Publications

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Journal Publications - Refereed

 
  • U. Sirin, U. Erdogdu, F. Polat, M. Tan, R. Alhajj, "Effective gene expression data generation framework based on multi-model approach," Artificial Intelligence in Medicine, 70: 41-61, 2016.
  • T. Oral, F. Polat, "MOD* Lite: An Incremental Path Planning Algorithm Taking Care of Multiple Objectives," IEEE Trans. Cybernetics, 46(1): 245-257, 2016.
  • E. Çilden, F. Polat, "Toward Generalization of Automated Temporal Abstraction to Partially Observable Reinforcement Learning," IEEE Trans. Cybernetics, 45(8): 1414-1425, 2015.
  • M. Tan, F. Polat, R. Alhajj , Subtree selection in kernels for graph classification, Int. J. of Data Mining and Bioinformatics, Vol.8, No.3, pp.294-310, 2013
  • U. Erdogdu, M. Tan, R. Alhajj, F. Polat, J. Rokne,  Integrating machine learning techniques into robust data enrichment approach and its application to gene expression data, Int. J. of Data Mining and Bioinformatics, Vol.8, No.3, pp.247-281, 2013
  • A. E. Bayrak, F. Polat, "Employment of an evolutionary heuristic to solve the target allocation problem efficiently," Information  Sciences, Vol. 222, pp. 675-695, 2013
  • A.G. Bayrak and F. Polat, "Formation preserving path finding in 3-D terrains,'' Applied Intelligence, Vol. 36 No. 2, pp. 348-368, 2012.
  • O.O. Isikman, T. Ozyer, O. Zarour, R. Alhajj, F. Polat, "TempoXML: Nested bitemporal relationship modeling and conversion tool for fuzzy XML," Information Sciences, Vol. 193, pp. 247-274, 2012.
  • M. Al-Shalalfa, M. Tan, G. Naji, R. Alhajj, F. Polat, J. G. Rokne, "Revealing miRNA Regulation and miRNA Target Prediction Using Constraint-Based Learning," IEEE Transactions on Systems, Man, and Cybernetics, Part C, Vol.42, No.6, pp.1354-1364, 2012
  • S. Bayili and F. Polat, ``Limited-Damage A*: A path search algorithm that considers damage as a feasibility criterion,'' Knowledge-Based Systems, Vol.24, No.4, pp.501-512, May 2011
  • M. Tan, M. Alshalalfa, R. Alhajj, F. Polat. ``Infuence of Prior Knowledge in Constraint-Based Learning of Gene Regulatory Networks,'' IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.8, No.1, pp.130-142, January/February 2011.
  • S.Girgin, F.Polat and R.Alhajj, ``Improving Reinforcement Learning by Using Sequence Trees,'' Machine Learning, Vol.81, No.3, pp.283-331, 2010.
  • C.Undeger and F.Polat, “Multiagent Real-Time Pursuit,” Autonomous Agents and Multiagent Systems, Vol.21, No.1, pp.69-107, 2010.
  • M.Tan, F.Polat, R.Alhajj, “Automated Large-Scale Control of Gene Regulatory Networks,” IEEE Transactions on Systems, Man, and Cybernetics, Part B, Vol.40, No.2, pp.286-297, April 2010.
  • M. Tan, R.Alhajj, F. Polat, “Scalable Approach for Effective Control of Gene Regulatory Networks,” Artificial Intelligence in Medicine, Vol.48, No.1, 2010, pp.51-59.
  • C.Undeger and F.Polat, ``Real-Time Edge Follow: A Real-Time Path Search Approach,'' IEEE Transaction on Systems, Man and Cybernetics, Part C, Vol.39, No.3,pp.366-372,  May 2009.
  • S.Girgin, F.Polat and R.Alhajj, ``Positive Impact of State Similarity on Reinforcement Learning Performance,''  IEEE Transaction on Systems, Man and Cybernetics, Part B, Vol.37, No.5, pp.1256-1270, Oct. 2007.
  • G.Erus and F.Polat, ``A layered approach to learning coordination knowledge in multiagent environments,'' Applied Intelligence, Vol.27, No.3, pp. 249-267, Dec. 2007.
  • C.Undeger and F.Polat, ``Real-Time Edge Follow: A Real-Time Path Search Approach,'' IEEE Transaction on Systems, Man and Cybernetics, Part C, Vol.37, No.5,pp.860-872, Sep. 2007.
