Click here for login.
Online visitors: 5
Publications
Publications
Name Authors Short Description Book Title

Improved Small Activity Determination via Centroid Nearest Neighbors Classification

P. Dao
F. Hormozdiari
H. Jowhari
and
S.C. Sahinalp
K. Byler
A. Cherkasov
Z.Cataltepe

In this study, we introduce the Combinatorial
Centroid Nearest Neighbor (CCNN) method which determines the representative compounds in a way that would
yield no classi cation errors on the training set. On a number of data sets CCNN method was applied, we observed
that CCNN provides the highest accuracy over the data sets of three di erent bioactivities among all classi ers we
tested.

CSB
2009, August 10-12, Stanford, CA.

On Utilizng Optimal and Information Theoretic Syntactic Modelling for Peptide Classification

Eser Aygün
John Oommen
Zehra Çataltepe

in this paper, we show that the
probability measure obtained from the OIT model can be perceived as a
sequence similarity metric, using which a Support Vector Machine
(SVM)-based peptide classifier, referred to as OIT SVM, can be
devised.

The classifier, which we have built has been tested for eight
different "substitution" matrices and for two different data sets,
namely, the HIV-1 Protease Cleavage sites and the T-cell Epitopes. The
results show that the OIT model performs significantly better than the
one which uses a Needleman-Wunsch sequence alignment score, and the
peptide classification methods that previously experimented with the
same two datasets.

PRIB 2009, Sheffield, England

Importance of Secondary Structure Elements for Prediction of GO Annotations

Zehra Çataltepe
Aslı Filiz
Eser Aygün
Özlem Keskin

In this study, importance of different secondary structure elements for protein function prediction is evaluated. In order to do that, first amino acid sequences are partitioned according to the actual secondary structure information. Instead of the whole sequence, portions of the amino acid sequence that belong to different secondary structure regions are used.

International Symposium on Health Informatics and Bioinformatics

Protein Function Prediction with Amino Acid Sequence and Secondary Structure Alignment Scores

Zehra Çataltepe
Eser Aygün
Caner Kömürlü
Zafer Aydin

In this study, we use amino acid sequence and actual or predicted secondary structure for protein function prediction. We investigate both sequence-sequence and Hidden Markov Model (HMM) profile-profile similarity measures that use both sequence and secondary structure information

International Symposium on Health Informatics and Bioinformatics

Gene Ontology Prediction Using Compression Based Distances
and Alignment Scores on Both Amino Acid Sequence and
Secondary Structure

Zehra Çataltepe
Aslı Filiz

In this study, we use NCD distance together with Smith-Waterman (SW) alignment scores of protein sequences for gene ontology prediction. We find out that, using secondary structure in addition to the amino acid sequence increases the prediction performance when using NCD or SW alignment scores alone.

International Symposium on Computer and Information Sciences

Protein Function Prediction Using Motifs, Sequence Features, Alignment Scores and Classifier Combination

Zehra Çataltepe
Uğur Ayan
Eser Aygün

In this study, our aim is to compare success of function prediction when sequence physiochemical properties, alignment scores or motifs are used

Research in Computational Molecular Biology

Gene Ontology (GO) Molecular Function
Prediction Based on Alignment Scores

Zehra Çataltepe
Eser Aygün

We investigate Gene Ontology (GO) Molecular Function prediction using alignment scores between protein sequences. We introduce a binary classification algorithm called Double Threshold Classifier (DTC).

International Symposium on Health Informatics and Bioinformatics.

Dimensionality Reduction for Protein Function Prediction

Zehra Çataltepe
Eser Aygün
Aslı Filiz
Özlem Keskin
Caner Kömürlü
Yücel Altunbaşak

In this study, we evaluate the effects of dimensionality reduction on protein function prediction. We evaluate three different classifiers (Naïve Bayes, kNN, SVC) and three different dimensionality reduction methods (PCA, Fisher’s LDA and FCBF (Fast Correlation-Based Filter) algorithm

Automated Function Prediction – Biosapiens Joint Special Interest Group Meeting

 

PUBLICATIONS:

 

(Organized by Topic, **:journal, *:book chapter, the conference papers have not been updated):

Book: (2010) D. Ünay, Z. Çataltepe and S. Aksoy, Recognizing Patterns in Signals, Speech, Images and Videos, ICPR 2010 Contests, Istanbul, Turkey, August 23-26, 2010, Contest Reports Lecture Notes in Computer Science, Volume 6388, 2010, DOI: 10.1007/978-3-642-17711-8.

