Immune System Modeling

"Engineering an immune system." S. Forrest and S. Hofmeyr. Graft Vol. 4:5 pp. 5-9 (2001).Postscript PDF

"Effective Feedback in the Immune System" C. Warrander, S. Forrest and L. Legal. In Genetic and Evolutionary Computation Conference Workship Program, Morgan Kaufman, pp. 329 - 332 (2001). Postscript PDF

"Immunology as information processing." S. Forrest and S.A. Hofmeyr. In Design Principles for the Immune System and Other Distributed Autonomous Systems, edited by L.A. Segel and I. Cohen. Santa Fe Institute Studies in the Sciences of Complexity. New York: Oxford University Press (2001). Postscript PDF

"Immunity by Design: An Artificial Immune System." S. Hofmeyr and S. Forrest. Proceedings of the Genetic and Evolutionary Computation Conference (GECCO), Morgan-Kaufmann, San Francisco, CA, pp. 1289-1296 (1999). Abstract Postscript PDF

"How the immune system generates diversity: Pathogen space coverage with random and evolved antibody libraries." M. Oprea and S. Forrest. 1999 Genetic and Evolutionary Computation Conference (GECCO) July 1999. Abstract Postscript PDF

"Variable efficacy of repeated annual influenza vaccination." D.J. Smith, S. Forrest and D.H. Ackley, and A.S.Perelson . Proceedings of the National Academy of Sciences 96:14001-14006 (1999). Abstract Postscript PDF

"Using lazy evaluation to simulate realistic-size repertoires in models of the immune system." D.J. Smith, S. Forrest and D.H. Ackley, and A.S.Perelson. Bulletin of Mathematical Biology Vol. 60, pp. 647-658 (1998). Abstract Postscript PDF

"Simulated evolution of antibody gene libraries under pathogen selection." M. Oprea and S. Forrest. 1998 IEEE International Conference on Systems, Man and Cybernetics. Abstract Postscript PDF

"Modeling the effect of prior infection on vaccine efficacy." D.J. Smith, S. Forrest and D.H. Ackley, and A.S.Perelson. In Artificial Immune systems and their Applications, Springer-Verlag, Berlin Germany (1998). Also presented at the 1997 IEEE International conference On Systems, man, and cybernetics. October, 1997. Abstract Postscript PDF

"Deriving shape-space parameters from immunological data for a model of cross-reactive memory." D.J. Smith, S. Forrest, R.R. Hightower, and A.S. Perelson . Journal of Theoretical Biology Vol.189, pp.141-150 (1997). Abstract Postscript PDF

"Evolution (and learning) of v-region genes." A. Perelson, R. Hightower, and S. Forrest. Research in Immunology Vol. 147, pp. 202-208 (1996). Abstract Postscript PDF

"The Evolution of Emergent Organization in Immune System Gene Libraries." R. Hightower, S. Forrest, and A.S. Perelson. In L.J. Eshelman (Ed.) Proc. of the Sixth Int. Conf. on Genetic Algorithms, Morgan Kaufmann, San Francisco, CA. Postscript PDF

"The Baldwin effect in the immune system: learning by somatic hypermutation." R. Hightower, S. Forrest, and A.S. Perelson. In R.K. Belew and M. Mitchell, (eds.), Adaptive Individuals in Evolving Populations, Addison-Wesley ,Reading, MA, pp. 159-167 (1996). Postscript PDF

Immune System Applications and Computer Security

"Revisiting LISYS: Parameters and Normal Behavior." J. Balthrop, S. Forrest, and M. Glickman.. Proceedings of the 2002 Congress on Evolutionary Computation (in press). Postscript PDF

"Architecture for an Artificial Immune System." S. Hofmeyr and S. Forrest. Evolutionary Computation 7(1), Morgan-Kaufmann, San Francisco, CA, pp. 1289-1296 (2000). Abstract Postscript PDF

"Automated Response Using System-Call Delays." A. Somayaji and S. Forrest. Usenix 2000. Abstract Postscript PDF

