Student Research Projects

Our collaborative research involves modern drug discovery, the design, synthesis, and evaluation of potential enzyme inhibitory chemical compounds. Computational Intelligence and Computer Aided Molecular Modeling represent essential components of this endeavor. We are using Sybyl molecular modeling in conjunction with neural-networks - fuzzy logic - genetic algorithms techniques to design de novo structures which can become lead compounds for further drug development, and possibly future therapeutic agents.

Razvan Andonie, Ph.D.; Levente Fabry-Asztalos, Ph.D.

CWU Alumni: Christopher B. Abdul-Wahid (graduated 2009, PhD); Grant Barker (graduated 2009); Sarah Abdul-Wahid, M.S. (graduated 2006); Catharine J. Collar, M.S. (graduated 2006, PhD); Nicholas Salim (graduated 2006); Heather N. Biles (graduated 2006); Lukas Magill (graduated 2008).

External collaborators: Istvan Lorentz, PhD, Siemens, Romania; Bogdan Crivat, PhD, VP  Microsoft, USA; Lucian Sasu, PhD, "Transilvania" University, Romania.

Publications

• Lorentz, I., Andonie, R., Fabry-Asztalos, L. Accelerating Molecular Structure Determination based on Inter-atomic Distances using OpenCL, IEEE Transactions on Parallel & Distributed Systems, 26, 2015, 3250-3263.

• Andonie R., Fabry-Asztalos L., Sasu, L. Bayesian ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors using A Small Molecular Dataset, Proceedings of the IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB 2014), May 21-24, 2014, Honolulu, Hawaii, USA.

• Lorentz I., Andonie R., Fabry-Asztalos L. Solving Molecular Distance Geometry Problems in OpenCL, Proceedings of the 13th International Conference on Optimization of Electrical and Electronic Equipment, (OPTIM'2012), Brasov, Romania, May 24-26, 2012, 1421-1428.

• Fabry-Asztalos, L., Lorentz I., Andonie, R. Molecular Distance Geometry Optimization using Geometric Build-up and Evolutionary Techniques on GPU, Proceedings of the IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB 2012), May 9-12, 2012, San Diego, USA, 321-328.

• Razvan Andonie, Levente Fabry-Asztalos, C. Badi‘ Abdul-Wahid, Sarah Abdul-Wahid, Grant Barker, Lukas Magill. Fuzzy ARTMAP Prediction of Biological Activities for Potential HIV-1 Protease Inhibitors using A Small Molecular Dataset, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8, 2011, 80-93.

• Andonie R., Fabry‑Asztalos L., Crivat B., Abdul‑Wahid S., Abdul‑Wahid B. Fuzzy ARTMAP Rule Extraction in Computational Chemistry, Proceedings of the IEEE International Joint Conference on Neural Networks (IJCNN 2009), Atlanta, June 14-19, 2009, 157-163, Best Poster Award Runner-up.

• Fabry-Asztalos, L., Andonie, R., Collar, C., Abdul-Wahid, S., Salim, N. A Genetic Algorithm Optimized Fuzzy Neural Network Analysis of the Affinity of Inhibitors for HIV-1 Protease, Bioorganic & Medicinal Chemistry, 16, 2008, 2903-2911.

• Andonie R., Fabry‑Asztalos L., Magill L., Abdul‑Wahid S. A New Fuzzy ARTMAP Approach for Predicting Biological Activity of Potential HIV‑1 Protease Inhibitors, Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007), San Jose, CA, Nov 2-4, 2007, IEEE Computer Society Press, ISBN 0-7695-3031-1, 56-61.

• Andonie, R., Fabry-Asztalos, L., Abdul-Wahid, S., Collar, C., Salim, N. An Integrated Soft Computing Approach for Predicting Biological Activity of Potential HIV-1 Protease Inhibitors, Proceedings of the IEEE International Conference on Neural Networks (IJCNN 2006), Vancouver, BC, Canada, July 16-21, 2006, 7495-7502, Best Session Presentation Award.