Classification of Networked Data:

  1. **(2015) İ. Gunes, S. Gunduz-Oguducu, Z. Cataltepe,  Link Prediction Using Time-Series of Neighborhood-based Static Node Similarity Metrics, Data Mining and Knowledge Discovery, accepted, DOI: 10.1007/s10618-015-0407-0.
  2. **(2014) İ. Gunes, Z. Cataltepe, S. Gunduz-Oguducu, GA-TVRC-Het: Genetic Algorithm enhanced Time Varying Relational Classifier for Evolving Heterogeneous Networks, Data Mining and Knowledge Discovery, 28:670-701.
  3. **(2014) Z. Cataltepe, A. Sonmez, B. Senliol, Feature Enrichment and Selection for Transductive Classification of Networked Data, Pattern Recognition Letters, Pattern Recognition Letters, 37:41-53.
  4. *(2014) Z. Cataltepe, A. Sonmez, Classification in Social Networks, Book Chapter in: Social Network Analysis:Tutorials and Case Studies, S. Gunduz-Oguducu, S. Etaner-Uyar eds., Springer, ISBN: 978-3709117965.
  5. (2013) Ergur, B., and Z. Cataltepe. "Relational stock market network analysis/İlişkisel Borsa Ağı Analizi" Signal Processing and Communications Applications Conference (SIU), 2013 21st. IEEE, 2013.
  6. (2012) J. Li, A. Sonmez, Z. Cataltepe, E. Bax, Validation of Network Classifiers, Structural, Syntactic, and Statistical Pattern Recognition Lecture Notes in Computer Science Volume 7626, 2012, 448-457.
  7. (2011) Z. Cataltepe, A. Sonmez, K. Baglioglu, and A. Erzan, Collective Classification Using Heterogeneous Classifiers, 7th International Conference on Machine Learning and Data Mining MLDM 2011, August 30-September 3, 2011, New York/USA.
  8. (2011) I. Gunes, Z. Cataltepe, and S. Gunduz-Oguducu, GA-TVRC: A Novel Relational Time Varying Classifier to Extract Temporal Information Using Genetic Algorithms, 7th International Conference on Machine Learning and Data Mining MLDM 2011, August 30-September 3, 2011, New York/USA.
  9. (2009) B. Senliol, Z. Cataltepe and A. Sonmez, Collective Classification with Content and Link Noise, NIPS 2009 Workshop on Analyzing Networks and Learning with Graphs, December 11, 2009 in Whistler, BC, Canada.
  10. (2009) B. Senliol, A. Aral and Z. Cataltepe, Feature Selection for Collective Classification , ISCIS 2009, Sept 14-16, Cyprus.

Human Learning:

  1. **(2014) C. Doenyas, E. Şimdi, E. Ç. Özcan, Z. Çataltepe, B. Birkan, Autism and tablet computers in Turkey: Teaching picture sequencing skills via a web-based iPad application,International Journal of Child-Computer Interaction, 2.1 (2014): 60-71, DOI: 10.1016/j.ijcci.2014.04.002.
  2. (2014) Aslan, S., Cataltepe, Z., Diner, I., Dundar, O., Esme, A., Ferens, R., …. and Yener, M. (2014, December). Learner Engagement Measurement and Classification in 1: 1 Learning. In Machine Learning and Applications (ICMLA), 2014 13th International Conference on (pp. 545-552). IEEE.
  3. (2012) M. E. Alper and Z. Cataltepe, Improving Course Success Prediction Using Abet Course Outcomes And Grades, CSEDU (The 4th International Conference on Computer Supported Education), Porto, Portugal, April 16-18, 2012.
  4. (2012) A. Aral and Z. Cataltepe, Learning Styles For K-12 Mathematics E-Learning, CSEDU (The 4th International Conference on Computer Supported Education), Porto, Portugal, April 16-18, 2012.

