Last Update: October, 2000

Paper topics:

Immune System Modeling

Immune System Applications & Computer Security

Ecology and Artificial Life

Genetic Algorithms and Classifier Systems

Cancer as an Evolutionary System

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 (2000). Postscript

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 Bulletin of Mathematical Biology

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



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

Architecture for an Artificial Immune System. S. Hofmeyr and S. Forrest. Evolutionary Computation 7(1), Morgan-Kaufmann, San Francisco, CA, pp. 1289-1296 (1999). Abstract Postscript

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

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

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

"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

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).

The mutability of cancer genes. Maley, C.C., M. Oprea, and S. Forrest. Submitted to the Journal of Molecular Biology.

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

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

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