  • C.Undeger and F.Polat, ``RTTES: Real-Time Search in Dynamic Environments'' Applied Intelligence, Vol.27, No.2, pp.113-129, Oct 2007.
  • O.Abul, R.Alhajj and F. Polat “A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes,” IEEE/ACM Transaction on Computational Biology and Bioinformatics, Vol.3, No.3, pp.220- 231, July-Sept. 2006.
  • S.Kucukpetek, F.Polat and H.Oguztuzun, “Multilevel Graph Partitioning: An Evolutionary Approach,” Journal of Operations Research Society, Palgrave-Macmillan, Vol.56, No.5, pp.549-562, May 2005.
  • M.O.Baykal, R.Alhajj and F. Polat, “Cooperation Framework of Case-Based Reasoning Agents for Automated Product Recommendation,” International Journal of Experimental and Theoretical Artificial Intelligence, Vol.17, No.3, pp., July-Sept 2005.
  • R.Alhajj, F.Polat and Cem Yilmaz, “Views as First-Class Citizens in Object-Oriented Databases,” The VLDB Journal, Springer-Verlag , Vol.14, No.2, pp.155-169,  April 2005.
  • O.Abul, R.Alhajj, F. Polat and K.Barker, “Finding Differentially Expressed Genes: Pattern Generation,” Bioinformatics, Vol.21, No.4, pp.445-450, Feb 2005.
  • R. Alhajj and F. Polat, “Multiple-Agents to Identify and Separate Touching Digits in Unconstrained Handwritten Hindi Numerals,” International Journal of Experimental and Theoretical Artificial Intelligence, Vol.15, No.4, pp.461-471, October-December 2003.
  • R.Alhajj and F.Polat, “Rule-Based Schema Evolution in Object-Oriented Databases,” Knowledge-Based Systems, Elsevier, Vol.16,  No.1, pp.47-57, Jan. 2003.
  • S. Senkul and F. Polat, “Learning Intelligent Behavior in a Non-Stationary and Partially Observable Environment,” Artificial Intelligence Review, Kluwer, Vol.18:2, Oct. 2002.
  • A.Cakir and F.Polat, “Coordination of Intelligent Agents in Real-Time Search,” Expert Systems, Blackwell Pub., Vol. 19, No.2, 2002, pp.80-87.
  • F. Polat and O. Abul,  “Learning Sequences of Compatible Actions Among Agents,” Artificial Intelligence Review, Kluwer, Vol.17:1, March 2002, pp. 21-37.
  • F. Polat, A. Cosar and R. Alhajj, “Semantic Information-Based Alternative Plan Generation for Multiple Query Optimization,” Information Sciences, Elsevier, Vol 137/1-4, pp.103-133, 2001.
  • O. Abul, F. Polat and R. Alhajj, “Multi-Agent Reinforcement Learning Using Function Approximation,” IEEE Transaction on Systems, Man and Cybernetics, Part C, IEEE Press,  Vol.30, No.4 pp.485-497, Nov.2000.
  • R. Alhajj and F. Polat, “Using Object-Oriented Materialized Views to Answer Selection-Based Complex Queries,” Information Sciences, Elsevier, Vol.118: (1-4), pp.75-99, Sept.1999.
  • F. Polat and R. Alhajj, “A Multi-Agent Tuple-Space Based Problem Solving Framework,” Journal of Systems and Software, Elsevier, Vol. 47, pp. 11-17, 1999.
  • R. Alhajj and F. Polat, “Incremental View Maintenance in Object-Oriented Databases,” Data Base for Advances in Information Systems, ACM Press, Vol.29, No.3, pp.52-64, 1998.
  • R. Alhajj and F. Polat, “Proper Handling of Query Results Towards Maximizing Reusability in Object-Oriented Databases,” Information Sciences, Elsevier, Vol. 107, pp.247-272, 1998.
  • F. Polat, S. Shekhar and A. Guvenir,  “A Negotiation Platform for Cooperating Multi-Agent Systems,” International Journal of Concurrent Engineering: Research & Applications (CERA), Sage Publications, No.3, pp.179-187, 1993.
  • F. Polat and A. Guvenir, “UVT: Unification Based Tool for Knowledge Base Verification,” IEEE Intelligent Systems & Their Applications, IEEE Press, Vol.8, No.3, pp. 69-75, June 1993.
