Department of Computer Science University of Sharjah
Sharjah, United Arab Emirates [email protected]
Institute of Information Science and Technology, Pisa, Italy.
Education
Post-doc. in Data mining, June 2006-March 2007.
Advisor: Prof.Dr Fosca Giannotti.
Norwegian University of Science and Technology, Trondheim, Norway.
Post-doc. in Bioinformatics, September 2005-May 2006.
Advisor: Prof.Dr Finn Drabløs.
Middle East Technical University, Ankara, Turkey.
Ph.D. in Computer Engineering, January 2005.
Thesis title: Controlling Discrete Genetic Regulatory Networks.
Advisors: Prof.Dr Faruk Polat, Prof.Dr Reda Alhajj.
University of Calgary, Calgary, Alberta, Canada.
Pre-doc. in Bioinformatics, Department of Computer Science, December 2002-December 2003.
Middle East Technical University, Ankara, Turkey.
M.Sc. in Computer Engineering, August 1999.
Thesis title: Multi-Agent Reinforcement Learning using Function Approximation.
Advisor: Prof.Dr Faruk Polat.
Hacettepe University, Ankara, Turkey.
M.Sc. student, Department of Computer Science and Engineering, August 1996-July 1997.
Hacettepe University, Ankara, Turkey.
B.Sc. in Computer Science and Engineering, June 1996.
Databases, Machine learning, (Privacy Preserving) Data Engineering, Artificial Intelligence, Research
interests Bioinformatics.
August 2023-..., Department of Computer Science, University of Sharjah, Sharjah, UAE.
Work
experience Associate professor
Research area: Privacy preserving data publishing/mining, machine learning, bioinfor- matics
Teaching area: Database systems, Operating systems, Programming,
March 2007-..., Department of Computer Engineering, TOBB University of Economics and Technology, Ankara, Turkey.
Assistant/Associate/Full professor
Research area: Privacy preserving data publishing/mining, machine learning, bioinfor- matics
Teaching area: Database systems, Data structures, Operating systems, Programming languages, Compilers, Theory of computation, Artificial intelligence
September 2005-March 2007, ERCIM (European Research Consortium in Informatics and Mathematics) Fellowships.
Two fellowship periods (each 9 months); (1st) Norwegian University of Science and Technology (NTNU) , Trondheim, Norway and (2nd) Institute of Information Science and Technology (ISTI), Pisa, Italy
Research area (at NTNU): computational DNA motif discovery
Research area (at ISTI): Constrained privacy preserving frequent itemset/sequence/structure mining/publication
January 2004-August 2005, Microwave and Systems Technologies Division, Aselsan Inc., Ankara, Turkey.
Worked in a large-scale air defense command&control system project as a senior sys- tem/software analyzer and designer
December 2002-December 2003, Department of Computer Science, University of Cal- gary, Calgary, Alberta, Canada.
Teaching assistant of courses Database Management Systems and Research Topics in Databases
Member of Advanced Database Systems and Applications (ADSA) laboratory
Research area: Data mining and Bioinformatics
August 2001-November 2002, Turkish Land Forces Headquarter, Ankara, Turkey.
Compulsory military service
August 1997-July 2001, Microwave and Systems Technologies Division, Aselsan Inc., Ankara, Turkey.
Worked in several system projects as software (senior) designer/developer
Programmed extensively in C/C++ for Win32 and Solaris platforms
July 1996-July 1997, Department of Computer Science and Engineering, Hacettepe Uni- versity, Ankara, Turkey.
