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Ofer M. Shir –List of Publications 1. Cohen, H., Shir, O.M., Yu, Y., Hou, W., Sun, S., Han, T., Amir, R.: Genetic background and environmental conditions drive metabolic variation in wild type and transgenic soybean (Glycine max) seeds. Plant, Cell & Environment doi: 10.1111/pce.12748 (2016) 2. Gal, M., Bloch, I., Shechter, N., Romanenko, O., Shir, O.M.: Efficient Isothermal Titration Calorimetry Technique Identifies Direct Interaction of Small Molecule Inhibitors with the Target Protein. Combinatorial Chemistry and High Throughput Screening 19(1) (2016) 4-13 3. Nanduri, A., Shir, O.M., Donovan, A., Ho, T.-S., Rabitz, H.: Exploring the complexity of quantum control optimization trajectories. Physical Chemistry Chemical Physics 17(1) (2015) 334—347. 4. Shir, O.M., Roslund, J., Whitley, D., Rabitz, H.: Efficient Retrieval of Landscape Hessian: Forced Optimal Covariance Adaptive Learning. Physical Review E 89(6) (2014) 063306 5. Shir, O.M., Roslund, J., Leghtas, Z., Rabitz, H.: Quantum Control Experiments as a Testbed for Evolutionary Multi-Objective Algorithms. Genetic Programming and Evolvable Machines 13(4) (2012) 445—491 6. Shir, O.M.: Niching in Evolutionary Algorithms. In: Handbook of Natural Computing: Theory, Experiments, and Applications. Springer-Verlag, Berlin-Heidelberg, Germany (2012) 1035—1069 7. Roslund, J., Shir, O.M., Dogariu, A., Miles, R., Rabitz, H.: Control of Nirtomethane Photoionization Efficiency with Shaped Femtosecond Pulses. The Journal of Chemical Physics 134(15) (2011) 154301 8. Cabrera, R., Shir, O.M., Wu, R., Rabitz, H.: Fidelity Between Unitary Operators and the Generation of Gates, Robust Against Off-Resonance Perturbations. Journal of Physics A: Mathematical and Theoretical 44(9) (2011) 095302 9. Laforge, F.O., Roslund, J., Shir, O.M., Rabitz, H.: Multiobjective Adaptive Feedback Control of Two-Photon Absorption Coupled with Propagation through a Dispersive Medium. Physical Review A 84(1) (2011) 013401 10. Rouzée, A., Ghafur, O., Vidma, K., Gijsbertsen, A., Shir, O.M., Bäck, T., Meijer, A., van der Zande, W.J., Parker, D., Vrakking, M.J.J.: Evolutionary Optimization of Rotational Population Transfer. Physical Review A (Atomic, Molecular, and Optical Physics) 84(3) (2011) 033415 11. Shir, O.M., Emmerich, M., Bäck, T.: Adaptive Niche-Radii and Niche-Shapes Approaches for Niching with the CMA-ES. Evolutionary Computation 18(1) (2010) 97– 126 12. Shir, O.M., Bäck, T.: Niching Methods: Speciation Theory Applied for Multimodal Function Optimization. In: Algorithmic BioProcesses. Springer-Verlag, Berlin Heidelberg, Germany (2009) 705–730 13. Roslund, J., Shir, O.M., Bäck, T., Rabitz, H.: Accelerated Optimization and Automated Discovery with Covariance Matrix Adaptation for Experimental Quantum Control. Physical Review A (Atomic, Molecular, and Optical Physics) 80(4) (2009) 043415 14. Shir, O.M., Beltrani, V., Bäck, T., Rabitz, H., Vrakking, M.J.: On the Diversity of Multiple Optimal Controls for Quantum Systems. Journal of Physics B: Atomic, Molecular and Optical Physics 41(7) (2008) 074021 15. Shir, O.M., Bäck, T.: Niching with Derandomized Evolution Strategies in Artificial and Real-World Landscapes. Natural Computing: An International Journal 8(1) (2009) 171– 196 16. Bäck, T., Emmerich, M., Shir, O.M.: Evolutionary Algorithms for Real-World Applications [Application Notes]. Computational Intelligence Magazine IEEE 3(1) (2008) 64-67 17. Shuang, F., Zhou, M., Pechen, A., Wu, R., Shir, O.M., Rabitz, H.: Control of Quantum Dynamics by Optimized Measurements. Physical Review A (Atomic, Molecular, and Optical Physics) 78(6) (2008) 063422 18. Siedschlag, C., Shir, O.M., Bäck, T., Vrakking, M.J.J.: Evolutionary Algorithms in the Optimization of Dynamic Molecular Alignment. Optics Communications 264 (2006) 511–518 Peer-Reviewed Computer Science Conference Proceedings: 19. Shir, O.M., Roslund, J., Yehudayoff, A.: On the Capacity of Evolution Strategies to Statistically Learn the Landscape. