Ph.D. in Civil & Environmental Engineering
Dissertation: "Efficient Data Inversion for Large Multi-Dimensional Problems Using an Approximate Extended Kalman Filter with Data Driven Zonation"

Advisor: Dr. David E. Dougherty

University of Vermont, 1997.

Continuing Education

New England Complex Systems Institute Summer School (5-day): Complex Physical, Biological and Social Systems, MIT, Cambridge, MA, June 2005.

New England Complex Systems Institute Summer School (5-day): Modeling, Networks and Evolution of Complex Systems, MIT, Cambridge, MA, June 2005.

New Directions in Bioinformatics and Biotechnology Workshop, Chautauqua Short Course #65 (3-day), RPI, July 2002.

NPACI Parallel Computing Workshop (1-day), San Diego Supercomputer Center, San Diego, CA. January, 2002

Inter-Institute Workshop on In Vivo Optical Imaging at NIH (2-day), October, 1999.

Parallel Virtual Machine Workshop (1-day) at the 6^th SIAM Conference on Parallel Processing for Scientific Computing, Norfolk, VA, March, 1993.

Follow-up Parallel Processing Workshop (4-day), Colgate University, Hamilton, NY. 1992.

Parallel Processing for Undergraduate Educators (2-week), Colgate University, Hamilton, NY. 1991.

Workshop for the Foundations of Artificial Intelligence (2-day), New Mexico State University, Las Cruces, NM. 1986.

Awards and Honors

Best Student Paper Award (my graduate student is 1^st author, I am 2^nd author), IEEE Symposium on Artificial Life, 2007.

The American Association of Physicists in Medicine Sylvia Sorkin Greenfield Award for the best paper (other than radiation dosimetry) published in Medical Physics in 2004.

Outstanding Student Paper Award, American Geophysical Union, Fall 1996.

American Association of University Women Career Development Award, 1993.

Finalist for the U.V.M. Kroepsch-Maurice Teaching Award, 1992.

U.V.M. graduate student travel mini-grants, 1982 and 1994.

National Science Foundation 3-year graduate fellowship, 1980-1983.

Initiated as Member, Upsilon Pi Epsilon, Computer Science Honor Society, 1983.

Member, Michigan State University Honor’s College, 1974-1979

Initiated as Member Phi Kappa Phi Honor Society, 1978.

Professional Positions

(in reverse chronological order)

2008-present Associate Professor (Primary Appointment), Department of Computer Science, University of Vermont, Burlington, Vermont.

2002-2008 Assistant Professor (Primary Appointment 2002-2008), Department of Computer Science, University of Vermont, Burlington, Vermont.

2006-present founding Director, Complex Systems Center at the University of Vermont. College of Engineering and Mathematical Sciences, University of Vermont, Burlington, Vermont.

2006-present Adjunct Member, Computational Genetics Laboratory, Dartmouth College, Lebanon, NH.

2005-present Assistant Professor (Secondary Appointment), Department of Biology, University of Vermont, Burlington, VT.

2001-2003 Adjunct Assistant Professor, Department of Chemical Engineering, Texas A&M University, College Station, TX.

2001-present Member, Vermont Cancer Center.

1997-2002 Research Assistant Professor (Primary Appointment 1998-2002), Department of Computer Science, University of Vermont, Burlington, VT.

1998-2003 Research Assistant Professor (Secondary Appointment), Department of Civil & Environmental Engineering, University of Vermont, Burlington, VT.

1983-2001 Lecturer (Primary Appointment 1983-1998), Department of Computer Science, University of Vermont, Burlington, VT.

1993-1997 Graduate Research Assistant, Department of Civil & Environmental Engineering, University of Vermont, Burlington, VT.

1990 Consultant, Digital Equipment Corporation, S. Burlington, VT.

1987-1988 Bioinformatics Software Engineer, International Biotechnologies, Inc., New Haven, CT (telecommuted).