Dimensionality Reduction:

  1. **(2015) Ümit Ekmekçi, Zehra Çataltepe, Extended multimodal Eigenclassifiers and criteria for fusion model selection, Information Sciences, Volume 298, 20 March 2015, Pages 53-65, ISSN 0020-0255, http://dx.doi.org/10.1016/j.ins.2014.11.034.
  2. **(2010) Y. Yaslan and Z. Cataltepe, Co-training with Relevant Random Subspaces, Neurocomputing, Volume 73, Issues 10-12, June 2010, pp 1652-1661.
  3. **(2005) Z. Cataltepe, E. Cetin and T. Pearson, Identification of Insect Damaged Wheat Kernels Using Transmittance Images , Electronics Letters, vol 41, no 5, pp 23-24. 
  4. (2013) H. Gündüz, Z. Cataltepe. Prediction Of Istanbul Stock Exchange (ISE) Direction Based On News Articles, In The Third International Conference on Digital Information Processing and Communications (ICDIPC2013) (pp. 320-330). The Society of Digital Information and Wireless Communication.
  5. (2013) Ekmekci, Ü.,  Cataltepe, Z. Classifier combination with kernelized eigenclassifiers. In Information Fusion (FUSION), 2013 16th International Conference on (pp. 743-749). IEEE.
  6. (2012) D. Polat, Z. Çataltepe, , Feature selection and classification on brain computer interface (BCI) data, SIU 2012, 18-20 May 2012, Mugla, Turkey.
  7. (2009) G. Gulgezen, Z. Cataltepe, L. Yu, Stable and Accurate Feature Selection, ECML/PKDD 2009, Bled, Slovenia.
  8. (2011) Z. Cataltepe, S. Ozer, V. Unutmaz Barin, Feature Selection for Price Change Prediction , International Conference on Mathematical Finance and Economics, July 6-8, 2011, Istanbul, Turkey.
  9. (2009) Y. Yaslan and Z. Cataltepe, Selection of Relevant and Non-Redundant Feature Subspaces for Co-training , IDEAL Conference, Burgos, Spain, 23-26 September, 2009.
  10.  (2009) E. Avsar, M. Kamasak, Z. Cataltepe, Tek-Sinif Destek Vektor Makineleri Kullanilarak EEG Isaretlerinin Siniflandirilmasi/EEG Signal Classification Using One-Class Support Vector Machines, BIYOMUT 2009, Izmir, Turkey.
  11. (2009) G. Gülgezen, Z. Çataltepe and L. Yu, Stable Feature Selection Using MRMR Algorithm/MRMR Algoritmasi Kullanilarak Kararli Oznitelik Secimi, 17th IEEE Conference on Signal Processing and Communications Applications (SIU 2009), Antalya, Turkey.
  12. (2009) Y. Yaslan, Z. Cataltepe, Audio Genre Classification with Co-MRMR/Muzik Turlerinin Co-MRMR ile Siniflandirilmasi, 17th IEEE Conference on Signal Processing and Communications Applications (SIU 2009), Antalya, Turkey.
  13. (2008) B. Senliol, G. Gulgezen, L. Yu, Z. Cataltepe, Fast Correlation Based Filter (FCBF) with a Different Search Strategy, poster presentation at ISCIS 2008 Conference, 27-29 October 2008, Istanbul, Turkey.
  14. (2007) M. Turan and Z. Cataltepe, Clustering and Dimensionality Reduction to Determine Important Software Quality Metrics, ISCIS 2007, Ankara, Turkey.
  15. (2007) Z. Cataltepe, H. M. Genc, T. Pearson, A PCA/ICA Based Feature Selection Method and its Application for Corn Fungi Detection, Eusipco (European Signal Processing Conference) 2007, 3-7 September, Poland.
  16. (2007) H. M. Genc, Z. Cataltepe, T. Pearson, A New PCA/ICA Based Feature Selection Method/Yeni Bir Temel/Bagimsiz Bilesen Analizi(TBA/BBA) Tabanli Oznitelik Secme Yontemi, SIU 2007, Eskisehir, Turkey.
  17. (2004) Z. Cataltepe, T. Pearson and E. Cetin, Fast Insect Damage Detection in Wheat Kernels Using Transmittance Images, IEEE IJCNN (International Joint Conference on Neural Networks) 2004, Budapest, Hungary.
  18. (2004) Z. Cataltepe, E. Cetin and T. Pearson, Identification of Insect Damaged Wheat Kernels Using Transmittance Images, IEEE ICIP (International Conference on Image Processing) 2004, Singapore.

