Abstract
Many algorithms in natural computing and computational biology are population-based: genetic algorithms evolve candidate solutions for optimization problems; artificial immune systems and learning classifier systems maintain populations of rules. Using such algorithms at very large population sizes (e.g., millions or billions) is computationally expensive. Here, we develop a methodology for implementing population-based models using weighted finite state machines (WFSMs) with exact rational weights. For populations that can be represented as weighted sets of strings, WFSMs can reduce memory use and runtime of population-based algorithms by orders of magnitude. We demonstrate the generality of our approach by constructing an immune-inspired anomaly detector for string data and an evolutionary algorithm that solves Boolean satisfiability problems. The WFSM approach allows repurposing of advanced algorithms developed for natural language processing, and should be applicable to other population-based algorithms such as learning classifier systems.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Allauzen, C., Riley, M., Schalkwyk, J., Skut, W., Mohri, M.: OpenFst: a general and efficient weighted finite-state transducer library. In: Holub, J., Zdarek, J. (eds.) CIAA 2007. LNCS, vol. 4783, pp. 11–23. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-76336-9_3
Baluja, S., Caruana, R.: Removing the genetics from the standard genetic algorithm. In: Machine Learning Proceedings 1995, pp. 38–46. Elsevier (1995)
Blum, C.: Ant colony optimization: introduction and recent trends. Phys. Life Rev. 2(4), 353–373 (2005). https://doi.org/10.1016/j.plrev.2005.10.001
Blum, C., Roli, A.: Metaheuristics in combinatorial optimization: overview and conceptual comparison. ACM Comput. Surv. 35(3), 268–308 (2003). https://doi.org/10.1145/937503.937505
Borisovsky, P., Eremeev, A.: Comparing evolutionary algorithms to the (1+1)-ea. Theoret. Comput. Sci. 403(1), 33–41 (2008). https://doi.org/10.1016/j.tcs.2008.03.008
Cheeseman, P.C., Kanefsky, B., Taylor, W.M., et al.: Where the really hard problems are. In: IJCAI, vol. 91, pp. 331–337 (1991)
D’haeseleer, P.: An immunological approach to change detection: theoretical results. In: Proceedings 9th IEEE Computer Security Foundations Workshop. IEEE Computer Society Press (1996). https://doi.org/10.1109/csfw.1996.503687
D’haeseleer, P., Forrest, S., Helman, P.: An immunological approach to change detection: algorithms, analysis and implications. In: Proceedings 1996 IEEE Symposium on Security and Privacy. IEEE Computer Society Press (1996). https://doi.org/10.1109/secpri.1996.502674
Dunning, T.: Statistical Identification of Language. Tech. Rep. MCCS 94-273, New Mexico State University (1994)
Eisner, J.: Simpler and more general minimization for weighted finite-state automata. In: Proceedings of the 2003 Human Language Technology Conference of the North American Chapter of the Association for Computational Linguistics, pp. 64–71 (2003). https://doi.org/10.3115/1073445.1073454
Elberfeld, M., Textor, J.: Efficient algorithms for string-based negative selection. In: Andrews, P.S., et al. (eds.) ICARIS 2009. LNCS, vol. 5666, pp. 109–121. Springer, Heidelberg (2009). https://doi.org/10.1007/978-3-642-03246-2_14
Elberfeld, M., Textor, J.: Negative selection algorithms on strings with efficient training and linear-time classification. Theor. Comput. Sci. 412, 534–542 (2011). https://doi.org/10.1016/j.tcs.2010.09.022
Forrest, S., Perelson, A., Allen, L., Cherukuri, R.: Self-nonself discrimination in a computer. In: Proceedings of 1994 IEEE Computer Society Symposium on Research in Security and Privacy. IEEE Computer Society Press (1994). https://doi.org/10.1109/risp.1994.296580
Gad, A.G.: Particle swarm optimization algorithm and its applications: a systematic review. Archiv. Comput. Methods Eng. 29(5), 2531–2561 (2022). https://doi.org/10.1007/s11831-021-09694-4
Boost. Boost C++ libraries. https://www.boost.org
Harik, G.R., Lobo, F.G., Goldberg, D.E.: The compact genetic algorithm. IEEE Trans. Evol. Comput. 3(4), 287–297 (1999). https://doi.org/10.1109/4235.797971
Hoos, H.H., Stützle, T.: Satlib: an online resource for research on sat. Sat 2000, 283–292 (2000)