1986 System Graphics Software Engineer, Vermont Microsystems, Inc., Winooski, VT.

1986 Consultant, Computing Research Laboratory, New Mexico State University, Las Cruces, NM.

1982 Graduate Teaching Assistant, Department of Computer Science, University of Vermont, Burlington, VT.

1982 Programmer, Academic Computing Center, University of Vermont, Burlington, VT.

1981-1982 Graduate Teaching Assistant, Department of Zoology, University of Vermont, Burlington, VT.

1979-1980 Research Associate, Department of Zoology, Michigan State University, E. Lansing, MI.

1977 Undergraduate Teaching Assistant, Department of Mathematics, Michigan State University, E. Lansing, MI.

1975-1979 Archaeologist for various institutions, including the Department of Anthropology at Michigan State University, the Tennessee Valley Authority, the State of Tennessee, and the U.S. Army Corps of Engineers.

Research

Research Interests

In keeping with my interdisciplinary educational background in biology, computer science, and environmental engineering, my research interests involve computational forward and inverse modeling and analysis of biological and environmental problems. Most of my research has focused on developing novel computational methods for large-scale, nonlinear, multi-scale tomographic inverse image reconstruction problems in subsurface hydrology, geophysics, and deep-tissue near-infrared fluorescence imaging. However, in the past couple of years I have shifted my research towards modeling and analysis of complex adaptive systems in a variety of biological and environmental systems. Current projects include developing, studying, and using novel evolutionary and agent-based computational approaches for a wide range of important problems, including plant species’ invasiveness in ecological communities, biological speciation, the impact of spatial topologies on information flow through complex interaction networks, identifying nonlinear interactions between single nucleotide polymorphisms that predispose for complex disease traits, and agent-based integrated assessment modeling of transportation energy alternatives.

Publications (in reverse chronological order)

Refereed Journal Publications

Published or accepted:

Payne, J.L. and Eppstein, M.J. “Pair Approximations of Takeover Dynamics in Regular Population Structures”, Evolutionary Computation (in press).

Eppstein, M.J., Payne, J.L., White, B.C., and Moore. J.H. "Genomic mining for complex disease traits with 'Random Chemistry'", Genetic Programming and Evolvable Machines (special issue on Medical Applications), 8:395-411, 2007. (DOI 10.1007/s10710-007-9039-5) pdf

Zhu, B., Eppstein, M.J., Sevick-Muraca, E.M., and Godavarty, A. "Noise pre-filtering techniques in fluorescence-enhanced optical tomography", Optics Express, 15(18):11285-11300, 2007. pdf

Eppstein, M.J. and Molofsky, J. "Invasiveness in plant communities with feedbacks". Ecology Letters, 10:253-263, 2007. pdf

Eppstein, M.J., Bever, J.D., and Molofsky, J., "Spatio-temporal community dynamics induced by frequency dependent interactions", Ecological Modelling, 197:133-147, 2006. pdf

Fedele, F., Eppstein, M.J., Laible, J.P., Godavarty, A., and Sevick-Muraca, E.M., “Fluorescence Photon Migration by the Boundary Element Method”, J. Computational Physics, 210(1):109-132, 2005. pdf

Godavarty, A., Sevick-Muraca, E.M., and Eppstein, M.J. "Three-dimensional fluorescence lifetime tomography", Medical Physics, 32(4): 992-1000, 2005. pdf

Godavarty, A., Eppstein, M.J., Zhang, C., and Sevick-Muraca, E.M., "Detection of single and multiple targets in tissue phantoms using fluorescence-enhanced optical imaging", Radiology, 235: 148-154, 2005. pdf

Godavarty, A., Thompson, A.B., Roy, R., Gurfinkel, M., Eppstein, M.J., Zhang, C., and Sevick-Muraca, E.M., “Diagnostic imaging of breast cancer using fluorescence-enhanced optical tomography: phantom studies,” J. Biomed. Opics.: Special edition on Biomedical Optics and Women’s Health 9:488-496, 2004. pdf

