Modeling Early Neurogenesis in Drosophila", G. Marnellos and E. Mjolsness, in Pacific Symposium on Biocomputing, eds. R. B. Altman, A. K. Dunker, L. Hunter and T. Klein, World Scientific, 1998.

C11 "A Convergence Proof for the Softassign Quadratic Assignment Algorithm", Anand Rangarajan, Alan Yuille, Steven Gold and Eric Mjolsness, Advances in Neural Information Processing Systems 9. M. Mozer, M. Jordan, and T. Petsche, eds. MIT Press, 1997.

C10 "A Multiscale Attentional Framework for Relaxation Neural Networks", Dimitris I. Tsioutsias and Eric Mjolsness, Advances in Neural Information Processing Systems 8, MIT Press, 1996.

C9 "New Algorithms for 2D and 3D Point Matching: Pose Estimation and Correspondence", Steven Gold, Chien- Ping Lu, Anand Rangarajan, Suguna Pappu and Eric Mjolsness. Advances in Neural Information Processing Systems 7, editors Tesauro, Touretzky, Leen, MIT Press 1995.

C8 "Learning with Preknowledge: Clustering with Point and Graph Matching Distance Measures", Steven Gold, Anand Rangarajan, and Eric Mjolsness. Advances in Neural Information Processing Systems 7, editors Tesauro, Touretzky, Leen, MIT Press, 1995.

C7 "Clustering with a Domain-Specific Distance Measure", Steven Gold, Anand Rangarajan, and Eric Mjolsness, Advances in Neural Information Processing Systems 6, editors Cowan, Tesauro, Alspector, Morgan-Kaufmann 1994.

C6 "Two-Dimensional Object Localization by Coarse-to-Fine Correlation Matching", Chien-Ping Lu and Eric Mjolsness, Advances in Neural Information Processing Systems 6, editors Cowan, Tesauro, Alspector, Morgan-Kaufmann 1994.

C5 "Animation of Plant Development", Przemyslaw Prusinkiewicz, Mark S. Hammel, and Eric Mjolsness, SIGGRAPH '93 Conference Proceedings, ACM 1993.

C4"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.

C3 "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.

C2 "Connectionist Variable-Binding by Optimization", P. Anandan, Stanley Letovsky, and Eric Mjolsness. August 1989 Cognitive Science conference proceedings.

C1 "Neural Networks for Model Matching and Perceptual Organization", Eric Mjolsness, Gene Gindi, and P. Anandan. Advances in Neural Information Processing Systems 1, editor David S. Touretsky, Morgan- Kaufman 1989.

REFEREED CONFERENCES (more peripheral conferences)

PC15 “Model Fitting and Parameter Optimization for Biological Dynamical

Pathway Systems”, Li Zhang and Eric Mjolsness. International Conference on Bio-Nano-Informatics (BNI) Fusion, Marina del Rey. July 2005.

PC14 “Training of a crater detection algorithm for Mars crater imagery”, Vinogradova T., Burl M., and Mjolsness E., IEEE Aerospace Conference, Big Sky MT, March 2002.

PC13 “Novel Analysis Methods for Biosignature Data”, E. Mjolsness, T. Mann, R. Castaño, B. Wold, First NASANCI Workshop on Sensors for Bio-Signatures (talk), Pasadena June 1999.

PC12 "Connectionist Models of Cell Fate Patterning Involving Cell-Cell Communication", G. Marnellos and E. Mjolsness, First Annual In Silico Biology Conference (poster), Cambridge Healthtech Institute, San Francisco, June 1999.

PC11 "Use of Processing-In-Memory (PIM) Technology to Enable On-Site `Geologist's Assistant' " , Peter Kogge, Jay Brockman, Eric Mjolsness, Robert Ferraro, Paul Kapcio, Joseph Marshall, conference paper at the NASA Mars Micromission Workshop, Pasadena (Jeffrey Plescia, organizer), 1998.

PC10 "Automated Calibration of 2D Electrophoresis Images", Tom Brotherton, Alan Thompson and Eric Mjolsness, Annual Meeting of the Biomedical Engineering Society (poster), San Diego CA 1997.

PC9 "A Gene Network Model of Early Neurogenesis in Drosophila", G. Marnellos and E. Mjolsness, Proceedings of the Fourth Joint Symposium on Neural Computation, University of California San Diego and California Institute of Technology, vol. 7, page 142, 1997.

PC8 "Labelled Matching Problems and Imaging Models", Eric Mjolsness and Richard Calmbach, Proceedings of the Third Joint Symposium on Neural Computation, University of California San Diego and California Institute of Technology, page 231, June 1 1996.

PC7 "A Robust Point Matching Algorithm for Autoradiograph Alignment", Anand Rangarajan, Eric Mjolsness, Suguna Pappu, Lila Davachi, Patricia S. Goldman-Rakic, and James S. Duncan, Visualization in Biomedical Computing (VBC) '96, K. H. Hohne and R. Kikinis editors, pp. 277-286, Springer-Verlag, 1996.

PC6 "A Lagrangian Relaxation Network for Graph Matching", Anand Rangarajan and Eric Mjolsness, IEEE International Conference on Neural Networks (ICNN), vol 7, pp 4629-4634, IEEE Press 1994.

