Wayne Hayes: Curriculum Vitae Assistant Professor Dept. of Computer Science University of California, Irvine, CA, 92697-3425 Phone: (B)949-824-1753, (C)949-981-2222. FAX: 949-824-4056 Citizenship: Canadian Web Page: http://www.ics.uci.edu/~wayne E-mail: wayne@ics.uci.edu Research Interests - complex systems: dynamical systems; scientific computing; numerical analysis - parallel, distributed, and grid computing - computational biology -- genome assembly, protein folding - operating systems and compilers - software engineering - optimization Education Ph.D. Computer Science, University of Toronto, 2001. Rigorous Shadowing of Numerical Solutions of Ordinary Differential Equations by Containment. Advisory Committee: Computer Science: Ken Jackson (supervisor), Wayne Enright, Tom Fairgrieve. Physics: Ted Shepherd. Astronomy: Scott Tremaine. M.Sc. Computer Science. University of Toronto, January 1995, under Ken Jackson. Efficient Shadowing of High Dimensional Chaotic Systems with the Large Astrophysical N-body Problem as an Example. Honours B.Sc. Computer Science, Physics & Astronomy. University of Toronto, June 1993. Publications Invited, Refereed Journal Publications 1. Wayne Hayes. "Computer simulations, exact trajectories, and the gravitational $N$-body problem". American Journal of Physics 72:9, pp. 1251-1257 (September 2004). Refereed Journal Publications 1. Wayne Hayes and Ken Jackson. "A Survey of Shadowing Methods for Numerical Solutions of Ordinary Differential Equations". Applied Numerical Mathematics 53, pp. 299-321 (2005). (doi:10.1016/j.apnum.2004.08.011) 2. Michael Roberts, Wayne Hayes, Brian R. Hunt, Stephen M. Mount, James A. Yorke. "Reducing storage requirements for biological sequence comparison." Bioinformatics 20:3363--3369 (Dec 2004). 3. Wayne Hayes and Ken Jackson, "Rigorous Shadowing of Numerical Solutions of Ordinary Differential Equations by Containment". SIAM J. of Numerical Analysis, 41:5 pp. 1948-1973 (2003). 4. Wayne Hayes. "Shadowing-based reliability decay in collisionless n-body simulations". Astrophysical Journal Letters 587:L59-L62 (2003). 5. Wayne Hayes. "Shadowing high-dimensional Hamiltonian systems: the gravitational N-body problem". Physics Review Letters 90:5 (2003) 6. Wayne Hayes and Scott Tremaine. "Fitting Selected Random Solar Systems to Titius-Bode Laws." Icarus 135, 549--557 (1998). 7. Bill Katz, Dan Driscoll, Kai Millyard, Bruce Waters, Mark Zalcik, Joe Adair, Andreas Gada, Wayne Hayes, Richard Kelsch, Richard McWaters, Richard Rokosz, John Zehethofer, Alex Fullerton, Ron Lyons, Marshall McCall. "Optical flashes in Perseus." Astrophysical Journal Letters, 307:L33-L37 (1986). 8. Wayne Hayes and Wayne Enright. "Robust defect control for continuous RK-methods with high-order interpolants". Submitted. 9. Carmen Young, Wayne Hayes, Ken Jackson. ``Rigorous shadowing of ODEs by containment: the general case''. Accepted to Discrete and Continious Dynamical Systems. 10. Michael Roberts, Wayne Hayes, Cevat Ustun, Brian Hunt, James Yorke, Paul Havlak. "Assembling the rat with extended and error corrected reads." Submitted. 11. Wayne Hayes and Kenneth R. Jackson. ``A Fast Shadowing Algorithm for High Dimensional ODE Systems''. Submitted. Refereed Conference Publications - Wayne B. Hayes & Kenneth R. Jackson. "Global error measures for the large gravi- tatonal N-body problem." Proceedings of the 12th "Kingston" Meeting on Theoretical Astrophysics: Computational Astrophysics. ASP Conference Series Vol. 123 (1997), D. A. Clarke and M. J. West, Eds. Halifax, Nova Scotia, Oct 1996. - Wayne Hayes and Mart L. Molle. "Solving Capture in Switched Two-Node Ethernets by Changing Only One Node." Proceedings of the 20th Annual Conference on Local Computer Networks, LCN '95, Oct 1995. Minneapolis, Minnesota, USA. Invited/Refereed Talks - Wayne Hayes. ``From Butterflies to Galaxies: Validating Simulations of Large Chaotic Systems''. Dept. of Electrical and Computer Engineering, University of California, Santa Barbara. 2005-Mar-4. - Wayne Hayes. ``From Butterflies to Galaxies: Validating Simulations of Large Chaotic Systems''. San Diego Supercomputer Centre and Department of Computer Science, UCSD. 2005-Feb-11. - Wayne Hayes and Kenneth Jackson. ``Rigorous Shadowing of numerical solutions to ordinary differential equations by containment.'' Joint Sherbrooke-Bishop's-CRM Colloquium Series in Analysis and Related Topics. Sherbrooke, Quebec, Canada, Feb 16--17, 2005. - Wayne Hayes. ``A shadowing-based timestep criterion for softened gravitational n-body simulations''. AIMS Fifth International Conference on Dynamical Systems and Differential Equations, June 16-19, 2004. California State Polytechnic University, Pomona, California. - Wayne Hayes, ``A shadowing-based timestep criterion for softened gravitational n-body simulations''. Dept. of Computer Science, University of California, Irvine. 2004-Mar-12. - Wayne Hayes, ``A shadowing-based timestep criterion for softened gravitational n-body simulations''. School of Science, University of Ontario Institute of Technology. 