• Andonie, R., Fabry-Asztalos, L., Collar, C., Abdul-Wahid, S., Salim, N. Neuro-fuzzy Prediction of Biological Activity and Rule Extraction for HIV-1 Protease Inhibitors, Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB'05), San Diego, November 14-15, 2005, 113-120.

Presentations

• Levente Fabry-Asztalos, Razvan Andonie. Fuzzy neural network analysis of the affinity of inhibitors for HIV-1 protease, Oral presentation at the 243rd American Chemical Society National Meeting, San Diego, CA, March 27, 2012.

• Kristoffer Hepler, Forrest Williamson, Zachary Haberman, Razvan Andonie, Levente Fabry-Asztalos. Bee Colony Optimization of Protein Folding, Symposium on University Research and Creative Expression (SOURCE 2011), Ellensburg, May 19, 2011.

• Forrest Williamson,  Kristoffer Hepler, Zachary Haberman, Levente Fabry-Asztalos, Razvan Andonie. Analysis of Cathepsin-D Inhibitory Compounds by Computational Intelligence Methods, Symposium on University Research and Creative Expression (SOURCE 2011), Ellensburg, May 19, 2011.

• Badi’ Adbul-Wahid, Grant I. Barker, Sarah Abdul-Wahid, Luke Magill, Catharine Collar, Nicholas  Salim, Razvan Andonie*, Levente Fabry-Asztalos*. Using Computational Intelligence as Predictive Tool for Biological Activities of Drug Candidates Targeted Towards Therapeutically Important Enzymes for Rapid Screening, Posters on the Hill, Council on Undergraduate Research, Capitol Hill, Washington DC, May 5th, 2009. The posters are presented to the members of Congress.

• Badi‘ Abdul-Wahid, Razvan Andonie, Levente Fabry-Asztalos, Bogdan Crivat, Sarah Abdul-Wahid. Fuzzy ARTMAP Rule Extraction in Computational Chemistry, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

• Badi' Abdul-Wahid, Gene Roseberry, Zacharias Thompson, Branden Lopez, Levente Fabry-Asztalos, Razvan Andonie. Applications of Graph Matching for Chemical Structures, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

• Badi' Abdul-Wahid, Grant Barker, Razvan Andonie, Levente Fabry-Asztalos. Predictive Software as a Rapid Screening Tool for Potential Drug Candidates, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

• Badi' Abdul-Wahid, Levente Fabry-Asztalos, Razvan Andonie. Prediction of Biological Efficacy for Potential Plasmodium Falciparum Plasmepsin IV Inhibitors, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

• Badi’ Adbul-Wahid, Levente Fabry-Asztalos, Razvan Andonie. Prediction of Biological Efficacy for Potential Plasmodium Falciparum Plasmepsin IV Inhibitors,  Seattle Parasitology Conference, Seattle Biomedical Research Institute, May 14-15, 2009.

• Grant I. Barker, Razvan Andonie, Levente Fabry-Asztalos. Computer modeling and neural networks used in the design of novel HIV-1 protease inhibitors for the therapeutic treatment of HIV/AIDS, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008.

• Badi’Adbul-Wahid, Razvan Andonie, Levente Fabry-Asztalos. Prediction of novel inhibitors targeting P. Falciparum Plasmepsin IV, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008.

• Badi’Adbul-Wahid, Grant I. Barker, Razvan Andonie, Levente Fabry-Asztalos. Ordered Fuzzy ARTMAP for predicting HIV-1 protease inhibitor activity, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008, Outstanding Oral Presentation Award.

• Badi’ Adbul-Wahid, Grant Barker, Levente Fabry-Asztalos, Razvan Andonie, Ordered Fuzzy ARTMAP for Predicting HIV-1 Protease Inhibitors, 2008 American Chemical Society – Puget Sound Section Undergraduate Research Symposium, The Evergreen State College, Olympia, WA, April 26th, 2008.

• Lukas Magill, Razvan Andonie, Levente Fabry-Asztalos, Genetic Algorithm Optimized Fuzzy ARTMAP with Relevancies for HIV-1 Protease Prediction, Symposium on University Research and Creative Expression (SOURCE 2007), Ellensburg, May 17, 2007.