Teaching assistant of coursesMicroprocessorsandDigital Systems Professional
1. IOI (International Olympiad in Informatics) Turkish team coach (January 2011-January 2016).
2. Invited speaker: IEEE International Conference on the Applications of Digital Infor- mation and Web Technologies (ICADIWT ’08)
3. Reviewer: Knowledge and Information Systems Journal (KAIS), Springer 4. Reviewer: Data and Knowledge Engineering Journal (DKE), Elsevier 5. Reviewer: Turkish Journal of Electrical Engineering and Computer Sciences 6. Reviewer: Data Mining and Knowledge Discovery Journal
7. Reviewer: IEEE SMC-C 8. Reviewer: IEEE TKDE
9. Reviewer: International Journal of Data Mining and Bioinformatics (IJDMB)
10. PC member: International Symposium on Networks, Computers and Communications (ISNCC ’18, ’19)
11. PC member: The International Workshop on Privacy and Anonymity in the Informa- tion Society (PAIS ’12, ’13, ’14, ’15, ’16, ’17)
12. PC member: International Conference on Data Mining (ICDM ’06, ’08, ’11, ’18) 13. PC member: International Symposium on Health Informatics and Bioinformatics (HI-
BIT ’10, ’11)
14. PC member: Int. Conf. on Health Informatics (HealthInf ’08, ’09, ’10)
15. PC Member: European Conference on Machine Learning and Conference on Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD ’09, ’10)
16. PC Member/reviewer: International Conference on Database and Expert Systems Ap- plications (DEXA ’09, ’10).
17. PC Member/reviewer: Pacific-Asia Conference on Knowledge Discovery and Data Min- ing (PAKDD ’07, ’09, ’10)
18. Reviewer: IFAC International Conference on Intelligent Control Systems and Signal Processing (ICONS’09)
19. PC Member: International Conference on e-Business (ICE-B’09)
20. PC Member/reviewer: International Symposium on Computer and Information Sci- ences (ISCIS ’05, ’09)
21. PC member: IEEE Int. Conf. on Bioinformatics and Bioengineering (BIBE ’07, ’08) 22. PC member: International Multi-Topic Conference (IMTIC’08)
23. PC member: Int. Work. on Practical Privacy-Preserving Data Mining (P3DM ’08), (in conjunction with SDM ’08)
24. Reviewer: SIAM Conference on Data Mining (SDM ’08)
25. Reviewer: International Conference on Information Visualization (IV ’10)
Teaching
1. Design and Analysis of Algorithms (undergraduate/graduate).
2. Automata Theory and Formal Languages (undergraduate).
3. Artificial Intelligence (undergraduate/graduate).
4. Database Systems (undergraduate).
5. Data Structures (undergraduate).
6. Unix/C++ Programming (undergraduate).
7. Programming Languages (undergraduate).
8. Theory of Computation (graduate).
9. Combinatorics (undergraduate).
10. Compilers (graduate).
11. Operating Systems (undergraduate).
Thesis
supervised 1. Zeynep Tufekci (MS, April 2023). ”Distinguishing True and False Buy/Sell Triggers from Financial Technical Indicators”, TOBB University.
2. Ozan Berk Bitirgen (MS, April 2022). ”Anonymous Location Sharing in Urban Area Mobility”, TOBB University.
3. Furkan Savsatli (MS, April 2021). ”Geo-spatial radar deployment optimization”, TOBB University.
4. Ugur Sopaoglu (PhD, August 2020). ”Privacy Preserving Anonymization of Big Data and Data Streams”, TOBB University.
5. Kutlu Emre Yilmaz (MS, April 2019). ”Inferring Political Alignments of Twitter Users:
A case study on 2017 Turkish constitutional referendum”, TOBB University.
6. Batuhan Karatas (MS, April 2018). ”Driver Classification with Machine Learning Methods on Vehicle Driving Data”, TOBB University.
7. Aytun Onay (PhD, August 2017). ”Formation of A Drug Classification Framework via Data Mining Techniques”, TOBB University.
8. Cansin Bayrak (MS, December 2016). ”Providing Location and Location Pattern Pri- vacy on Location-Based Applications”, TOBB University.
9. Kasim Ali Gul (MS, August 2016). ”Privacy and Safety Aware Traffic Data Generator”, TOBB University.
10. Mete Uzun (MS, April 2016). ”End-To-End Internet Speed Analysis of Mobile Net- works with MapReduce”, TOBB University.
