Download Complete List of Publications

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