Godavarty, A., Zhang, C., Eppstein, M.J., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical imaging of large phantoms using single and simultaneous dual point illumination geometries", Medical Physics 31(2):183-190, 2004. (Awarded the American Association of Physicists in Medicine Sylvia Sorkin Greenfield Award for the best paper published in Medical Physics in 2004) pdf

Eppstein, M.J., Fedele, F., Laible, J.P., Zhang, C., Godavarty, A., and Sevick-Muraca, E.M., "A comparison of exact and approximate adjoint sensitivities in fluorescence tomography", IEEE Transactions on Medical Imaging, 22(10):1215-1223, 2003. pdf

Godavarty, A., Eppstein, M.J., Zhang, C., Thompson, A.B., Gurfinkel, M., Theru, S., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical imaging in large tissue volumes using a gain modulated ICCD camera, Physics in Medicine and Biology, 48:1701-1720, 2003. pdf

Fedele, F. Laible, J. P., and Eppstein, M.J., "Coupled complex adjoint sensitivities for frequency-domain fluorescence tomography: theory and vectorized implementation", J Computational Physics, 187(2):597-619, 2003. pdf

Godavarty, A., Hawrysz, D.J., Roy, R., Sevick-Muraca, E.M., and Eppstein, M.J., "The influence of the refractive index-mismatch at the boundaries measured in fluorescence-enhanced frequency-domain photon migration imaging", Optics Express, 10(15):653:662, 2002. pdf

Eppstein, M.J., Hawrysz, D.J., Godavarty, A., and Sevick-Muraca, E.M., "Three-dimensional, Bayesian image reconstruction from sparse and noisy data sets: Near-infrared fluorescence tomography", Proc. Natl. Acad. Sci. USA, 99(15):9619-9624, 2002. pdf

Hawrysz, D.J., Eppstein, M.J., Lee, J., and Sevick-Muraca, E.M., "Error Consideration in Contrast-Enhanced Three Dimensional Optical Tomography", Optics Letters, 26(10):704-706, 2001.

Eppstein, M.J., Dougherty, D.E., Hawrysz, D.J., Sevick-Muraca, E.M., "3-D Bayesian optical image reconstruction with domain decomposition", IEEE Transactions on Medical Imaging, 20(3):147-163, 2001. pdf

Eppstein, M.J., Dougherty, D.E., Troy, T.L, and Sevick-Muraca, E.M., "Biomedical optical tomography using dynamic parameterization and Bayesian conditioning on photon migration measurements", Applied Optics, 38:2138-2150, 1999 (cover article). pdf

Eppstein, M.J. and Dougherty, D.E., "Efficient 3-D data inversion: Soil characterization and moisture monitoring from crosswell GPR at a Vermont test site", Water Resources Research, 34(8):1889-1900, 1998. pdf

Eppstein, M.J. and Dougherty, D.E., "Optimal 3-D traveltime tomography", Geophysics, 63(3):1053-1061, 1998.

Eppstein, M.J. and Dougherty, D.E., "Simultaneous estimation of transmissivity values and zonation", Water Resources Research, 32(11):3321-3336, 1996. pdf

Eppstein, M.J. and Dougherty, D.E., "A comparative study of PVM workstation cluster implementations of a two-phase subsurface flow model", Adv. In Water Resources, 17:181-195, 1994.

Heinrich, B. and Heinrich (née Eppstein), M.J.E., "The pit-trapping foraging strategy of the ant lion, Myrmeleon immaculatus", Behav. Ecol. and Sociobiol., 14:151-160, 1984.

Heinrich, B. and Heinrich (née Eppstein), M.J.E., "Size and caste in temperature regulation by bumblebees", Phys. Zool., 56:552-562, 1983.

Heinrich, B. and Heinrich (née Eppstein), M.J.E., "Heterothermia in foraging workers and drones of the bumblebee Bombus terricola", Phys. Zool., 56: 563-567, 1983.

