Edwin de Jong
Edwin de Jong is a former member of the ADA group.
Gene Interaction Networks
Within bio-informatics, my research focus is on inferring networks of interactions between genes from data. A major source of data in this is micro-array gene-expression data. I have compared a number of different interaction measures, and evaluated their efficacy in extracting gene expression networks. A central finding is that while there is variability between the different measures, there also exists substantial variability between the various interaction databases. Furthermore, for a given interaction measure and data source, different types of interactions can be extracted with differing accuracy. These findings suggest that different types of interactions may benefit from different sources of data. An interesting research question now therefore is which data sources are most relevant for different types of genetic interactions.

Modularity and Hierarchy
If the design of complex systems is viewed as a process of arranging large numbers of primitive elements in a specific manner, then the space of possible designs is prohibitively large. However, if some choices concerning aspects of a design can be made independent of other choices, then the required size of the effective search space can be greatly reduced by recursively combining such independently made choices, resulting in a hierarchical structure. A substantial reduction is still possible if choices are not independent, but if the dependencies are merely reduced compared to the case where each choice depends on all other choices. Problems exhibiting this property are called modular, and the principle of modularity is seen in a wide variety of design processes. I am interested in seeing how this principle can be achieved by means of an automatic search process.

Edwin is a post-doctoral researcher at the ADA group since 2005.

Selected Bookchapters

2007
de Jong, E.D. & Bucci, A. Objective Set Compression, Chapter of: J. Knowles, D. Corne, K. Deb & D. Raj (eds.) Multiobjective Problem Solving from Nature: From Concepts to Applications, Springer, Berlin, 2007.
Bosman, P.A.N & de Jong, E.D. Adaptation of a Success Story in GAs: Estimation-of-Distribution Algorithms for Tree-based Optimization Problems, Chapter of: Yang, A. & Shan, Y. (eds.) Success in Evolutionary Computation, Springer Verlag, Berlin, 2007.

Selected Refereed Publications

2007
de Jong, E.D., Franke, L. & Siebes, A. On the Measurement of Genetic Interactions. In: Proceedings of the 3rd international symposium on Computational Life Science (CompLife'07), 2007.
van de Koppel, E., Slavkov, I., Astrahantseff, K., Schramm, A., Schulte, J., Vandesompele, J., de Jong, E., Dzeroski, S., Knobbe, A. Knowledge Discovery in Neuroblastoma-related Biological Data. In: Data Mining in Functional Genomics and Proteomics Workshop (DMFGP'07), pp 45-56, 2007.
Yo, T.-S. & de Jong, E.D. A comparison of evaluation methods in coevolution. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'07), pp 479-487, 2007.
de Jong, E.D. Objective Fitness Correlation. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'07), pp 440-447, 2007. (Best paper award, Coevolution track)
Wiering, M.A. & de Jong, E.D. Computing Optimal Stationary Policies for Multi-Objective Markov Decision Processes. In: Proceedings of the IEEE International Symposium on Approximate Dynamic Programming and Reinforcement Learning (ADPRL'07), 2007.
de Jong, E.D. A Monotonic Archive for Pareto-Coevolution. In: Evolutionary Computation, vol.15(1), pp 61-93, MIT Press, 2007.
2006
de Jong, E.D. & Bucci, A. DECA: Dimension Extracting Coevolutionary Algorithm. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'06), 2006.
Oliehoek, F.A., de Jong, E.D. & Vlassis, N. The Parallel Nash Memory for Asymmetric Games. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'06), 2006.
Bosman, P.A.N. & de Jong, E.D. Combining gradient techniques for numerical multi-objective evolutionary optimization. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'06), 2006.
Snijders, P., de Jong, E.D., de Boer, B. & Weissing, F. Multi-Objective Diversity Maintenance. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'06), 2006.
de Back, W., de Jong, E.D. & Wiering, M.A. Red Queen dynamics in a predator-prey ecosystem. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO'06), 2006.
Franke, L., van Bakel, H., Fokkens, L., de Jong, E.D., Egmont-Petersen, M. & Wijmenga, C. Gene Networks and Gene Prioritization. In: American Journal of Human Genetics, vol.78(), pp 1011-1025, 2006.
de Jong, E.D., Franke, L. & Siebes, A. A comparison of gene interaction measures. In: Proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB'06), 2006.
de Jong, E.D. & Siebes, A. Evaluation of a Gene Network Extraction Method on Synthetic Data. In: Proceedings of the International Symposium on Networks in Biology (ISNB'06), 2006.
van Diggelen, J., de Jong, E.D. & Wiering, M.A. Strategies for Ontology Negotiation: Finding the Right Level of Generality. In: Proceedings of the International Workshop on Agent Communication at AAMAS'06 (IWAC'06), 2006.
Zwanepol Klinkmeijer, L. J., de Jong, E.D. & Wiering, M.A. A serial population genetic algorithm for dynamic optimization problems. In: Proceedings of the Annual Machine Learning Conference of Belgium and The Netherlands (BeNeLearn'06), 2006.

Selected Unrefereed Publications

2007
de Jong, E.D. & Bucci, A. Objective Set Compression, Chapter of: J. Knowles, D. Corne, K. Deb & D. Raj (eds.) Multiobjective Problem Solving from Nature: From Concepts to Applications, Springer, Berlin, 2007.
Bosman, P.A.N & de Jong, E.D. Adaptation of a Success Story in GAs: Estimation-of-Distribution Algorithms for Tree-based Optimization Problems, Chapter of: Yang, A. & Shan, Y. (eds.) Success in Evolutionary Computation, Springer Verlag, Berlin, 2007.