11. Yigit Cetin (MS, June 2014). ”Implementation of Distributed RDFS Reasoning with MapReduce”, TOBB University.
12. Emre Yigitoglu (MS, August 2012). ”Privacy-preserving sharing of sensitive semantic locations”, TOBB University.
13. Ibrahim Gumus (MS, June 2012). ”Human Computation and Archive Digitization with Computer Games”, TOBB University.
14. Elif Tugce Ors (MS, August 2011). ”Soft Constraints based Clustering”, TOBB Uni- versity.
15. Engin Sahin (MS, June 2011). ”Human Computation and Image Tagging with Com- puter Games”, TOBB University.
16. Harun Gokce (MS, November 2010). ”Knowledge Hiding from Tree and Graph Databases”, TOBB University.
17. Gulistan Ozdemir Ozdogan (MS, January 2010). ”Implementation of Parallel FP- Growth Algorithm on Cluster Computers”, TOBB University.
18. Sertel Asim Unsal (MS, December 2009). ”Design and Implementation of an Institu- tional Change Management System”, TOBB University.
19. Arzu Kutukcu (MS, December 2009). ”Efficient Querying of Spatial Databases”, TOBB University.
Project
1. ”Sensitive knowledge hiding in data publication”, June 2008-December 2010, funded by TUBITAK (Turkish scientific research council) under 1001 (scientific and technological research projects support) programme (Principal investigator).
2. ”Protecting Location and Location Pattern Privacy for Location-Based Services”, Oc- tober 2014-April 2017, funded by TUBITAK (Turkish scientific research council) under 1001 (scientific and technological research projects support) programme (Principal in- vestigator).
3. ”Location Privacy Preserving Querying of Urban Area Proximity-based Services”, February 2019-May 2021, funded by TUBITAK (Turkish scientific research council) under 1001 (scientific and technological research projects support) programme (Prin- cipal investigator).
Profiles.
Publication
Google scholar: https://scholar.google.com/citations?user=fG9v1bwAAAAJ&hl=tr&oi=ao dblp: https://dblp.org/pers/hd/a/Abul:Osman
Theses.
1. O. Abul. ”Controlling Discrete Genetic Regulatory Networks”, PhD thesis, Dept. of Computer Engineering, Middle East Technical University, Ankara, 2005.
2. O. Abul. ”Multi-agent Reinforcement Learning using Function Approximation”, Mas- ters thesis, Dept. of Computer Engineering, Middle East Technical University, Ankara, 1999.
Book chapters.
1. O.Abul, ”Knowledge Hiding in Emerging Application Domains” in ”Privacy-Aware Knowledge Discovery: Novel Applications and New Techniques”, January 2011, CRC Press. (F. Bonchi and E. Ferrari editors)
Refereed Journals.
1. M.B.Bilgen, O.Abuland K.Bicakci. ”Authentication-enabled attribute-based access control for smart homes”, International Journal of Information Security, Vol. 22(2), Pages 479–495, 2023.
2. M. Uzun and O.Abul. ”Proactive Metering of Mobile Internet User Experience”, Balkan Journal of Electrical and Computer Engineering, Vol. 10.3, Pages 264–272, 2022. [Non-SCI]
3. O.Abul. ”Location-privacy preserving partial nearby friends querying in urban areas”, Data and Knowledge Engineering, Vol. 139, 2022.
4. U. Sopaoglu andO.Abul. ”Classification Utility Aware Data Stream Anonymization”, Applied Soft Computing, Vol. 110, 2021.
5. O.Abul and O. Bitirgen. ”Anonymous Location Sharing in Urban Area Mobility”, Knowledge and Information Systems (KAIS), Vol. 63, Pages 1849—1871, 2021.
6. O.Abuland B. Karatas. ”Can Driving Patterns Predict Identity and Gender?”, Jour- nal of Ambient Intelligence and Humanized Computing, Vol. 12, Pages 151-–166, 2021.