Published Refereed Conference Proceedings

Eppstein, M.J. and Haake, P., “Very Large Scale ReliefF for Genome-Wide Association Analysis”, IEEE Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), accepted, 2008.

Payne, J.L. and Eppstein, M.J. “The influence of Scaling and Assortativity on Takeover Times in Scale-Free Topologies”, Genetic and Evolutionary Computation Conference (GECCO), pp. 241-248, 2008 (Nominated for a Best-Paper Award).

Payne, J.L, and Eppstein, M.J. "Parameterizing Pair Approximations for Takeover Dynamics", Genetic and Evolutionary Computation Conference (GECCO), late-breaking papers, pp.. 2199-2204, 2008.

Payne, J.L, and Eppstein, M.J. "Using Pair Approximations to Predict Takeover Dynamics in Spatially Structured Populations", Genetic and Evolutionary Computation Conference (GECCO), late-breaking papers pp. 2557-2563, 2007.

Payne, J.L. and Eppstein, M.J., “Takeover Times on Scale-Free Topologies”, Genetic and Evolutionary Computation Conference (GECCO), pp. 308-315, 2007.

Payne, J.L., Eppstein, M.J., and Goodnight, C.J. “Sensitivity of Self-Organized Speciation to Long Distance Dispersal”, Proceedings of the 2007 IEEE Symposium on Artificial Life (Alife’07), pp. 1-7, 2007 (best student paper award).

Eppstein, M.J., Payne, J.L., White, B.C., and Moore. J.H., "Hill-climbing through ‘random chemistry’ for detecting epistasis", Genetic and Evolutionary Computation Conference (GECCO), late-breaking papers, 2006.

Eppstein, M.J., Payne, J.L, and Goodnight, C.J. "Speciation by Self-Organizing Barriers to Gene Flow in Simulated Populations with Localized Mating", Workshop Proceedings for Genetic and Evolutionary Computation Conference (GECCO), 2006.

J.L. Payne and M.J. Eppstein, "Emergent Mating Topologies in Spatially Structured Genetic Algorithms", Proceedings of Genetic and Evolutionary Computation Conference (GECCO) 2006, pp. 207-214.

J.L. Payne and M.J. Eppstein, “A Hybrid Genetic Algorithm with Pattern Search for finding Heavy Atoms in Protein Crystals”, Genetic and Evolutionary Computation Conference (GECCO) 2005, Part 1, Eds. H-G Bayer et al., pp. 377-384, 2005. (nominated for a best-paper award).

Godavarty, A., Eppstein, M.J., Zhang, C., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical tomography on large phantoms using dual point illumination geometry", OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, April, 2004.

Godavarty, A., Eppstein, M.J., and Sevick-Muraca, E.M., "Fluorescence-enhanced optical tomography: Absorption and lifetime contrast studies", OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, April, 2004.

Fedele, F., Laible, J.P., and Eppstein, M.J., "Boundary Element Solution of the Coupled Fluorescence Diffusion Equations", OSA Biomedical Topical Meetings, OSA Technical Digest, Optical Society of America, Washington, DC, April, 2004.

Gilbert, J., and Eppstein, M.J., "Codons in Evolutionary Computation", Genetic and Evolutionary Computation Conference (GECCO) 2003, Part 1, Eds. E. Cantu-Paz et al., Lecture Notes in Computer Science, 2723:967-978, 2003.

Eppstein, M.J., Zhang, C., Godavarty, A., and Sevick-Muraca, E.M.,"Advances in 3-D frequency domain fluorescence tomography", Proc SPIE 4955:211-218, 2003.

Zhang, C., Eppstein, M.J., Godavarty, A., and Sevick-Muraca, E.M., "A hybrid approach to Bayesian image reconstruction", SPIE 2003 ProcSPIE 4955:591-599, 2003.

Eppstein, M.J., and Laible, J.P., "The benefits of vectorization in optical tomography", Proc SPIE 4955:59-69, 2003.