2004-Feb-16. - Ken Jackson and Wayne Hayes, ``Rigorous Shadowing of Numerical Solutions of Ordinary Differential Equations by Containment'', a 50 minute talk presented at {\em NUMDIFF 10}, a tri-annual conference on the numerical solution of differential and differential-algebraic equations, Halle, Germany, September, 2003. - Michael Roberts, James Yorke, Brian Hunt, Wayne Hayes, Aleksey Zimin, Cevat Ustun, Paul Havlak. "Improving Sequence Assemblies Using High- quality Overlaps" Third Annual RECOMB Satellite Meeting on DNA Sequencing Technologies and Computation} May 17-18, 2003, Stanford University. - Michael Roberts, James Yorke, Brian Hunt, Wayne Hayes, Aleksey Zimin, Cevat Ustun, Paul Havlak. "Improving Sequence Assemblies Using High- quality Overlaps" Poster at The Intelligent Systems for Molecular Biology (ISMB). Brisbase, Australia, June 29-July 3, 2003. - Wayne Hayes, ``A shadowing-based timestep criterion for softened gravitational n-body simulations''. Dept. of Computer Science, University of Guelph. 2002-May-2. - Wayne Hayes. "Rigorous Shadowing of Numerical Trajectories of Dynamical Systems". Informal Working Group on Validated Methods for ODEs and DAEs. Fields Institute, Sept. 10-14, 2001. - Wayne Hayes & Ken Jackson. "Rigorous shadowing of numerical trajectories of dynamical systems". Minisymposium on validated numerics, SciCADE 2001, Vancouver, B.C. July 2001. - Wayne Hayes. "Shadowing the gravitational N-body problem". Ontario Research Centre for Computer Algebra, University of Western Ontario. 4 April 2000. - Wayne Hayes. "Rigorous shadowing of numerical solutions of ODEs". Argonne National Labs. Chicago, Illinois. 4 Feb, 2000. Contributed Conference Talks - Wayne Hayes & Ken Jackson. "Rigorous shadowing of Numerical Solutions to Ordinary Differential Equations by Containment". Southern Ontario and Western New York Numerical Analysis Day, 29 Apr 1999, McMaster University, Hamilton, Ontario. - Wayne Hayes. "Can we trust numerical simulations of galaxy dynamics?" Galaxy Dynamics Conference, Rutgers University, 8-12 August 1998. - Wayne Hayes & Ken Jackson. "Rigorous Containment of Shadows of High-Dimensional Dynamical Systems". SIAM 1998 Annual Meeting, Toronto, Canada, July 13-17 1998. - Wayne Hayes. "A Fast Shadowing Algorithm for High Dimensional ODE Systems." Seminar, Department of Computer Science, University of Toronto, March 1996. - Wayne Hayes. "Shadowing the Large Gravitational N-body Problem." G2000 Seminar, Department of Astronomy, University of Toronto, January 1996. - Wayne Hayes & Kenneth R. Jackson. "A Fast Shadowing Algorithm for High Dimensional ODE Systems." Dynamical Numerical Analysis Conference, Georgia Tech, Atlanta, December 1995. - Wayne Hayes & Ken Jackson. "High-dimensional shadowing and the large gravitational N-body problem." Ontario Numerical Analysis Day, University of Waterloo, 1995. Technical Reports - Wayne Hayes & Kenneth R. Jackson. "A Fast Shadowing Algorithm for High Dimensional ODE Systems." (1995) Software - "libwayne: A portable, re-usable code library of data structures and algorithms for discrete and continuous systems". Available at http://www.cs.toronto.edu/"wayne/libwayne/. Experience July 2004--present: Assistant Professor, Dept. of Computer Science, University of California, Irvine. At U.C. Irvine, I am collaborating with astronomers such as James Bullock at UCI and John Dubinski at the University of Toronto to test whether their gravitational $n$-body simulations of galaxies and cosmological structure are shadowable. With my new graduate student I am also beginning to study the applications of parallel computing to Lattice Gauge Theory, which is a branch of quantum mechanics. Such studies need to be numerical since the strong dynamics of quarks and gluons is beyond the reach of the traditional perturbative methods of quantum field theory. Nov. 2002--present: Research Associate, Institute for Physical Sciences and Technology, University of Maryland. Genome assembly is the computational problem of re-assembling millions of pieces of a genome which has been chemically shattered for the purpose of sequencing. Although sequencing is extremely expensive (100M$ (U.S.) for the mouse, 58M$ for the rat), existing algorithms to assemble the sequences are computationally very crude. I am a member of the genome sequence assembly group under James Yorke at the University of Maryland, working in collaboration with Celera Genomics, Inc., The Institute for Genomic Research, and the Baylor College of Medicine to improve the most CPU-intensive step in sequence assembly. Compared to existing algorithms, ours produce a 100-fold decrease in runtime, while simultaneously achieving a 100-fold decrease in the error rate, resulting in a better, more-quickly produced draft genome. Further dramatic algorithmic improvements are likely to occur, and this is clearly an area where Computer Science can significantly contribute to the broader advancement of human knowledge. Our algorithms are inspired by (surprisingly) dynamical systems and