7. U. Sopaoglu andO.Abul. ”A utility based approach for data stream anonymization”, Journal of Intelligent Information Systems, Vol. 54, No.3, Pages 605–631, 2020.
8. O.Abuland C. Bayrak. ”From location to location pattern privacy in location-based services”, Knowledge and Information Systems (KAIS), Vol. 56/3, Pages 533–557, September 2018.
9. A. Onay, M. Onay and O.Abul. ”Classification of nervous system withdrawn and approved drugs with ToxPrint features via machine learning strategies”, Computer Methods and Programs in Biomedicine, Vol. 142, Pages 9-19, February 2017.
10. T. Can, IO. Girci, O.Abul and MF. Demirci. ”Informatics Olympiads in Turkey:
team selection and training”, Olympiads in Informatics, 2015. [Non-SCI]
11. O.Abuland H. Gokce. ”Knowledge Hiding from Tree and Graph Databases”, Data and Knowledge Engineering, Vol.72, Pages 148-171, February 2012.
12. S. Gundersen, M. Kalas,O.Abul, A. Frigessi, E. Hovig, and G. K. Sandve. ”Identifying elemental genomic track types and representing them uniformly”, BMC Bioinformatics, Vol. 12 No.494, 2011.
13. O.Abul, F. Bonchi and F. Giannotti. ”Hiding Sequential and Spatio-temporal Pat- terns”, IEEE TKDE Vol.22, No.12, December 2010.
14. O.Abul, F. Bonchi and M. Nanni. ”Anonymization of Moving Objects Databases by Clustering and Perturbation”, Information Systems, Vol.35, No.8, December 2010.
15. G. K. Sandve, O. Abul and F. Drablos. ”Compo: composite motif discovery using discrete models”, BMC Bioinformatics, Vol.9, No.527, 2008.
16. K. Klepper, G.K. Sandve, O. Abul, J. Johansen, V. Walseng and F. Drablos. ”As- sessment of composite motif discovery methods”, BMC Bioinformatics, Vol.9, No.123, 2008.
17. G.K. Sandve,O. Abul, V. Walseng and F. Drablos, ”Improved Benchmarks for Com- putational Motif Discovery”, BMC Bioinformatics, Vol.8, No.163, 2007.
18. O. Abul, R. Alhajj and F. Polat. ”A Powerful Approach for Effective Finding of Signif- icantly Differentially Expressed Genes”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.3, No.3, pp. 220-231, 2006.
19. O. Abul, R. Alhajj, F. Polat and K. Barker. ”Finding differentially expressed genes for pattern generation”, Bioinformatics, Vol.21, No.4, pp. 445-450, 2005.
20. F. Polat and O. Abul. ”Learning Sequences of Compatible Actions Among Agents”, Artificial Intelligence Review, Kluwer, Vol.17:1, pp. 21-37, March 2002.
21. O. Abul, F. Polat and R. Alhajj. ”Multi-Agent Reinforcement Learning Using Func- tion Approximation”, IEEE Transactions on Systems, Man and Cybernetics-C, Vol.30, No. 4, pp. 485-497, Nov. 2000.
Refereed International Conferences.
1. M.D. Turkmen, D. Dogan,O. Abuland M. Kutlu. ”Stance Detection of Turkish Twit- ter Accounts”, 31st Signal Processing and Communications Applications Conference (SIU), 2023.
2. O. Abuland F. Savsatli. ”Geospatial Radar Deployment Optimization”, 6th Interna- tional Conference on Computer Science and Engineering (UBMK), 2021.
3. Z. Tufekci and O. Abul. ”Distinguishing True and False Buy/Sell Triggers from Financial Technical Indicators”, Innovations in Intelligent Systems and Applications Conference (ASYU), October 2020, Istanbul.
4. K.E. Yilmaz andO. Abul. ”Inferring Political Alignments of Twitter Users: A case study on 2017 Turkish constitutional referendum”, ISNCC 2018, June 2018, Rome.