Bioinformatics:

  1. **(2010) E. Aygun, B. J. Oommen and Z. Cataltepe, “Peptide Classification Using Optimal and Information Theoretic Syntactic Modeling, doi:10.1016/j.patcog.2010.05.022, Pattern Recognition.
  2. (2009) E. Aygun, J. Oommen, Z. Cataltepe, On Utilizing Optimal and Information Theoretic Syntactic Modeling for Peptide Classification, PRIB 2009, Sheffield, England.
  3. (2009) P. Dao, F. Hormozdiari, H. Jowhari, S.C. Sahinalp, K. Byler, A. Cherkasov, Z. Cataltepe, Improved Small Molecule Activity Determination via Centroid Nearest Neighbors Classification, CSB 2009, August 10-12, Stanford, CA.
  4. (2009) B. Senliol, Z. Cataltepe, Score Matrix Optimization for Quartz Binding Peptides Using Evolutionary Strategy/Kuvarsa Baðlanabilen Peptitler için Evrimsel Strateji ile Skor Matris Optimizasyonu, 17th IEEE Conference on Signal Processing and Communications Applications (SIU 2009), Antalya, Turkey.
  5. (2008) A. Filiz, Z. Cataltepe, Gene Ontology Prediction Using Compression Based Distances and Alignment Scores on Both Amino Acid Sequence and Secondary Structure, ISCIS 2008 Conference, 27-29 October 2008, Istanbul, Turkey.
  6. (2008) A. Filiz, E. Aygün, O. Keskin, Z. Cataltepe, Importance of Secondary Structure Elements for Prediction of GO Annotations, HIBIT 2008, Istanbul, Turkey.
  7. (2008) E. Aygün, C. Komurlu, Z. Aydin, Z. Cataltepe, Protein Function Prediction with Amino Acid Sequence and Secondary Structure Alignment Scores, HIBIT 2008, Istanbul, Turkey.
  8. (2007) Z. Cataltepe, U. Ayan and E. Aygun, Protein Function Prediction Using Motifs, Sequence Features and Alignment Scores, poster presentation at RECOMB (International Conference on Research in Computational Molecular Biology), April 2007, San Fransisco.
  9. (2007) Z. Cataltepe, E. Aygun, A. Filiz, O. Keskin, C. Komurlu and Y. Altunbasak, Dimensionality Reduction for Protein Function Prediction, poster presentation at Automated Function Prediction – Biosapiens Joint Special Interest Group Meeting, Vienna, Austria July 2007.
  10. (2007) E. Aygun and Z. Cataltepe, Gene Ontology (GO) Molecular Function Prediction Based on Alignment Scores, HIBIT (International Symposium on Health Informatics and Bioinformatics), May 2007, Antalya, Turkey.