PC5 "Mean Field Point Matching by Vernier Network and by Generalized Hough Transform", Chien-Ping Lu and Eric Mjolsness, proceedings of the World Conference on Neural Networks, Portland OR July 1993.

PC4 "Visual Grammars and Their Neural Networks", proceedings of the SPIE conference on the Science of Artificial Neural Networks, Orlando, Florida, April 21 1992.

PC3 "A Neural Net for Reconstruction of Multiple Curves with a Visual Grammar", Eric Mjolsness, Anand Rangarajan, Charles Garrett, International Joint Conference on Neural Networks, Seattle, June 1991.

PC2 "Multiscale Optimization in Neural Nets: Preliminary Report", Eric Mjolsness, Charles Garrett, Willard L. Miranker, International Joint Conference on Neural Networks, San Diego, June 1990.

PC1 "A Preliminary Analysis of Recursively Generated Networks", Eric Mjolsness and David H. Sharp. In John Denker, editor, Neural Networks for Computing, American Institute for Physics, 1986. Proceedings. Snowbird, Utah.

SELECTED TECHNICAL REPORTS

R18 “Variable-structure systems from graphs and grammarsEric Mjolsness, UCI ICS TR# 05-09. http://www.ics.uci.edu/~emj/ à papers /vbl-Struct_GG_TR.pdf. July 2005.

R17 “Labeled graph notations for graphical models: Extended Report”, Eric Mjolsness, UCI ICS TR# 04-03. http://www.ics.uci.edu/~emj/ à papers /graphNotationsTR.pdf . March 2004.

R16 "Multi-Parent Clustering Algorithms from Stochastic Grammar Data Models", E. Mjolsness, R. Castaño, A. Gray. Technical Report JPL-ICTR-99-5, 1999.

R15 "Clustering Methods for the Analysis of C. elegans Gene Expression Array Data", E. Mjolsness, R. Castaño, T. Mann, J. Roden, A. Gray, B. Wold, Technical Report JPL-ICTR-99-1, 1999.

R14 "Finding Globally Convergent Trajectories in Large-Scale Relaxation Neural Networks" Dimitris I. Tsioutias and Eric Mjolsness, UCSD Department of Computer Science Technical Report 97-563, 1997.

R13 "A Model of Optimal Resource Allocation to Growth and Reproduction Using Gene Networks", George Marnellos and Eric Mjolsness, UCSD Department of Computer Science December 1997.

R12 "Mean Field Point Matching by Vernier Network and by Generalized Hough Transform", Chien-Ping Lu and Eric Mjolsness, Report YALEU/DCS/TR-974, February 1993.

R11 "Mean Field Point Matching by Vernier Network and by Generalized Hough Transform: Preliminary Report", Chien-Ping Lu and Eric Mjolsness, Proceedings of the World Conference on Neural Networks, Portland Oregon, July 1993. Also Report YALEU/DCS/TR-949, February 1993.

R10 "Greedy Lagrangians for Neural Networks: Three Levels of Optimization in Relaxation Dynamics", Eric Mjolsness and Willard Miranker, Report YALEU/DCS/TR-945, January 1993. Also IBM Research Division RC 18769 (82097), 3/9/93.

R9 "Automated Fingerprint Identification: An Independent Study", Eric Mjolsness and Carol Crawford, Report YALEU/DCS/TR-920, October 1991.

R8 "Bayesian Inference on Visual Grammars by Neural Nets that Optimize", Eric Mjolsness, Report YALEU/DCS/TR- 854, May 1991.

R7 "Neural Networks for Object Recognition with Compositional Hierarchies: Initial Experiments", Joachim Utans, Gene Gindi, Eric Mjolsness and P. Anandan. Yale EE Center for Systems Science Report No. 8903, February 1989.

R6 "Recursively Generated Neural Networks", Eric Mjolsness, David H. Sharp, and Bradley K. Alpert. Yale Computer Science Research Report YALEU/DCS/RR-549. Proceedings of the IEEE First Annual International Conference on Neural Networks, June 1987, p. III-165.

R5 "Control of Attention in Neural Networks", Eric Mjolsness, Proceedings of the IEEE First Annual International Conference on Neural Networks, June 1987, p. II-567.

R4 "A Preliminary Analysis of Recursively Generated Networks", Eric Mjolsness and David H. Sharp. Yale Computer Science Research Report YALEU/DCS/RR-476.

R3 "Neural Networks, Pattern Recognition, and Fingerprint Hallucination", Eric Mjolsness, Caltech Physics Ph.D. Thesis, 1985.

R2 SMP Handbook, C.A. Cole, S. Wolfram, G.C. Fox, J.M. Greif, E.D. Mjolsness, L.J. Romans, T. Shaw, and A.E. Terrano, California Institute of Technology 1981.

R1 "A Novel Approach to the Solution of Boundary Layer Problems", C.M. Bender, F. Cooper, G.S. Guralnick, E. Mjolsness, H.A. Rose, and D.H. Sharp, Los Alamos Preprint LA-UR-80-512 (1980).