point-set topology. Nov. 2002--Jul. 2003: Research Associate, Samuel Lunenfeld Research Insitute, Mount Sinai Hospital, Toronto. I completed a small protein folding project under Christopher Hogue utilizing a large-scale distributed computing platform called TraDES (http://bioinfo.mshri.on.ca/trades/index.html). Aug. 2001-2002: Post-Doctoral Fellow, Fields Institute for Research in Mathe- matical Sciences. During the Thematic Year on Numerical and Computational Challenges in Science and Engineering, I collaborated with W. Enright to produce several new robust high-order Runge-Kutta integrators with asymtotically correct defect estimates, resulting in a publication. I also visited James Yorke at the U. of Maryland to investigate computational challenges in gene sequencing, leading to my current position there; and discussed distributed environmental modelling with Z. Zlatev of the University of Denmark. As well, I continued to pursue extensions of both of my theses, resulting in 3 publications. Aug. 2000-July 2001 Software Engineer, Member of the Technical Staff, Altera Corporation. In the research and development group, I aided in the development of Altera's next-generation of programmable microchips. I worked with a group of about 10 highly mo- tivated M.Sc.- and Ph.D.-educated co-workers to continue development of complex heuristics to approximately solve several NP-complete optimization problems arising from fitting ar- bitrary circuits onto programmable logic devices. I observed first-hand how productive a well-managed software engineering group can be. 1996-2000: Lecturer (Part Time) During my PhD I prepared and taught the following University of Toronto Computer Science courses. CSC209H, Software Tools and Systems Programming in Unix and C (Spring 1998 & Fall 1996). Topics: Advanced Unix shell programming, Unix System Programming in C. In the final assignment, students wrote a Unix shell from scratch, complete with piping and I/O redirection. CSC270H, Fundamental Data Structures and Techniques (Summer & Spring 2000, Summer 1999). Topics: Graph Theory, Dynamic Programming, Simulation, Numeri- cal Methods, C, C++. I have also been a teaching assistant for at least 19 courses, including courses on introductory programming, computer organization, databases, operating systems, systems programming, data structures and algorithms, dynamic programming, programming languages, computer networks, symbolic and scientific computing, and numerical analysis. My teaching evaluations are typically above averge: 6 out of 7 when the departmental average was 5, and many of my students tend to write rave comments on the evaluations. 1999-2000: CollegeHire.com Qualifier: I interviewed and evaluated the technical knowl edge of at least 50 undergraduate candidates from the University of Toronto and Princeton University. Jan-Aug 1995: Software Engineer, Algorithmics, Inc. As a programmer who was also mathematically fluent, I facilitated communication between the financial engineers, who built customized risk models for financial derivatives, and the programmers responsible for implementing them. 1989-1993: Undergraduate Summer Research Assistant Under Prof. Mart Molle, I devised and wrote communications networks simulations and analyzed protocols. A resulting publication is listed below. 1990-1991: IBM Canada Toronto Lab. As a student intern for 16 months, I coded a Smalltalk library for an OS/2 database project, ported the build environment for the RISC/6000 optimizing compiler from CMS to Unix, and studied optimizing compiler tech- nology. 1989-1995: McLaughlin Planetarium. Wrote hypertext describing hundreds of images in a computerized question-and-answer display; lectured to the public about astronomy and ran and maintained automated shows in the main theatre. Academic Honours Popular article about my work in Physics Focus, 2003-Feb-27. Available at http://focus.aps.org/story/v11/st8 Ontario Graduate Scholarship ($12,000) 1997-98 academic year University of Toronto Open Fellowship ($11,000) 1996-97 academic year Professional Activities o Member of ACM, SIAM, AMS, AAS, CAS. o Spring 1999: Expert Witness, software source code theft. o 1993-2000 Computing Insights: Each summer, I lecture to gifted high-school students about chaos and fractals, describing algorithms for creating images such as fractal landscapes. o 1993-1999: Member of U. of T. Department of Computer Science Graduate Committee. In addition, I have been a member of the Computer Science Graduate Student Society, which organizes social activities for graduate students. o Referee for papers in the following journals: - Physics Letters A - Earth, Moon, and Planets. - Monthly Notices of the Royal Astronomical Society. - Journal of the Royal Astronomical Society of Canada. - 20th Annual Conference on Local Computer Networks Volunteer Activities 1995-2000: Organizer, Numerical Analysis Area Meeting. 1999-2000: Director, University of Toronto Outing Club. 1995-2000: Mentor for new Comp. Sci. graduate students. References available on request.