Movie/WebPage/Music/Document Classification and Recommendation:

  1. **(2013) Cataltepe, Z., Uluyağmur, M. E. Tayfur, E. (2013). Feature Selection for Movie Recommendation. Turkish Journal of Electrical Engineering and Computer Sciences.
  2. *(2009) Z. Cataltepe and B. Altinel, Music Recommendation by Modeling User’s Preferred Perspectives of Content, Singer/Genre and Popularity in "Collaborative and Social Information Retrieval and Access: Techniques for Improved User Modeling" edited by M. Chevalier, C. Julien and C. Soulé-Dupuy, IGI Global, pp. 203-221, ISBN: 978-1-60566-306-7,
  3. *(2007) Z. Cataltepe, Y. Yaslan and A. Sonmez, Music Genre Classification Using MIDI and Audio Features, EURASIP Journal of Advances in Signal Processing, vol. 2007 (January), Article ID 36409, 8 pages.
  4. (2015) E. Gülşen, H. Gündüz, Z. Çataltepe, L. Serinol, Big Data Feature Selection And Projection For Gender Prediction Based On User Web Behaviour/Internet Kullanıcı Davranısları Tabanlı Cinsiyet Tahmini icin Buyuk Veri Uzerinde Oznitelik Secimi ve Indirgemesi Yapılması, accepted, SIU 2015 Conference, Malatya, Turkey, May 16-19, 2015.
  5. (2012) M. Uluyagmur, Z. Cataltepe and E. Tayfur, Content-Based Movie Recommendation Using Different Feature Sets, Proceedings of the World Congress on Engineering and Computer Science 2012 Vol I WCECS 2012, October 24-26, 2012, San Francisco, USA. 
  6. (2012) Z. Çataltepe, M. Uluyağmur, E. Tayfur, TV program recommendation using implicit feedback with adaptive regularization, SIU 2012, 18-20 May 2012, Mugla, Turkey.
  7. (2009) Z. Cataltepe, B. Dilber, H. Germiyan, Better User Interest Estimation to Increase Web Banner Ad Click Rate/ Daha Iyi Kullanici Ilgi Alani Belirleme ile Webde Reklam Tiklamanin Iyilestirilmesi, SIU 2010, Diyarbakir, Turkey.
  8. (2009) Y. Yaslan and Z. Cataltepe, Audio Genre Classification with SemiSupervised Feature Ensemble Learning, MML Workshop at ECML/PKDD, 7-11 September, 2009, Bled Slovenia.
  9. (2007) Z. Cataltepe and B. Altinel, Hybrid Music Recommendation Based on Different Dimensions of Audio Content and Entropy Measure, Eusipco (European Signal Processing Conference) 2007, 3-7 September, Poland.
  10. (2007) Z. Cataltepe and B. Altinel, Music Recommendation Based on Adaptive Feature and User Grouping, ISCIS 2007, Ankara, Turkey.
  11. (2007) Z. Cataltepe, Y. Turan, F. Kesgin, Turkish Document Classification Using Shorter Roots/Türkçe’de Daha Kisa Kök Kullanarak Doküman Siniflandirma, SIU 2007, Eskisehir, Turkey.
  12. (2007) Z. Cataltepe and E. Aygun, An Improvement of Centroid-Based Classification Algorithm for Text Classification, DBMI Workshop within ICDE (International Conference on Data Engineering), April 2007, Istanbul.
  13. (2007) Y. Yaslan, Z. Çataltepe, A Comparison Framework of Similarity Metrics Used for Web Access Log Analysis, poster presentation at MLDM (Machine Learning and Data Mining) 2007, July 18-20, 2007, Leipzig/Germany.
  14. (2006) Y. Yaslan, Z. Çataltepe, Audio Music Genre Classification Using Different Classifiers and Feature Selection, ICPR 2006, Hong-Kong.
  15. (2005) Z. Cataltepe, A. Sonmez and E. Adali, Music Classification Using Kolmogorov Distance, Representation in Music/Musical Representation Congress, Istanbul, Turkey, October 2005.