"Novelty Detection in Time Series Data using Ideas from Immunology." D. Dasgupta and S. Forrest. In Proceedings of The International Conference on Intelligent Systems (1999). Abstract Postscript PDF

"Detecting intrusions using system calls: Alternative data models." C. Warrender, S. Forrest, B. Pearlmutter. 1999 IEEE Symposium on security and Privacy (1999). Abstract Postscript PDF

"Artificial Immune Systems in Industrial Applications." D. Dasgupta and S. Forrest. Accepted for presentation at the International conference on Intelligent Processing and Manufacturing Material (IPMM). Honolulu, HI (July 10-14, 1999). Postscript PDF

"Intrusion Detection Using Sequences of System Calls." S. Hofmeyr, S. Forrest, and A. Somayaji Journal of Computer Security Vol. 6, pp. 151-180 (1998). Abstract Postscript PDF

"Principles of a Computer Immune System." A. Somayaji, S. Hofmeyr, and S. Forrest. 1997 New Security Paradigms Workshop pp. 75-82 (1998). Abstract Postscript PDF

"A Distributed Approach to Anomaly Detection." P. D'haeseleer, S. Forrest, and P. Helman (1997). Abstract Postscript PDF

"Computer Immunology." (DRAFT) S. Forrest, S. Hofmeyr, and A. Somayaji. Communications of the ACM Vol. 40, No. 10, pp. 88-96 (1997). Postscript PDF

"Building Diverse Computer Systems." S. Forrest, A. Somayaji, and D. Ackley. In Proceedings of the Sixth Workshop on Hot Topics in Operating Systems (1997). Abstract Postscript PDF

"An Immunological Approach to Change Detection: Algorithms, Analysis, and Implications."P. D'haeseleer, S. Forrest, and P. Helman. In Proceedings of the 1996 IEEE Symposium on Computer Security and Privacy (1996). Abstract Postscript PDF

"A Sense of Self for Unix Processes." S. Forrest, S. A. Hofmeyr, A. Somayaji, and T. A. Longstaff. In Proceedings of 1996 IEEE Symposium on Computer Security and Privacy (1996). Abstract Postscript PDF

"Self-Nonself Discrimination in a Computer." S. Forrest, A.S. Perelson, L. Allen, R. and Cherukuri. In Proceedings of the 1994 IEEE Symposium on Research in Security and Privacy, Los Alamitos, CA: IEEE Computer Society Press (1994). Abstract Postscript PDF

Ecology and Artificial Life

"Book review of The Computational Beauty of Nature by G. Flake". M. Moses and S. Forrest. Artificial Intelligence. 128:239-242 (2001).Postscript PDF

"John Holland's invisible hand: An artificial immune system." S. Forrest, and S. Hofmeyr. Presented at the Festschrift held in honor of John Holland, University of Michigan (1999). Abstract Postscript PDF

"The ecology of Echo." P. Hraber, T. Jones, and S. Forrest. Artificial Life Vol. 3, No. 3, pp. 165-190 (1994). Abstract Postscript PDF

"Modeling complex adaptive systems with Echo." S. Forrest and T. Jones. In Complex Systems: Mechanism of Adaptation, R.J. Stonier and X.H. Yu (eds.), Amsterdam, The Netherlands: IOS Press, pp. 3-21 (1994). Abstract Postscript PDF

Genetic Algorithms and Classifier Systems

Genetic Algorithms for Finding Polynomial Orderings Jurgen Giesl, Fernando Esponda, and Stephanie Forrest. TR-CS-2001-26 University of New Mexico, Albuquerque, NM (2001) Postscript PDF

"Fitness Landscapes: Royal Road Functions." M. Mitchell and S. Forrest. In Back, Fogel, and Michalewicx (Eds.) Handbook of Evolutionary Computation. Institute of Physics Publishing, Phiuladelphia and Bristol UK, B2.7:1-25 (1997). Postscript PDF

"Genetic Algorithms" S. Forrest. Computing Surveys Vol. 28:1, pp. 77-80 (1996). Postscript PDF