  • F. Polat, S. Shekhar and A. Guvenir, “Distributed Conflict Resolution Among Cooperating Expert Systems,” Expert Systems, Blackwell Pub., Vol.10, No.4, pp.147-163, 1993.
  • F. Polat and A. Guvenir, “A Unification-Based Approach for Knowledge Base Verification,” Expert Systems,  Blackwell Pub., Vol.8, No.4, pp.251-259, November 1991. 


Conference Publications - Refereed (2000 – )

 
  • C. Sahin, E. Cilden, F. Polat, "Memory efficient factored abstraction for reinforcement learning, CYBCONF 2015: 18-23, 2015.
  • M. G. Ozsoy, F. Polat, R. Alhajj, "Inference of gene regulatory networks via multiple data sources and a recommendation method," BIBM 2015: 661-664, 2015.
  • M. Gulcin Ozsoy, F. Polat, R. Alhajj: Modeling Individuals and Making Recommendations Using Multiple Social Networks. ASONAM 2015: 1184-1191, 2015
  • E.Cilden and F.Polat, “Employing Automatic Temporal Abstractions to Accelerate Utile Suffix Memory Algorithm,” Multiagent System Technologies (MATES), LNAI, Springer, pp.156-169, 2014.
  • A. E. Bayrak and F. Polat. “Contextual Feature Analysis to Improve Link Prediction for Location Based Social Network,” Proceedings of the 8th Workshop on Social Network Mining and Analysis (SNAKDD'14). ACM, New York, NY, USA
  • M.G. Ozsoy,  F. Polat, R. Alhajj, R, "Multi-objective optimization based location and social network aware recommendation," IEEE Int. Conf on Collaborative Computing: Networking, Applications and Worksharing (CollaborateCom),  Florida, US, pp. 233-242, Oct. 2014.
  • U. Sirin, F. Polat, R. Alhajj, “Employing Batch Reinforcement Learning to Control Gene Regulation Without Explicitly Constructing Gene Regulatory Networks,” International Joint Conference in Artificial Intelligence, IJCAI 2013, Beijing, China, August 3-9,  pp.2042-2048, 2013.
  • E. Cilden, F. Polat, “Abstraction in Model Based Partially Observable Reinforcement Learning using Extended Sequence Trees,” IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology, pp.401-408, Macau, China, December 2012.
  • T. Oral, F. Polat, “A Multi-Objective Incremental Path Planning Algorithm for Mobile Agents,” IEEE/WIC/ACM International Conferences on Web Intelligence and Intelligent Agent Technology, pp.401-408, Macau, China, December 2012.
  • U. Erdogdu, F. Polat, R. Alhajj, “Partially Observable Gene Regulatory Network Control With- out a Boundary on Horizon,” IEEE International Conference on Tools with Artificial Intelligence (ICTAI), pp.81-88, Athens, Greece, November 2012.
  • U. Sirin, U. Erdogdu, M. Tan, F. Polat, R. Alhajj, “Effective Enrichment of Gene Expression Data Sets,” International Conference on Machine Learning and Applications (ICMLA), IEEE Computer Society, pp.76-81, Boca Raton, FL, USA, December 2012.
  • U. Erdogdu, M. Tan, R. Alhajj, F. Polat, D. J. Demetrick, J. G. Rokne, "Employing Machine Learning Techniques for Data Enrichment: Increasing the Number of Samples for Effective Gene Expression Data Analysis," IEEE International Conference on Bioinformatics & Biomedicine (BIBM),  BIBM 2011, 238-242, 2011, Atlanta, USA
  • U. Erdogdu, R. Alhajj, F. Polat, "The Benefit of Decomposing POMDP for Control of Gene Regulatory Networks," IEEE/WIC/ACM International Conference on Intelligent Agent Technology, IAT 2011, Campus Scientifique de la Doua, Lyon, France, August 22-27, 2011. IEEE Computer Society 2011, pp.381-385
  • M.Tan, F.Polat and R.Alhajj,``Feature Selection for Graph Kernels,'' IEEE International Conference on Bioinformatics and Biomedicine  (IEEE BIBM), Dec 18-21, 2010, Hong Kong, pp.632-637
  • I. Suleiman, T. Salman, S. Gao, F. Polat, M. Arslan, R. Alhajj, ``The Power of Genetic Algorithm in Automated Assessment of School Readiness,'' IEEE International Conference on Information Reuse and Integration (IEEE IRI'10), Aug 4-6, 2010, Las Vegas, NV, pp.280-285
  • M.Tan, F.Polat and R.Alhajj, “Derivation of Transcriptional Regulatory Relationships by Partial Least Squares Regression,” IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Nov 1 - 4, 2009, Washington D.C.
