Abstract
Multiagent systems and data mining techniques are being frequently used in genome projects, especially regarding the annotation process (annotation pipeline). This paper discusses annotation-related problems where agent-based and/or distributed data mining has been successfully employed.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Baldi, P., Søren, B.: Bioinformatics: the machine learning approach, 351 p. MIT Press, Cambridge (1998)
Batista, G.E.A.P.A., Monard, M.C., Bazzan, A.L.C.: Improving rule induction precision for automated annotation by balancing skewed data sets. In: López, J.A., Benfenati, E., Dubitzky, W. (eds.) KELSI 2004. LNCS, vol. 3303, pp. 20–32. Springer, Heidelberg (2004)
Bazzan, A.L.C., Ceroni da Silva, S., Engel, P.M., Schroeder, L.F.: Automatic annotation of keywords for proteins related to mycoplasmataceae using machine learning techniques. Bioinformatics 18(S2), S1–S9 (2002)
Bazzan, A.L.C., Duarte, R., Pitinga, A.N., Schroeder, L.F., Silva, S.C., Souto, F.A.: ATUCG-an agent-based environment for automatic annotation of genomes. International Journal of Cooperative Information Systems 12(2), 241–273 (2003)
Bazzan, A.L.C., Santos, C.T.: Selection of data sets of motifs as attributes in the process of automating the annotation of proteins’ keywords in bioinformatics. In: Setubal, J.C., Verjovski-Almeida, S. (eds.) BSB 2005. LNCS (LNBI), vol. 3594, pp. 230–233. Springer, Heidelberg (2005)
BenHur, A., Brutlag, D.: Sequence motifs: highly predictive features of protein function. In: Feature extraction, foundations and applications. Springer, Heidelberg (2005)
Bryson, K., Luck, M., Joy, M., Jones, D.: Applying agents to bioinformatics in GeneWeaver. In: Klusch, M., Kerschberg, L. (eds.) CIA 2000. LNCS, vol. 1860, pp. 60–71. Springer, Heidelberg (2000)
Cai, C.Z., Han, L.Y., Ji, Z.L., Chen, Y.Z.: Enzyme family classification by support vector machines. Proteins: Structure, Function, and Bioinformatics 55(1), 66–76 (2004)
Cao, L., Luo, C., Zhang, C.: Agent-mining interaction: An emerging area. In: Gorodetsky, V., Zhang, C., Skormin, V.A., Cao, L. (eds.) AIS-ADM 2007. LNCS, vol. 4476, pp. 60–73. Springer, Heidelberg (2007)
Craven, M.W., Shavlik, J.W.: Machine learning approaches to gene recognition. IEEE Expert 9(2), 2–10 (1994)
Decker, K., Zheng, X., Schmidt, C.: A multi-agent system for automated genomic annotation. In: Proc. of the Int. Conf. Autonomous Agents, Montreal. ACM Press, New York (2001)
des Jardins, M., Karp, P.D., Krummenacker, M., Lee, T.J., Ouzounis, C.A.: Prediction of enzyme classification from protein sequence without the use of sequence similarity. In: Proceedings of the International Conference on Intelligent Systems Molecular Biology, pp. 92–99 (1997)
dos Santos, C.T., Bazzan, A.L.C.: Integrating knowledge through cooperative negotiation – a case study in bioinformatics. In: Gorodetsky, V., Liu, J., Skormin, V.A. (eds.) AIS-ADM 2005. LNCS (LNAI), vol. 3505, pp. 277–288. Springer, Heidelberg (2005)
dos Santos, C.T., Bazzan, A.L.C., Lemke, N.: Automatic classification of enzyme family in protein annotation. In: Proc. of the Brazilian Symposium on Bioinformatics 2009. Springer, Heidelberg (2009)
dos Santos, D.S., Bazzan, A.L.C.: A bee inspired clustering algorithm. In: Proc. of the 2009 IEEE Swarm Intelligence Symposium, Nashville, pp. 160–167. IEEE, Los Alamitos (2009)
dos Santos, D.S., de Oliveira, D., Bazzan, A.L.C.: A multiagent, multiobjective clustering algorithm. In: Cao, L. (ed.) Data Mining and Multiagent Integration. Springer, Heidelberg (2009)
Faceli, K., Carvalho, A.C.P.L.F., Souto, M.C.P.: Multi-objective clustering ensemble. In: Proceedings of the Sixth International Conference on Hybrid Intelligent Systems (HIS 2006), Washington, DC, USA, p. 51. IEEE Computer Society, Los Alamitos (2006)
Kretschmann, E., Fleischmann, W., Apweiler, R.: Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics 17, 920–926 (2001)
Schroeder, L.F., Bazzan, A.L.C.: A multi-agent system to facilitate knowledge discovery: an application to bioinformatics. In: Proceedings of the Workshop on Bioinformatics and Multi-Agent Systems (BIXMAS 2002), Bologna, Italy, pp. 44–50 (2002)
Setúbal, J.C., Meidanis, J.: Introduction to Computational Molecular Biology. PWS Publishing Company (1997)
Weinert, W.R., Lopes, H.S.: Neural networks for protein classification. Applied Bioinformatics 3(1), 41–48 (2004)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bazzan, A.L.C. (2009). Agents and Data Mining in Bioinformatics: Joining Data Gathering and Automatic Annotation with Classification and Distributed Clustering. In: Cao, L., Gorodetsky, V., Liu, J., Weiss, G., Yu, P.S. (eds) Agents and Data Mining Interaction. ADMI 2009. Lecture Notes in Computer Science(), vol 5680. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-03603-3_1
Download citation
DOI: https://doi.org/10.1007/978-3-642-03603-3_1
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-03602-6
Online ISBN: 978-3-642-03603-3
eBook Packages: Computer ScienceComputer Science (R0)