"Genetic operators for the DNA fragment-assembly problem." R. Parsons, S. Forrest, and C. Burks. Machine Learning Vol. 21:1/2, pp. 11-33 (1995). Abstract Postscript PDF

"Fitness Distance Correlation as a Measure of Problem Difficulty for Genetic Algorithms." T. Jones and S. Forrest. In L.J. Eshelman (Ed.) Proc. of the Sixth Int. Conf. on Genetic Algorithms Morgan Kaufmann, San Francisco, CA, pp. 184-192 (1995). Abstract Postscript PDF

"Genetic algorithms and artificial life." M. Mitchell and S. Forrest. Artificial Life, Vol. 1, No. 3 (1994), pp. 267-289. Reprinted in C. G. Langton (Ed.) Artificial Life: an Overview, MIT Press, Cambridge, MA (1995). Abstract Postscript PDF

"When will a genetic algorithm outperform hill climbing?." M. Mitchell, J.H. Holland, and S. Forrest. In J.D. Cowan, G. Tesauro, and J. Alspector, (eds.), Advances in Neural Information Processing Systems , Vol. 6, San Mateo, CA: Morgan Kaufmann (1994). Postscript PDF

"Genetic algorithms: Principles of adaptation applied to computation." S. Forrest. Science, Vol. 261, Aug. 1993, pp. 872-878. Science Reprints

"Using genetic algorithms to explore pattern recognition in the immune system." S. Forrest, B. Javornik, R.E. Smith, and A.S. Perelson. Evolutionary Computation, Vol. 1, No. 3 (1993), pp. 191-211. Abstract Postscript PDF

"What makes a problem hard for a genetic algorithm? Some anomalous results and their explanation." S. Forrest and M. Mitchell. Machine Learning, Vol. 13, No. 2/3 (1993).

"Towards a stronger building-blocks hypothesis: Effects of relative building-block fitness on GA performance." S. Forrest and M. Mitchell. In Proceedings of a Workshop on Foundations of Genetic Algorithms, Los Altos, CA: Morgan Kaufmann (1993).

"Genetic algorithms for DNA sequence assembly." R. Parsons, S. Forrest, and C. Burks. In L. Hunter, et al., (eds.), Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, Menlo Park, CA: AAAI/MIT Press (1993).

"Searching for diverse, cooperative populations with genetic algorithms." R.E. Smith, S. Forrest, and A.S. Perelson. Evolutionary Computation, Vol. 1, No. 2, pp. 127-149 (1993). Abstract Postscript PDF

"The royal road for genetic algorithms: Fitness landscapes and GA performance." M. Mitchell, S. Forrest, and J.H. Holland. In Proceedings of the First European Conference on Artificial Life, Cambridge, MA: MIT Press (1992).

"Using genetic algorithms for controller design: Simultaneous stabilization and eigenvalue placement in a region." W.E. Schmitendorf, O. Shaw, R. Benson, and S. Forrest. In Proceedings of AIAA Guidance Navigation and Control Conference, Hilton Head, SC, Aug. 1992.

"Genetic algorithms, nonlinear dynamical systems, and global stability models." S. Forrest and G. Mayer-Kress. In L. Davis, (ed.), The Handbook of Genetic Algorithms, New York, NY: Van Nostrand Reinhold (1991).

Cancer as an Evolutionary System

"Reconstructing the evolutionary history of neoplastic cells." C. C. Maley, F. Esponda, S. Forrest, L. Prevo, and B. J. Reid. Abstract presented at the conference on Oncogene 2000: Evolution of the Cancer Cell. Salk Institute, San Diego, CA (June, 2000). Abstract (.ps) Abstract (.pdf)

"Exploring the relationship between neutral and selective mutations in cancer." Maley, C.C. and S. Forrest. 2000. In Artificial Life. In press.Postscript PDF

"Modeling the role of neutral and selective mutations in cancer."  Maley, C.C. and S. Forrest. In: Artificial Life 7. M. Bedau, J. McCaskill, N. Packard, and S. Rasmussen (eds.).  Cambridge, MA:   MIT Press.  pp. 395-404. Postscript PDF