  • A.Galip Bayrak and F.Polat, ``Formation Preserving Navigation of Agent Teams in 3-D Terrains,''  Proc. of the EUROSIS Industrial Simulation Conference 2008 (ISC 2008), June 9-12 2008, Lyon, Paris, pp.148-155.
  • M.Tan, R.Alhajj and F. Polat, ”Large-scale Approximate Intervention Strategies for Probabilistic Boolean Networks as Models of Gene Regulation,'' Proc of 8th IEEE International Conference on Bioinformatics and Bioengineering (BIBE'08), Oct 8-10, 2008, Athens, Greece. pp.1-6.
  • M.Tan, M. AlShalalfa, R. Alhajj and F. Polat, ``Combining Multiple Types of Biological Data in Constraint-Based Learning of Gene Regulatory Networks,'' Proc. of IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2008), September 15-17, 2008, Sun Valley, Idaho, USA, pp.90-97.
  • C.Undeger and F.Polat, ``Real-Time Moving Target Search,'' PRIMA 2007, Lecture Notes in Artificial Intelligence, Springer, Bangkok, Nov.21-23, 2007.
  • M.Tan, F.Polat and R.Alhajj, ``Feature Reduction for Gene Regulatory Network Control '' IEEE 7th Symposium on Bioinformatics and Bioengineering (BIBE'07), Oct 14-17, 2007, Boston MA, pp.1260-1264.
  • S.Girgin, F.Polat and R.Alhajj, “State Similarity Based Approach for Improving Performance in RL,” International Joint Conference in  Artificial Intelligence (IJCAI'07), Jan 6-12, 2006, Hyderabad, India,  pp.817-822.
  • O.Abul, R.Alhajj and F.Polat, “Optimal Multi-Objective Control Method for Discrete Genetic Regulatory Networks,” IEEE 6th Symposium on Bioinformatics and Bioengineering (BIBE'06), Oct 16-18, 2006, Washington D.C.
  • O.Abul, R.Alhajj and F.Polat, “Asymptotical Lower Limits on Required Number of Examples for Learning Boolean Networks,” The 21st International Symposium on Computer and Information Sciences, November 1-3, 2006 - Istanbul, Turkey
  • S. Girgin, F. Polat and R. Alhajj, ``Effectiveness of Considering State Similarity for Reinforcement Learning,'' Proc. of 7th Int'l Conference on Intelligent Data Engineering and Automated Learning (IDEAL-06), Sept 20-23, 2006, Burgos, Spain.
  • S. Girgin, F. Polat and R. Alhajj, ``Learning by Automatic Option Discovery from Conditionally Terminating Sequences,'' Proc. of the 17th European Conference on Artificial Intelligence (ECAI), Aug 28-Sept 1, 2006,  Riva del Garda, Italy.
  • U.Erdogdu and F. Polat, ``Dynamic Cooperation Using Resource Based Planning,'' Proceedings of the Fifth International Joint Conference on Autonomous Agents & Multi Agent Systems (AAMAS), May 8-12 2006, Hakodate, Japan.
  • C.Undeger and F. Polat, ``Real-Time Target Evaluation Search,'' Proceedings of the Fifth International Joint Conference on Autonomous Agents & Multi Agent Systems (AAMAS), May 8-12 2006, Hakodate, Japan.
  • S.Girgin and F. Polat, “Option Discovery in Reinforcement Learning Using Frequent Common Subsequences of Actions,” Proc. of International Conference on Intelligent Agents Web Technologies and Internet Commerce, IAWTIC, Vienna, Nov.28-30, 2005.
  • O. Abul, R. Alhajj and F. Polat, “Importance of Monitoring in Developing Optimal Control Policies for Probabilistic Boolean Genetic Networks,” Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU2004),  Perugia, Italy, pp.1145-1152, July 2004.
  • O. Abul, R. Alhajj and F. Polat, “Markov Decision Processes Based Optimal Control Policies for Probabilistic Boolean Networks,” Proc. of IEEE Symposium on Bioinformatics and Bioengineering (BIBE2004), Taichung, Taiwan, May 19-21, pp.337-344, 2004.