5. K.E. Yilmaz andO. Abul. ”Extraction of Environment Related Topics from Social Media using Latent Dirichlet Allocation”, ISEM 2018, June 2018, Sarajevo.
6. U. Sopaoglu andO. Abul. ”A top-down k-anonymization implementation for apache spark”, BigData 2017, pp. 4513-4521, December 2017, Boston.
7. M. Uzun andO. Abul. ”End-to-end internet speed analysis of mobile networks with mapReduce”, ISNCC 2016, May 2016, Tunisia. (Best paper award)
8. D.D. Yavuz and O. Abul. ”Implicit Location Sharing Detection in Social Media Turkish Text Messaging”, MOD 2016, pp. 341-352, August 2016, Volterra-Italy.
9. A. Soylev and O. Abul. ”REFBSS: Reference based similarity search in biological network databases”, CIBCB 2015, August 2015, Niagara Falls-Canada.
10. Y. Cetin andO. Abul. ”Distributed RDFS Reasoning with MapReduce”, ISCIS 2014, pp. 305-313, October 2014, Krakow.
11. O. Abul. ”Anonymity in Multi-Instance Micro-Data Publication”, ISCIS 2013, pp.
325-337, October 2013, Paris.
12. E.Yigitoglu, M.L. Damiani, O. Abul and C. Silvestri. ”Privacy-preserving sharing of sensitive semantic locations under road-network constraints”, MDM 2012: 186-195, July 2012, Bengaluru-India.
13. C. Silvestri, E.Yigitoglu, M.L. Damiani, O. Abul. ”SAWLnet: Sensitivity Aware Location Cloaking on Road-NETworks”. MDM 2012: 336-339, July 2012, Bengaluru- India. (Best demonstration award)
14. I.Gumus andO.Abul. ”Turkish archive digitization by human computation approach”, INISTA 2012, July 2012, Trabzon-Turkey.
15. R. Ozcan, F. Orhan, M. F. Demirci andO. Abul. ”An Adaptive Smoothing Method for Sensor Noise in Augmented Reality Applications on Smartphones”, Mobilware 2011, June 2011, London.
16. D. Vitale, E. E. Kuruoglu and O. Abul. ” Long Range Correlations Between Nu- cleotide Triplets”, Int. Symp. on Health Informatics and Bioinformatics (HIBIT’11), pp. 241-244, May 2011, Izmir.
17. H. Gokce and O. Abul. ”A Tradeoff Balancing Algorithm for Hiding Sensitive Fre- quent Itemsets”, Int. Conf. on Knowlede Discovery and Information Retrieval (KDIR’10), October 2010, Valencia.
18. G. O. Ozdogan and O. Abul. ”Task-Parallel FP-Growth on Cluster Computers”, 25th International Symposium on Computer and Information Sciences (ISCIS’10) , September 2010, London.
19. O. Abul. ”Hiding Co-Occurring Frequent Itemsets”, 2nd International Workshop on Privacy and Anonymity in the Information Society (PAIS’09), In conjunction with ICDT/EDBT’09, St. Petersburg, Russia, March 2009.
20. O. Abul. ”Motifhider: A Knowledge Hiding Approach To Sequence Masking”. The 21st International Symposium on Computer and Information Sciences (ISCIS’09), Cyprus, Sept. 2009.
21. O. Abul, H. Gokce and Y. Sengez. ”Frequent Itemsets Hiding: A Performance Evalu- ation Framework”. The 21st International Symposium on Computer and Information Sciences (ISCIS’09), Cyprus, Sept. 2009.
22. O. Abul, F. Bonchi and M. Nanni. ”Never Walk Alone: Uncertainty for Anonymity in Moving Objects Databases”, IEEE 24th International Conference on Data Engineering (ICDE’08), Cancun, Mexico, April 2008.