Monitoring (of Traffic, Power Plants, Motors):

  1. (2010)Ü. Yildirim, Z. Cataltepe, Oruntu Tanima ve Oznitelik Secme Yontemleri Kullanarak Kisa Zaman Sonraki Yol Trafik Hiz Ongorusu, Türkiye Bilisim Vakfı, Bilgisayar Bilimleri ve Mühendisliği Dergisi, 2010, Sayı 3, Sayfa 21-28.
  2. (2008) Ü. Yildirim, Z. Cataltepe, Short Time Traffic Speed Prediction Using Data from a Number of Different Sensor Locations, ISCIS 2008 Conference, 27-29 October 2008, Istanbul, Turkey.
  3. (2008) Ü. Yildirim, Z. Cataltepe, Short Time Traffic Speed Prediction Using Pattern Recognition and Feature Selection Method/Oruntu Tanima ve Oznitelik Secme Yontemleri Kullanarak Kisa Zaman Sonraki Yol Trafik Hiz Ongorusu, SIU 2008, Didim, Turkey (one of the 9 finalists for the Alper Atalay Student Prize).
  4. (2007) E. Karatoprak, S. Seker, Z. Cataltepe and T. Sengüler, Using Bayes Decision Rule for Motor Fault Detection/Bayes Karar Verme Kuraminin Motor Ariza Tanisinda Kullanilmasi, SIU 2007, Eskisehir, Turkey.
  5. (2005) Z. Cataltepe, C. Yuan, C. Neubauer, Meltem Demirkus and H.Gerd-Brummel, A Robust Method to Identify Faults in Correlated Sensors in Machine Condition Monitoring, EUSIPCO (European Signal Processing Conference) September 2005, Antalya, Turkey.
  6. (2005) C. Yuan, C. Neubauer, Z. Cataltepe and H.Gerd-Brummel, Support Vector Methods and Use of Computed Sensors for Power Plant Monitoring, ICASSP (International Conf. on Acoustics, Speech and Signal Processing), Philadelphia, USA, March 2005.
  7. (2003) Z. Cataltepe, M. Chang, T. Stiefmeier, B. Chen and C. Neubauer, Using ROC Curve In the Absence of Positive Examples, CINC 6 (The 6th International Conference on Computational Intelligence and Natural Computing) Cary, North Carolina.
  8. (2003) Z. Cataltepe, P. Moghe, Characterizing Nature and Location of Congestion on the Public Internet, ISSC' (IEEE Symposium on Computers and Communication), Kemer, Antalya, Turkey.

See also the patents below.

Misc. Topics:

  1. **(1999) Z. Cataltepe, Y. S. Abu-Mostafa and M. Magdon-Ismail, No Free Lunch for Early Stopping, Neural Computation, vol 11, no 4, pp 995--1009.
  2. *(2009) B. Kurt and Z. Cataltepe, "Enterprise Server Platform" in "Handbook of Enterprise Integration", edited by M.H. Sherif, Auerbach Publications, ISBN: 978-1420078213.
  3. (1997) Z. Cataltepe and M. Magdon-Ismail, Incorporating Test Inputs into Learning, Proceedings of the Advances in Neural Information Processing Systems 10.
  4. (2012) H. Gumus, E.K. Ozay, I. Ari, Z. Cataltepe, An iterative approach for clustering optimization and validation, SIU 2012, 18-20 May 2012, Mugla, Turkey.
  5. (1997) E. Bax, Z. Cataltepe and J. Sill, The Central Classifier Bound -- A New Error Bound for the Classifier Chosen by Early Stopping, IEEE PACRIM, Victoria, B.C. 1997 conference proceedings.
  6. (1994) Z. Cataltepe and Y. S. Abu-Mostafa, Estimating Learning Performance Using Hints, Proceedings of the 1993 Connectionist Models Summer School, M. Mozer et. al. (Eds.), Lawrence Erlbaum Associates, Publishers, Hillsdale, NJ. pp.380-386.
  7. (2008) Y. Yaslan, Z. Cataltepe, Co-Training with Adaptive Bayesian Classifier Combination, poster presentation at ISCIS 2008 Conference, 27-29 October 2008, Istanbul, Turkey.
  8. (1997) R. A. Sahan, D. C. Albin, N. K. Sahan and Z. Cataltepe, Modelling Of Transitional Air Flow System In A Channel Using Artificial Neural Networks", Sixth Turkish Symposium on Artificial Intelligence and Neural Networks ( TAINN 97 ).