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2016, New York, NY, USA, ACM Press (2016) 151– 152 20. Shir, O.M.: Multilevel Evolution Strategies for Multigrid Problems. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2016, New York, NY, USA, ACM Press (2016) 33–34 21. Shir, O.M., Chen, Sh., Amid, D., Margalit, O., Masin, M., Anaby-Tavor, A., Boaz, D.: Pareto Landscapes Analyses via Graph-Based Modeling for Interactive DecisionMaking. Advances in Intelligent Systems and Computing volume 288 (EVOLVE-2014), Springer (2014) 97-113 22. Shir, O.M., Moor, D., Chen, Sh., Amid, D., Boaz, D., Anaby-Tavor, A.: Pareto Optimization and Tradeoff Analysis Applied to Meta-Learning of Multiple Simulation Criteria. In: Proceedings of the 2013 Winter Simulation Conference (INFORMS WSC2013), IEEE (2013) 89-100 23. Chen, Sh., Amid, D., Shir, O.M., Boaz, D., Schreck, T., Limonad, L.: Self-Organizing Maps for Multi-Objective Pareto Frontiers. In: Proceedings of the Pacific Visualization Symposium, PacificVis-2013, IEEE (2013) 153-160 24. Zadorojniy, A., Masin, M., Greenberg, L., Shir, O.M., Zeidner, L.: Algorithms for Finding Maximum Diversity of Design Variables in Multi-Objective Optimization. In: Conference on Systems Engineering Research. Volume 8 of Procedia Computer Science., Elsevier (2012) 171-176 25. Shir, O.M., Roslund, J., Rabitz, H.: Forced Optimal Covariance Adaptive Learning: Modified CMA-ES for Efficient Hessian Determination. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2010, New York, NY, USA, ACM Press (2010) 421–422 26. Klinkenberg, J.W., Emmerich, M., Deutz, A., Shir, O.M., Bäck, T.: A Reduced-Cost SMS-EMOA Using Kriging, Self-Adaptation, and Parallelization. In: Multiple Criteria Decision Making for Sustainable Energy and Transportation Systems: Volume 634 of Lecture Notes in Economics and Mathematical Systems., Springer Berlin Heidelberg (2010) 301—311 27. Shir, O.M., Roslund, J., Rabitz, H.: Evolutionary Multi-Objective Quantum Control Experiments with the Covariance Matrix Adaptation. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2009, New York, NY, USA, ACM Press (2009) 659–666 28. Shir, O.M., Preuss, M., Naujoks, B., Emmerich, M.: Enhancing Decision Space Diversity in Evolutionary Multiobjective Algorithms. In: Proceedings of Evolutionary Multi-Criterion Optimization: Fifth International Conference (EMO 2009). Volume 5467 of Lecture Notes in Computer Science., Springer (2009) 95–109 29. van der Goes, V., Shir, O.M., Bäck, T.: Niche Radius Adaptation with Asymmetric Sharing. In: Parallel Problem Solving from Nature - PPSN X. Volume 5199 of Lecture Notes in Computer Science., Springer (2008) 195–204 30. Li, R., Eggermont, J., Shir, O.M., Emmerich, M., Bäck, T., Dijkstra, J., Reiber, J.: Mixed-Integer Evolution Strategies with Dynamic Niching. In: Parallel Problem Solving from Nature - PPSN X. Volume 5199 of Lecture Notes in Computer Science., Springer (2008) 246–255 31. Shir, O.M., Roslund, J., Bäck, T., Rabitz, H.: Performance Analysis of Derandomized Evolution Strategies in Quantum Control Experiments. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2008, New York, NY, USA, ACM Press (2008) 519–526 32. Shir, O.M., Bäck, T., Rabitz, H., Vrakking, M.J.: On the Evolution of Laser Pulses under a Dynamic Quantum Control Environment. In: Proceedings of the 2008 IEEE World Congress on Computational Intelligence (WCCICEC), IEEE Computational Intelligence Society (2008) 2127–2134 33. Shir, O.M., Emmerich, M., Bäck, T.: Self-Adaptive Niching CMA-ES with Mahalanobis Metric. In: Proceedings of the 2007 IEEE Congress on Evolutionary Computation (CEC), IEEE Computational Intelligence Society (2007) 820–827 34. Shir, O.M., Emmerich, M., Bäck, T., Vrakking, M.J.: The Application of Evolutionary Multi-Criteria Optimization to Dynamic Molecular Alignment. In: Proceedings of the 2007 IEEE Congress on Evolutionary Computation (CEC), IEEE Computational Intelligence Society (2007) 4108–4115 35. Shir, O.M., Kok, J.N., Vrakking, M.J., Bäck, T.: Gaining Insight into Laser Pulse Shaping by Evolution Strategies. In: Proceedings of IWINAC-2007. Volume 4527 of Lecture Notes in Computer Science., Springer (2007) 467–477 36. Shir, O.M., Vrakking, M.J., Bäck, T.: On the Scalability of Evolution Strategies in the Optimization of Dynamic Molecular Alignment. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2007, New York, NY, USA, ACM Press (2007) 2266–2266 37. Shir, O.M., Bäck, T.: The Second Harmonic Generation Case Study as a Gateway for ES to Quantum Control Problems. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2007, New York, NY, USA, ACM Press (2007) 713– 721 38. Shir, O.M., Bäck, T.: Performance Analysis of Niching Algorithms Based on Derandomized ES Variants. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2007, New York, NY, USA, ACM Press (2007) 705– 712 39. Shir, O.M., Emmerich, M., Bäck, T., Vrakking, M.J.: Conceptual Designs in Laser Pulse Shaping Obtained by Niching in Evolution Strategies. In: Evolutionary and Deterministic Methods for Design, Optimization and Control. A Series of Handbooks on Theory and Engineering Applications of Computational Methods, CIMNE (2008) 152–157 40. Shir, O.M., Raz, V., Dirks, R.W., Bäck, T.: Classification of Cell Fates with Support Vector Machine Learning. In: Proceedings of EvoBIO 2007. Volume 4447 of Lecture Notes in Computer Science., Springer (2007) 258–269 41. Shir, O.M., Kok, J.N., Bäck, T., Vrakking, M.J.: Learning the Complete-Basis-Functions Parameterization for the Optimization of Dynamic Molecular Alignment by ES. In: Proceedings of IDEAL-2006. Volume 4224 of Lecture Notes in Computer Science., Springer (2006) 410–418 42. Shir, O.M., Bäck, T.: Niche Radius Adaptation in the CMA-ES Niching Algorithm. In: Parallel Problem Solving from Nature - PPSN IX. Volume 4193 of Lecture Notes in Computer Science., Springer (2006) 142–151 43. Shir, O.M., Siedschlag, C., Bäck, T., Vrakking, M.J.: Evolutionary Algorithms in the Optimization of Dynamic Molecular Alignment. In: Proceedings of the 2006 IEEE World Congress on Computational Intelligence, IEEE Computational Intelligence Society (2006) 9817–9824 44. Shir, O.M., Siedschlag, C., Bäck, T., Vrakking, M.J.: The Complete-Basis-Functions Parameterization in ES and its Application to Laser Pulse Shaping. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2006, New York, NY, USA, ACM Press (2006) 1769–1776 45. Shir, O.M., Siedschlag, C., Bäck, T., Vrakking, M.J.: Niching in Evolution Strategies and its Application to Laser Pulse Shaping. In: Artificial Evolution, 7th International Conference, Evolution Artificielle, EA 2005. Volume 3871 of Lecture Notes in Computer Science., Springer (2006) 85–96 46. Shir, O.M., Bäck, T.: Dynamic Niching in Evolution Strategies with Covariance Matrix Adaptation. In: Proceedings of the 2005 Congress on Evolutionary Computation CEC2005, Piscataway, NJ, USA, IEEE Press (2005) 2584–2591 47. Shir, O.M., Bäck, T.: Niching in Evolution Strategies. In: Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2005, New York, NY, USA, ACM Press (2005) 915–916 Patents: Leak detection in a fluid distribution network. U.S. Patent Number US8930150 B2, granted Jan 6, 2015 Self organizing maps for visualizing an objective space. U.S. Patent Number US US9104963 B2, granted Aug 11, 2015 Filed Patents: Identifying a highly diverse set of multi objective designs. U.S. Patent Number US 2013/0218526 A1, pub. Aug 22, 2013 Sensor placement for leakage location in liquid distribution networks. U.S. Patent Number US 2013/0262068 A1, pub. Oct 3, 2013 Multi objective design selection. U.S. Patent Number US 2014/0136460 A1, pub. May 15, 2014 Multiobjective optimization through user interactive navigation in a design space. U.S. Patent Number US 2015/0019173 A1, pub. Jan 15, 2015 Objective weighing and ranking. U.S. Patent Number US 2015/0227848 A1, pub. Aug 13, 2015 Automated multi-objective solution selection. U.S. Patent Number US 2015/0363703 A1, pub. Dec 17, 2015