Prof. Ofer Shir

Ofer Shir
Associate Professor of Computer Science
Principal Investigator
Research Group Leader
PhD
Phone
972-4-6489923

Lab Website

Full CV (PDF)
Research Interests:

Computational Intelligence, Experimental Optimization, Statistical Learning, Theory of Randomized Search Heuristics, Quantum ML

Quote
You are the outcome of 3.8 billion years of evolutionary success. Act like it.

The advent of modern laboratory and field experiments, as well as of computerized systems, enables researchers to control experiments and analyze their big-data in high-speed rates. Yet, algorithmic design of intelligent experiments for optimization and learning of prescribed objectives may constitute the next level. Very little is known today about the general usefulness of optimization heuristics and statistical learning methods in laboratory experiments, about their strengths and weaknesses when compared to traditional Design-of-Experiments approaches, or about any kind of guidelines which approach to prefer, depending upon the dimensionality of the search-space, the levels of uncertainty and the number of available trials.

We are interested in learning and optimization questions related to systems within the Natural Sciences. In particular, Operational Research and Machine Learning aspects of experimental domains, that is, practical physical- and life-sciences problems whose computerized models are unavailable or too expensive to be executed, and thus necessitate real-world experiments toward the end of their global optimization. Our research interests encompass in general the following topics:

  • AI-Driven Scientific Research and Algorithmically-Guided Experimentation
  • Artificial General Intelligence, Deep Learning, Self-Supervised Learning
  • Combinatorial Optimization (White/Grey/Black-box, including physical systems in the lab)
  • Quantum Computing
     

Our current activities include Experimental Combinatorial Optimization (with Dr. Dan Gamrasni and Dr. Or Shahar), Multi-Objective Mixed-Integer Quadratic Models (with Prof. Michael Emmerich), Effective Detection of Foliage Diseases in Vineyards (with Dr. Rakefet Sharon), and Deep Learning of Enzymes' Functionality (with Dr. Livnat Jurnou and Dr. Itai Sharon).

CV

Education

2008-2010 Postdoctoral Research Associate, Princeton University, USA
2008 Ph.D., Computer Science, Leiden University, The Netherlands
2004 M.Sc., Computer Science, Leiden University, The Netherlands
2003 B.Sc., Physics and Computer Science, The Hebrew University of Jerusalem, Israel

Academic and research positions

2022-2023 Visiting Associate Professor, Faculty of Mathematics, Technion - Israel Institute of Technology
2020- Associate Professor, Computer Science Department, Tel-Hai College
2013- Principal Investigator, MIGAL-Galilee Research Institute

Previously

2019-2022 Head, Computer Science Department, Tel-Hai College
2012-2020 Lecturer and Senior Lecturer, Computer Science Department, Tel-Hai College
2010-2013, Research Staff Member, IBM-Research

Funding
  1. [M.O.S.T.] An innovative AI-driven approach for the development of environmentally-friendly postharvest volatile fungicides (with Dr. Gamrasni/Migal)
  2. [M.O.A.G.] Innovative AI-driven approach for the development of postharvest protocols (with Dr. Gamrasni/Migal)
  3. [Migal-internal] Automated identification of enzymes with desirable traits for agriculture use in extreme climate conditions using machine learning (with Dr. I. Sharon and Dr. Afriat-Jurnou)

Scientific Publications

Multi-Objective Mixed-Integer Quadratic Models: A Study on Mathematical Programming and Evolutionary Computation

Ofer M. Shir and Michael Emmerich
This paper appears in: IEEE Transactions on Evolutionary Computation On page(s): 1-15 Print ISSN: 1089-778X Online ISSN: 1941-0026 Digital Object Identifier: 10.1109/TEVC.2024.3374519
2024

Towards AI Research Agents in the Chemical Sciences

Ofer M. Shir
ChemRxiv. Cambridge: Cambridge Open Engage; 2024
2024

On the Behavior of the Mixed-Integer SMS-EMOA on Box-Constrained Quadratic Bi-Objective Models

Shir, O.M., Emmerich, M.
2023

Saliency Can Be All You Need In Contrastive Self-Supervised Learning

Kocaman, V., Shir, O.M., Bäck, T., Belbachir, A.N.
2022

Toward an ImageNet Library of Functions for Global Optimization Benchmarking

Yazmir B., Shir, O.M.
arXiv preprint (2022)
2022

Algorithmically-guided postharvest by experimental combinatorial optimization

Shir, O.M., Yazmir, B., Israeli, A., Gamrasni, D.
Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2022, New York, NY, USA, ACM Press (2022) 2027–2035
2022