Jansen, T.: Analyzing Evolutionary Algorithms: The Computer Science Perspective. Springer, Incorporated (2013). https://doi.org/10.1007/978-3-642-17339-4
Kirkpatrick, S., Selman, B.: Critical behavior in the satisfiability of random Boolean expressions. Science 264(5163), 1297–1301 (1994). https://doi.org/10.1126/science.264.5163.1297
Liśkiewicz, M., Textor, J.: Negative selection algorithms without generating detectors. In: Proceedings of Genetic and Evolutionary Computation Conference (GECCO 2010), pp. 1047–1054. ACM (2010). https://doi.org/10.1145/1830483.1830673
Manso, A., Correia, L.: Genetic algorithms using populations based on multisets. New Trends Artif. Intell. EPIA 2009, 53–64 (2009)
Martin, O.C., Monasson, R., Zecchina, R.: Statistical mechanics methods and phase transitions in optimization problems. Theoret. Comput. Sci. 265(1–2), 3–67 (2001). https://doi.org/10.1016/s0304-3975(01)00149-9
Mitchell, D., Selman, B., Levesque, H.: Hard and easy distributions of sat problems. In: Proceedings of the Tenth National Conference on Artificial Intelligence (AAAI 1992), pp. 459–465. AAAI Press (1992)
Mohri, M.: On some applications of finite-state automata theory to natural language processing. Nat. Lang. Eng. 2(1), 61–80 (1996). https://doi.org/10.1017/S135132499600126X
Mohri, M.: Minimization algorithms for sequential transducers. Theoret. Comput. Sci. 234(1–2), 177–201 (2000). https://doi.org/10.1016/S0304-3975(98)00115-7
Schoning, T.: A probabilistic algorithm for k-sat and constraint satisfaction problems. In: 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039). SFCS-99. IEEE Computer Society (1999). https://doi.org/10.1109/sffcs.1999.814612
Schröder, G., Textor, J.: Population-based algorithms built on weighted automata (implementation). Zenodo (2024). https://doi.org/10.5281/zenodo.12205008
Sisson, S.A., Fan, Y., Tanaka, M.M.: Sequential Monte Carlo without likelihoods. Proc. Natl. Acad. Sci. 104(6), 1760–1765 (Feb 2007). https://doi.org/10.1073/pnas.0607208104
Stibor, T., Mohr, P., Timmis, J., Eckert, C.: Is negative selection appropriate for anomaly detection? In: Proceedings of the 7th Annual Conference on Genetic and Evolutionary Computation. ACM (2005). https://doi.org/10.1145/1068009.1068061
Textor, J.: A comparative study of negative selection based anomaly detection in sequence data. In: Coello Coello, C.A., Greensmith, J., Krasnogor, N., Liò, P., Nicosia, G., Pavone, M. (eds.) ICARIS 2012. LNCS, vol. 7597, pp. 28–41. Springer, Heidelberg (2012). https://doi.org/10.1007/978-3-642-33757-4_3
Textor, J., Dannenberg, K., Liśkiewicz, M.: A generic finite automata based approach to implementing lymphocyte repertoire models. In: Proceedings of the 2014 Annual Conference on Genetic and Evolutionary Computation, pp. 129–136 (2014). https://doi.org/10.1145/2576768.2598331
Timmis, J., Hone, A., Stibor, T., Clark, E.: Theoretical advances in artificial immune systems. Theor. Comput. Sci. 403(1), 11–32 (2008). https://doi.org/10.1016/j.tcs.2008.02.011
Timmis, J., Knight, T., de Castro, L.N., Hart, E.: An Overview of Artificial Immune Systems, pp. 51–91. Springer, Heidelberg (2004). https://doi.org/10.1007/978-3-662-06369-9_4
Urbanowicz, R.J., Moore, J.H.: Learning classifier systems: a complete introduction, review, and roadmap. J. Artif. Evol. Appl. 2009, 1–25 (2009). https://doi.org/10.1155/2009/736398
Wortel, I.M., Keşmir, C., de Boer, R.J., Mandl, J.N., Textor, J.: Is T cell negative selection a learning algorithm? Cells 9(3), 690 (2020). https://doi.org/10.3390/cells9030690
Acknowledgments
JT and GS were supported by NWO grant VI.Vidi.192.084 (to JT).
Disclosure of Interests. The authors do not declare any conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Schröder, G., Wortel, I., Textor, J. (2024). Population-Based Algorithms Built on Weighted Automata. In: Affenzeller, M., et al. Parallel Problem Solving from Nature – PPSN XVIII. PPSN 2024. Lecture Notes in Computer Science, vol 15150. Springer, Cham. https://doi.org/10.1007/978-3-031-70071-2_20
Download citation
DOI: https://doi.org/10.1007/978-3-031-70071-2_20
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-70070-5
Online ISBN: 978-3-031-70071-2
eBook Packages: Computer ScienceComputer Science (R0)