• Badi’ Adbul-Wahid, Levente Fabry-Asztalos, Sarah Abdul-Wahid, Razvan Andonie, Dimensional abstraction: Generating novel potential inhibitors of Malarial Plasmepsin IV using computational methodologies, Symposium on University Research and Creative Expression (SOURCE 2007), Ellensburg, May 17, 2007.

• Badi’ Adbul-Wahid, Sarah Abdul-Wahid, Levente Fabry-Asztalos, Razvan Andonie. In Silico Study of Plasmodium Falciparum Proteases Plasmepsin II and IV: Prediction of Biological Activity of Newly Designed Inhibitors, the 233th American Chemical Society National Meeting, Chicago, IL, March 25-29, 2007.

• Andonie, R. Predicting Biological Activity of Potential HIV-1 Protease Inhibitors – A Computational Intelligence Approach, November 10th, 2006, Old Dominium University, Norfolk, VA, invited tutorial presentation.

• Nicholas Salim, Catharine J. Collar, Sarah Abdul-Wahid, Levente Fabry-Asztalos, Razvan Andonie.  Fuzzy-neural network predictions of IC50 values for potential HIV-1 protease inhibitors, Symposium on University Research and Creative Expression (SOURCE 2006), Ellensburg, May 18, 2006.

• Sarah Abdul-Wahid, Catharine J. Collar, Nicholas Salim, Razvan Andonie, Levente Fabry-Asztalos.  An integrated computational intelligence approach for predicting biological activity of potential HIV-1 protease inhibitors, Symposium on University Research and Creative Expression (SOURCE 2006), Ellensburg, May 18, 2006.

• Nicholas Salim, Sarah Abdul-Wahid, Catharine J. Collar, Levente Fabry-Asztalos, Razvan Andonie. Application of a Fuzzy-Neural Network to Predict IC50 Values for Potential HIV-1 Protease Inhibitors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2006.

• Levente Fabry-Asztalos, Razvan Andonie, Catharine J. Collar, Sarah Abdul-Wahid, Nicholas Salim. Neuro-Fuzzy Prediction of Biological Activity and IF/THEN Rule Extraction for HIV-1 Protease Inhibitors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2006.

• Nicholas Salim, Catharine J. Collar, Sarah Abdul-Wahid, Levente Fabry-Asztalos, Rǎzvan Andonie. Application of fuzzy neural networks to predict IC50 values of novel HIV-1 protease inhibitors, oral presentation, the 14th Regional Murdock Conference on Undergraduate Research, Nampa, ID, November 12, 2005.

• Catharine J. Collar and Levente Fabry-Asztalos. Modeling Bioactivity for Aspartic Protease Inhibitors Using Bioavailability and Physicochemical Molecular Descriptors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2005.

• Heather Biles, Michael Ellis, Catharine J. Collar, Levente Fabry-Asztalos. Analyzing Force Field and Charge Conditions to Enhance Biological Activity Predictions of Cathepsin D Inhibitors, poster presentation, the 331th American Chemical Society National Meeting, Atlanta, GA, March 26-30, 2005.

• Sarah Abdul-Wahid, Catharine J. Collar, Nicholas Salim, Razvan Andonie, Levente Fabry-Asztalos. Explicit Knowledge Extraction from Properties of Chemical Structures, poster presentation, Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005.

• Catharine Collar, Sarah Abdul-Wahid, Nicholas Salim, Levente Fabry-Asztalos, Razvan Andonie. Neuro-Fuzzy and Multiple Regression IC50 Prediction of HIV-1 Protease Inhibitors, oral presentation,  Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005.

• Catharine Collar, Levente Fabry-Asztalos. Predicting Biological Activity of HIV-1 Protease Inhibitors Using Multi-Variable Molecular Mathematical Modeling, oral presentation, Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005.

• Sarah Abdul-Wahid, Nicholas Salim, Catharine J. Collar, Razvan Andonie, Levente Fabry-Asztalos. Predicting Biological Affinity of HIV-1 Protease Inhibitors Using A Neuro-Fuzzy Network, poster presentation, American Chemical Society Puget Sound Section Undergraduate Research Symposium, Seattle, WA, April 23, 2005.