Algorithmically-guided discovery of viral epitopes via linguistic parsing: Problem formulation and solving by soft computing

Shir, O.M., Israeli, A., Caftory, A., Zepko, G., Bloch, I.
Applied Soft Computing, Volume 129 (2022) 109509
2022

Introductory Mathematical Programming for EC

Shir, O.M.
Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2022, New York, NY, USA, ACM Press (2022)
2022

Sequential Experimentation by Evolutionary Algorithms

Shir, O.M., Bäck, T.
Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2022, New York, NY, USA, ACM Press (2022)
2022

The Unreasonable Effectiveness of the Final Batch Normalization Layer

Kocaman, V., Shir, O.M., Bäck, T.
Proceedings of the 16th International Symposium on Visual Computing, ISVC'21
2021

Locating the local minima in lens design with machine learning

Kononova, A.V., Shir, O.M., Tukker, T., Frisco, P., Zeng, S., Bäck, T.
Current Developments in Lens Design and Optical Engineering XXII 11814, 1181402
2021

Addressing the Multiplicity of Solutions in Optical Lens Design as a Niching Evolutionary Algorithms Computational Challenge

Kononova, A.V., Shir, O.M., Tukker, T., Frisco, P., Zeng, S., Bäck, T.
Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2021, New York, NY, USA, ACM Press (2021) 1596–1604
2021

Multi-level evolution strategies for high-resolution black-box control

Shir, O.M., Xi, X., Rabitz, H.
Journal of Heuristics (2021), Springer US
2021

Automated Feature Detection of Black-Box Continuous Search-Landscapes using Neural Image Recognition

Yazmir, B., Shir, O.M.
Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2021, New York, NY, USA, ACM Press (2021) 213–214
2021

Improving Model Accuracy for Imbalanced Image Classification Tasks by Adding a Final Batch Normalization Layer: An Empirical Study

Kocaman, V., Shir, O.M., Bäck, T.
Proceedings of the 25th International Conference on Pattern Recognition, ICPR2020 (2021) 10404–10411
2021

Benchmarking Discrete Optimization Heuristics with IOHprofiler.

Doerr, C., Ye, F., Horesh, N., Wang, H., Shir, O.M., Bäck, T.
Applied Soft Computing 88 (2020) 106027
2020

On the Covariance-Hessian Relation in Evolution Strategies.

Shir, O.M., Yehudayoff, A.
Theoretical Computer Science 801 (2020) 157—174
2020

Predict or Screen Your Expensive Assay? DoE vs. Surrogates in Experimental Combinatorial Optimization.

Horesh, N., Bäck, T., Shir, O.M.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 274?284
2019

Statistical Learning in Soil Sampling Design Aided by Pareto Optimization.

Israeli, A., Emmerich, M., Litaor, M., Shir, O.M.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 1198?1205
2019

Bayesian Performance Analysis for Black-Box Optimization Benchmarking.

Calvo, B., Shir, O.M., Ceberio, J., Doerr, C., Wang, H., Bäck, T., Lozano, J.A.
In Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2019 ,2019, Ed. ,ACM Press New York, NY, USA, Pages 1789?1797
2019

Compiling A Benchmarking Test-Suite For Combinatorial Black-Box Optimization: A Position Paper.

Shir, O.M., Doerr, C., Bäck, T.
In Proceedings of the Genetic and Evolutionary Computation Conference Companion, GECCO-2018 ,2018, ACM Press Ed. , New York, NY, USA,, Pages 1753?1760
2018

Evolution Strategies.

Emmerich, M.T.M., Shir, O.M., Wang, H.
In Handbook of Heuristics. ,2018, Martí R., Panos P., Resende M. Ed. ,Springer Cham , Pages 1-31
2018

Protein Design by Multiobjective Optimization: Evolutionary and Non-Evolutionary Approaches.

Belure, S.V., Shir, O.M., Nanda, V.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2017 ,2017, Ed. ,ACM Press New York, USA, Pages 1081?1088
2017

Searching for the Pareto frontier in multi-objective protein design.

Nanda, V., Belure, S.V., Shir, O.M.
Biophysical Reviews 2017 Volume 9 Issue 4 Pages 339?344
2017

Solving Structures of Pigment-Protein Complexes as Inverse Optimization Problems using Decomposition.

Lahav, Y., Shir, O.M., Noy, D.
In Proceedings of the Genetic and Evolutionary Computation Conference, GECCO-2017, ,2017, Ed. ,ACM Press New York, NY, USA,, Pages 1169?1176
2017