  • O. Baykal, R. Alhajj, F. Polat, “Automated Product Recommendation by Employing Case-Based Reasoning Agents,” Proceedings of International Conference on Enterprise Information Systems ICEIS (2), pp. 515-518, 2004.
  • O. Abul, R. Alhajj, F. Polat and K. Barker, “Finding Differentially Expressed Genes: Pattern Generation using q-values,” Proceedings of the ACM Annual Symposium on Applied Computing (SAC), Cyprus, Mar. 2004, pp.138-142.
  • O. Abul, A. Lo, R. Alhajj, F. Polat and K. Barker, “Cluster Validity Analysis Using Subsampling,” Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, Washington DC, Oct. 2003.
  • E.Gokturk and F.Polat, “Implementing Agent Communication for a Multiagent Simulation Infrastructure on HLA,” Proc. of the International Symposium on Computer and Information Science (ISCIS 2003), LNCS, Springer-Verlag, 2003.
  • M.Kaya, R.Alhajj, F.Polat and A.Arslan, “Efficient Automated Mining of Fuzzy Association Rules,” Database and Expert Systems Applications (DEXA), Lecture Notes in Computer Science (LNCS 2453), pp.133-142, 2002.
  • C.Undeger, M.Balci, S.Girgin, V.Koc, F.Polat, S.Bilir, and Z.Ipekkan, “Platform Optimization and Simulation for Surviellance of Large Scale Terrains,” Proc. of Interservice/Industry Training, Simulation and Education Conference, 2002, Orlando, FL
  • C. Undeger, F. Polat and Z. Ipekkan, “Real-Time Edge Follow: A New Paradigm to Real-Time Path Search,” Annual European Game-On Conference (GAME-ON 2001), London, UK, Nov.30-Dec.1, 2001.
  • R. Alhajj and F. Polat, ``Reengineering of Relational Databases into Object-Oriented: Constructing the Class Hierarchy and Migrating the Data,'' Proceedings of the IEEE Working Conference on Data Reverse Engineering WCRE 2001, IEEE Press, Stuttgart, Germany, Oct. 2001, pp.335-344.
  • R. Alhajj and F. Polat, “Transferring Database Contents from a Conventional Information System to a Corresponding Existing Object Oriented Information System,” Proceedings of the ACM Annual Symposium on Applied Computing, ACM Press, Las Vegas, USA, Mar. 2001, pp.220-224.
  • R. Alhajj, F. Polat and A. Elnagar, “Employing Multi-Agents to Identify Touching of Adjacent Digits in Handwritten Hindi Numerals,” Proceedings of IEEE International Conference on Systems, Man, and Cybernetics, IEEE Press, Vol.4, Nashville, Tennessee, USA, Oct. 2000, pp.2725-2730.
  • O. Abul, F. Polat and R. Alhajj, “Function Approximation Based Multi-Agent Reinforcement Learning,” Proceedings of IEEE International Conference on Tools with Artificial Intelligence (ICTAI-2000), IEEE Press, Nov 13, 2000, Vancouver, British, Columbia, CA, pp.36-39.
  • U. Kuter and F. Polat, “Learning Better in Dynamic, Partially Observable Environment,” Proc. of European Conf. on Artificial Intelligence (ECAI) Workshop on Modeling Artificial Societies and Hybrid Organization, (Ed. G.Lindemann), Berlin, Aug. 20-25, 2000, pp.50-68.
  • F. Polat and R. Alhajj, “A Comparative Study of the Linda Model with Other Alternative Models of Parallel Programming,” Proc. of Int'l Conference on Software Engineering Applied to Networking and Parallel/Distributed Computing, SNPD'00, Reims, France, May 2000, pp.61-68.
  • R. Alhajj and F. Polat, “Maximizing Reusability: Seeking Appropriate Positions for Derived Classes within the Class Hierarchy,” Proceedings of the ACM Annual Symposium on Applied Computing, ACM Press, Como, Mar. 2000, pp.351-355.
  • R. Alhajj and F. Polat, “The Impact of Utilizing Materialized Views to Answer Object-Oriented Queries on Performance,”  Proceedings of the International Conference on Computer Science and Informatics, Atlantic City, NJ, Feb. 2000, pp.295-298.