• Heather N. Biles, Catharine J. Collar, Levente Fabry-Asztalos. Molecular Modeling of Cathepsin-D Inhibitors; A Comparative Study with Pepstatin, poster presentation, the 14th Regional Murdock Conference on Undergraduate Research, Nampa, ID, November 19, 2004.

Swarms of mobile software agents, imitating the behavior of insects, can solve complex tasks. Such agents individually have simple behavior. However, as a collective unit, constructive behavior emerges, as it does in insect colonies. We intend to investigate distributed computing in a heterogeneous network using bio-inspired techniques. The system should be adaptive and completely distributed. It should perform dynamic, event-driven load balancing. Every node of the network should be capable of producing new events and introducing them into the network for computation. The architecture should be used as a general support for clustering and task allocation applications.

Razvan Andonie, PhD; James Schwing, PhD.

CWU Alumni: Brandon Wysocki (graduated 2010); Ben Sisson (graduated 2010); Joseph Lemnley (graduated 2006); Sarah Abdul-Wahid, M.S. (graduated 2006); Jonathan Widger (graduated 2006); Berk Erkul (graduated 2007); Sorin (Alex) Bucse (graduated 2008); Lukas Magill (graduated 2008); Michael Wilson (graduated 2008); Ben Woodard (graduated 2008); Badi` Abdul-Wahid (graduated 2009).

External collaborators: Istvan Lorentz, PhD, Siemens Romania; Mihai Dumitrescu,  Transilvania University, Romania, Mihaela Malita, PhD, Anselm College, USA.

Publications

• Dumitrescu, M., Andonie, R. Clustering Superpeers in P2P Networks by Growing Neural Gas, Proceedings of the Twentieth Euromicro Conference on Parallel, Distributed, and Network-Based Processing (PDP 2012), Feb. 15-17, Garching, Germany, IEEE Computer Society Press, Los Alamitos, 2012, 311-318, ISBN: 978-0-7695-44633-9.

• Lorentz I., Andonie, R., Malita, M. An Implementation of Evolutionary Computation Operators in OpenCL, in: Intelligent Distributed Computing V, Studies in Computational Intelligence 382, F. Brazier, K. Nieuwenhuis, G. Pavlin, M. Warnier, C. Badica (eds.), Springer-Verlag, Berlin, 2012, 103-113, ISBN 978-3-642-24012-6.

• Lorentz I., Malita, M. Andonie, R. Evolutionary Computation on the Connex Architecture, Proceedings of The 22nd Midwest Artificial Intelligence and Cognitive Science Conference (MAICS 2011), Cincinnati, USA, April 16-17, 2011, 146-153, ISSN: 1613-0073.

• Lorentz I., Malita M., Andonie R. Fitting FFT onto an Energy Efficient Massively Parallel Architecture, Proceedings of the Second International Forum on Next-Generation Multicore/Manycore Technologies (IFMT’10), ACM/IEEE International Symposium on Computer Architecture (ISCA 2010), Saint-Malo, France, June 19-23, 2010, ACM, ISBN  978-1-4503-0008-7.

• Andonie R., Magill, L., Schwing J., Sisson B., Wysocki B. An Adaptive Replication Algorithm in P2P File Systems with Unreliable Nodes, Proceedings of the 2009 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'09), Las Vegas, July 13-16, 2009, 398-404.

• Abdul-Wahid, S., Andonie, R., Lemley, J., Schwing, J., Widger, J. Adaptive Distributed Database Replication Through Colonies of Pogo Ants, Proceedings of the IEEE International Parallel & Distributed Processing Symposium (IPDPS 2007) , Long Beach, California, March 26-30, 2007, ISBN 1-4244-0909-8.

• Abdul-Wahid, S., Andonie, R., Lemley, J., Schwing, J., Widger, J. Event-Driven Load Balancing of Partially Replicated Objects through a Swarm of Mobile Agents, Proceedings of the IASTED International Conference on Computational Intelligence (CI 2006), B. Kovalerchuk (ed.), San Francisco, November 20-22, 2006, ACTA Press, ISBN 0-88986-603-1, 110-115.