23. O. Abul, G.K. Sandve and F. Drablos. ”False Discovery Rates in Identifying Func- tional DNA Motifs”, Proceedings of IEEE Symposium on Bioinformatics and Bioengi- neering (BIBE’07), Cambridge MA, Oct. 2007.
24. O. Abul, M. Atzori, F. Bonchi and F. Giannotti. ”Hiding Sensitive Trajectory Pat- terns”, 6th International Workshop on Privacy Aspects of Data Mining, In conjunction with ICDM’07, Omaha, Nebreska, Oct. 2007.
25. M. Atzori, F. Bonchi, F. Giannotti, D. Pedreschi and O. Abul. ”Privacy-Aware Knowledge Discovery from Location Data”,The International Workshop on Privacy- Aware Location-based Mobile Services (PALMS’07),Mannheim, Germany, May 2007.
26. O. Abul, M. Atzori, F. Bonchi and F. Giannotti. ”Hiding Sequences”, The 3rd In- ternational Workshop on Privacy Data Management, In conjunction with ICDE 2007, Istanbul, Turkey, April 2007. An extended abstract also appears in SEBD’07 (Italian Database Conference).
27. O. Abul, F. Polat and R. Alhajj. ”Asymptotical Lower Limits on the Required Number of Examples for Learning Boolean Networks”, The 21st International Sympo- sium on Computer and Information Sciences (ISCIS’06), Istanbul, Turkey, Nov. 2006 (LNCS, Vol 4263 pp. 154-164, Springer-Verlag).
28. O. Abul, F. Polat and R. Alhajj. ”Optimal Multi-Objective Control Method for Discrete Genetic Regulatory Networks”, Proceedings of IEEE Symposium on Bioinfor- matics and Bioengineering (BIBE), Washington DC, Oct. 2006.
29. G.K. Sandve, M. Nedland, O.B. Syrstad, L.A. Eidsheim, O. Abul and F. Drablos.
”Accelerating Motif Discovery: Motif Matching on Parallel Hardware”, 6th Workshop on Algorithms in Bioinformatics (WABI), Zurich-Switzerland, Sep. 2006 (LNCS, Vol 4175 pp. 197-206 Springer-Verlag).
30. O. Abul, G.K. Sandve and F. Drablos. ”A Methodology for Motif Discovery Employ- ing Iterated Cluster Re-assignment”, Computational Systems Bioinformatics Confer- ence (CSB), Stanford University CA, Aug. 2006 (Series on Advances in Bioinformatics and Computational Biology - Volume 4, 2006, Imperial College Press).
31. O. Abul, G.K. Sandve and F. Drablos. ”TSCAN: A two-step de novo Motif Discov- ery Method”, The 3rd annual RECOMB Satellite Workshop on Regulatory Genomics (RECOMB-RG), Singapore, July. 2006.
32. O. Abul, R. Alhajj and F. Polat. ”Importance of Monitoring in Developing Optimal Control Policies for Probabilistic Boolean Genetic Networks”, Proceedings of the In- ternational Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU), Italy, July 2004.
33. O. Abul, R. Alhajj and F. Polat. ”Markov Decision Processes Based Optimal Con- trol Policies for Probabilistic Boolean Networks”, Proceedings of IEEE Symposium on Bioinformatics and Bioengineering (BIBE), Taiwan, pp.337-344, May 2004.
34. 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, Cyprus, Mar. 2004.
35. O. Abul, A. Lo, R. Alhajj, F. Polat and K. Barker. ”Cluster Validity Analysis Using Subsampling”, Proceedings of IEEE International Conference on Systems, Man and Cybernetics, Washington DC, Oct. 2003.
36. O. Abul, F. Polat and R. Alhajj. ”Function Approximation Based Multi-Agent Re- inforcement Learning”, Proceedings of IEEE International Conference on Tools with Artificial Intelligence (ICTAI-2000), IEEE Press, Nov 13, 2000, Vancouver, British Columbia, Canada, pp.36-39.