 


Student Thesis:

  1. (2014) Abdullah Sonmez, Ph.D. in Computer Engineering, Thesis title: " Improving Collective Classification By Incorporating Directed Links, Feature Enrichment And Classifier Combination".
  2. (2014) Ismail Gunes, Ph.D. in Computer Engineering, Thesis title: "Node Classification And Link Prediction On Complex Evolving Networks " (co-advised with Sule Gunduz-Oguducu).
  3. (2010) Yusuf Yaslan, Ph.D. in Computer Engineering, Thesis title: "Supervised and Semi-Supervised Learning with Feature Ensembles".
  4. (2014) Bircan Ergur, M. Sc. in Computer Engineering, Thesis title: "Prediction of the Borsa Istanbul (BIST) Change Direction Using Relational Stock Networks/Borsa İstanbul (BIST) Hisse Fiyat Değişim Yönünün İlişkisel Borsa Aği Kullanilarak Tahmin Edilmesi".
  5. (2014) Umit Ekmekci, M. Sc. in Computer Engineering, Thesis title: "Classifier Fusion For Multimodal Correlated Classifiers and Video Annotation".
  6. (2014) Ismail Bilgen, M. Sc. in Computer Engineering, Thesis title: "Predicting Human-HIV1 Protein-Protein Interactions Using Random Forests In A Co-Training Approach".
  7. (2013) Kadriye Bağlıoğlu, M.Sc. in Computer Engineering, Thesis title: "Ağ Verisi Üzerinde İlgili ve Rastgele Altuzaylar Seçerek Birlikte Öğrenme".
  8. (2013) Hakan Gündüz, M.Sc. in Computer Engineering, Thesis title: "Borsa İstanbul 100 Endeksi Yönünün Ekonomi Haberleri İle Tahmin Edilmesi".
  9. (2012) Mahiye Uluyağmur, M.Sc. in Computer Engineering, Thesis title: "Hybrid Film Öneri Sistemi/Hybrid Movie Recommendation".
  10. (2011) Onur Sarkan, M.Sc. in Computer Engineering, Thesis title: "GSM Network Fault Management By Using Statistical Learning Methods/ GSM Şebekelerinde İstatistiksel Öğrenme Yöntemleri İle Aksaklık Yönetimi".
  11. (2010) Barış Şenliol, M.Sc. in Computer Engineering, Thesis title: "Kolektif Sınıflandırma Yöntemleri için Öznitelik ve Düğüm Seçimi/Feature and Node Selection for Collective Classification".
  12. (2010) Kenan Kule, M.Sc. in Computer Engineering, Thesis title: "Feature Selection Using Different Mutual Information Estimation Methods".
  13. (2009) Gökhan Gülgezen, M.Sc. in Computer Engineering, Thesis title: "Stable and Accurate Feature Selection".
  14. (2009) Eser Aygün, M.Sc. in Computer Engineering, Thesis title: " Improvement of Protein Function Prediction Using Structural Information and Peptite Classification Using Syntactic Transition Probabilities/Protein Islev Kestiriminde Yapisal Bilginin Katkisi ve Dizi Gecis Olasiliklari ile Peptit Siniflandirma".
  15. (2008) Asli Filiz, M.Sc. in Information Sciences, Thesis title: " Alignment and Compression-Based Protein Function Prediction Using Secondary Structure”
  16. (2008) Caner Kömürlü, M.Sc. in Information Sciences, Thesis title: " Protein Function Prediction Using Hidden Markov Models".
  17. (2008) Ümit Ülkem Yıldırım, M.Sc. in Computer Engineering, Thesis title: " Short Time Traffic Speed Prediction Using Pattern Recognition and Feature Selection/Örüntü Tanima ve Öznitelik Seçme Yöntemleri Kullanarak Kısa Zaman Sonraki Yol Trafik Hiz Öngörüsü".
  18. (2007) Berna Altınel, M.Sc. in Computer Engineering, Thesis title: "A Hybrid Music Recommender System Based on Different Features of Music and User".
  19. (2005) Abdullah Sönmez, M.Sc. in Computer Engineering, Thesis title: "Music Genre and Composer Identification by Using Kolmogorov Distance" (co-advised with E. Adali).