Presentations

• Brandon Wysocki, Ben Sisson, Razvan Andonie, James Schwing. An Adaptive Replication Algorithm in P2P File Systems with Unreliable Nodes, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

• Ben Woodward, Michael Wilson, Luke Magill, Sorin Bucse, James Schwing, Razvan Andonie, ANTS Need This Software, Symposium on University Research and Creative Expression (SOURCE 2008), Ellensburg, May 15, 2008.

• James Schwing, Old Dominium, Norfolk, VA - Invited Presentation, November 10, 2006.

• Joseph Lemley, Jonathan Widger, Virgil Mednick, Sarah Abdul-Wahid, James Schwing, Razvan Andonie, Biologically inspired solution for load balancing distributed data, Symposium on University Research and Creative Expression (SOURCE 2006), Ellensburg, May 18, 2006.

Writing a chess program is a notoriously difficult task. Our solution is to develop an adaptive distributed program that uses a genetic algorithm in combination with a neural network that can learn after each game it plays. The entire genetic algorithm/neural network component is part of the evaluation function used to rank each board. Given a board configuration, ten attributes are evaluated each of which is used as the input to the neural network. The weights of the neural network are optimized on a computer network, using a distributed genetic algorithm. Each time the evaluation function is called, the neural network calculates the value for a given board configuration which will then be used in a recursive search algorithm that uses Alpha-Beta pruning. The weights are adjusted at the end of the game based on its outcome. Work on parallelizing the alpha beta function to achieve greater search depths is partially complete. Our final goal is a fully distributed chess program which learns after each game it plays and analyzes in parallel strategies. CWU-Chess is integrated in the ARENA GUI. Approx. 250 chess engines run under Arena.

The free and publicly available UCI and Winboard protocols are used for the communication between CWU-Chess and Arena GUI. CWU-Chess can play against any of the Arena supported engines, against itself, and against a human partner.

Originally a final project in the CS457 Computational Intelligence course by Ashur Odah, Pushpinder Heer, and Joe Lemley, the CWU Chess program has turned in to a tradition for emerging research students.

Razvan Andonie, Ph.D.

CWU Alumni:  Ashur Odah (graduated 2004); Pushpinder Heer (graduated 2004); Joseph Lemnley (graduated 2006); Jonathan Widger (graduated 2006); Berk Erkul (graduated 2007;, Lukas Magill (graduated 2008;, Kyle Littlefield (graduated 2009). 

External Collaborator:  Michael Diosi (Germany), one of the ARENA developers. Thanks Michael for introducing us to ARENA and for your continuous support!

Publications and Presentations

• Lemley, J., Andonie, R., Odah, A., Heer, P., Widger, J., Erkul, B., Magill, L., Littlefield, K. CWU-Chess: An Adaptive Chess Program that Improves After Each Game, Proceedings of the IEEE Games, Entertainment, Media Conference (GEM), August 15-17, 2018, Galway, Ireland, 86-89.

• Kyle Littlefield, Razvan Andonie. Integrating CWU Chess in the ARENA Chess GUI, Symposium on University Research and Creative Expression (SOURCE 2009), Ellensburg, May 21, 2009.

• Lukas Magill, Joseph Lemley, Jonathan Widger, Berk Erkul, Razvan Andonie. Fuzzy ARTMAP for Chess Artificial Iintelligence, Symposium on University Research and Creative Expression (SOURCE 2006), Ellensburg, May 18, 2006. J

• Joseph Lemley, Jonathan Widger, Razvan Andonie. An Adaptive Chess Program Distributed Over A Network of Workstations, Symposium on University Research and Creative Expression (SOURCE 2005), Ellensburg, May 19, 2005 - Outstanding Undergraduate Student Oral Presentations Award. 

• Ashur Odah, Pushpinder Heer, Joe Lemley, Razvan Andonie. CWU-Chess - An Adaptive Chess Program, Student Poster Session of the Sixth Annual Northwestern Regional Conference of the Consortium for Computing Sciences in Colleges, Willamette University, Salem, Oregon, October 8 & 9, 2004.