ZEHRA CATALTEPE

Associate Professor

Istanbul Technical University, Computer Engineering Department, Maslak, Istanbul, Turkey

cataltepe at itu.edu.tr

www3.itu.edu.tr/~cataltepe

EDUCATION:

• 1998 : Ph.D in Computer Science at Caltech
  Thesis Title: "Incorporating Input Information into Learning and Augmented Objective Functions"
  Thesis Advisor: Prof. Yaser S. Abu-Mostafa
• 1994 : M.S. in Computer Science at Caltech
  Thesis Title: "The Scheduling Problem in Learning From Hints"
  Thesis Advisor: Prof. Yaser S. Abu-Mostafa
• 1991 : B.S. in Computer Engineering and Information Sciences at Bilkent University, Turkey (Graduated first in the class)
  Thesis Title: "Field: A Data Type for Automated Perception in Go"
  Thesis Advisor: Prof. Varol Akman

RESEARCH INTERESTS:

• Machine learning applications (bioinformatics, social network analysis, credit scoring, recommendation (web, music), web mining, music genre and composer classification, machine and plant condition monitoring, image classification).
• Machine learning algorithms (collective classification, HMMs, RBF Networks, SVMs, linear models).
• Machine learning theory (feature selection, classifier combination techniques, improving generalization by regularization or additional information about the problem).

PUBLICATIONS (Organized by Topic, *:journal/book chapter):

Bioinformatics:

1. *(2009) E. Aygun, B. J. Oommen and Z. Cataltepe, “Peptide Classification Using Optimal and Information Theoretic Syntactic Modeling”, accepted.
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 Bağlanabilen 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.

Machine Learning (Feature Selection):

11. *(2009) Y. Yaslan and Z. Cataltepe, "Co-training with Relevant Random Subspaces", accepted.
12. *(2009) B. Senliol, Z. Cataltepe, A. Sonmez, "Feature and Node Selection for Collective Classification", under preparation.
13. *(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.
14. (2009) Y. Yaslan and Z. Cataltepe, “Random, Relevant and Non-Redundant Feature Subspaces for Co-training “, IDEAL Conference, Burgos, Spain, 23-26 September, 2009.
15. (2009) B. Senliol, A. Aral and Z. Cataltepe, “Feature Selection for Collective Classification”, ISCIS 2009, Sept 14-16, Cyprus.
16. (2009) G. Gulgezen, Z. Cataltepe, L. Yu, “Stable and Accurate Feature Selection”, ECML/PKDD 2009, Bled, Slovenia.
17. (2009) E. Avsar, M. Kamasak, Z. Cataltepe, ” Tek-Sınıf Destek Vektör Makineleri Kullanılarak EEG İşaretlerinin Sınıflandırılması/EEG Signal Classification Using One-Class Support Vector Machines”, BIYOMUT 2009, Izmir, Turkey.
18. (2009) G. Gülgezen, Z. Çataltepe and L. Yu, "Stable Feature Selection Using MRMR Algorithm/MRMR Algoritması Kullanılarak Kararlı Öznitelik Seçimi", 17th IEEE Conference on Signal Processing and Communications Applications (SIU 2009), Antalya, Turkey.
19. (2009) Y. Yaslan, Z. Cataltepe, "Audio Genre Classification with Co-MRMR/Müzik Türlerinin Co-MRMR ile Sınıflandırılması", 17th IEEE Conference on Signal Processing and Communications Applications (SIU 2009), Antalya, Turkey.
20. (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.
21. (2007) M. Turan and Z. Cataltepe, "Clustering and Dimensionality Reduction to Determine Important Software Quality Metrics", ISCIS 2007, Ankara, Turkey.
22. (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.
23. (2007) H. M. Genc, Z. Cataltepe, T. Pearson, "A New PCA/ICA Based Feature Selection Method/Yeni Bir Temel/Bağımsız Bileşen Analizi(TBA/BBA) Tabanlı Öznitelik Seçme Yöntemi", SIU 2007, Eskisehir, Turkey.
24. (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.
25. (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.

Music/Document Classification and Recommendation:

26. *(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,
27. *(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.
28. (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.
29. (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.
30. (2007) Z. Cataltepe and B. Altinel, "Music Recommendation Based on Adaptive Feature and User Grouping", ISCIS 2007, Ankara, Turkey.
31. (2007) Z. Cataltepe, Y. Turan, F. Kesgin, " Turkish Document Classification Using Shorter Roots/Türkçe’de Daha Kısa Kök Kullanarak Doküman Sınıflandırma", SIU 2007, Eskisehir, Turkey.
32. (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.
33. (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.
34. (2006) Y. Yaslan, Z. Çataltepe, "Audio Music Genre Classification Using Different Classifiers and Feature Selection", ICPR 2006, Hong-Kong.
35. (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):

36. (2008) Ü. Yıldırım, 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.
37. (2008) Ü. Yıldırım, Z. Cataltepe, “Short Time Traffic Speed Prediction Using Pattern Recognition and Feature Selection Method/Örüntü Tanıma ve Öznitelik Seçme Yöntemleri Kullanarak Kısa Zaman Sonraki Yol Trafik Hız Öngörüsü”, SIU 2008, Didim, Turkey (one of the 9 finalists for the Alper Atalay Student Prize).
38. (2007) E. Karatoprak, S. Seker, Z. Cataltepe and T. Sengüler, "Using Bayes Decision Rule for Motor Fault Detection/Bayes Karar Verme Kuramının Motor Arıza Tanısında Kullanılması", SIU 2007, Eskisehir, Turkey.
39. (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.
40. (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.
41. (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.
42. (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.
43. (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 ).

See also the patents below.

Machine Learning (Other topics: Early Stopping of Training, Learning From Hints):

44. *(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.
45. (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.
46. (1997) Z. Cataltepe and M. Magdon-Ismail, "Incorporating Test Inputs into Learning" , Proceedings of the Advances in Neural Information Processing Systems 10 .
47. (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.
48. (2008) Y. Yaslan, Z. Cataltepe, "Co-Training with Adaptive Bayesian Classifier Combination", poster presentation at ISCIS 2008 Conference, 27-29 October 2008, Istanbul, Turkey.

Software:

49. *(2009) B. Kurt and Z. Cataltepe, "Enterprise Server Platform" in "Handbook of Enterprise Integration", edited by M.H. Sherif, Auerbach Publications, ISBN: 978-1420078213 .

ISSUED PATENTS :

1. (2009) Z. Cataltepe, C. Neubauer, C. Yuan, (Siemens Corporate Research), Method to use a receiver operator characteristics curve for model comparison in machine condition monitoring, US Pat No: 7,552,035.
2. (2008) C. Yuan, C. Neubauer, Z. Cataltepe, W. McCorckle, H.G. Brummel, M. Fang, (Siemens Corporate Research), Method to use a receiver operator characteristics curve for model comparison in machine condition monitoring, US Pat No: 7,457,674.
3. (2007) C. Yuan, Z. Cataltepe, C. Neubauer, M. Fang, (Siemens Corporate Research), “Joint approach of out-of-range detection and fault detection for power plant monitoring”, US Pat No: 7,305,317.
4. (2007) C. Yuan, C. Neubauer and Z. Cataltepe (Siemens Corporate Research), “Apparatus and methods for detecting system faults using hidden process drivers,” US Pat No: 7,216,061.
5. (2007) Z. Cataltepe, M. Fang; Ming, C. Neubauer, C. Yuan (Siemens Corporate Research), “Tool for sensor management and fault visualization in machine condition monitoring,” US Pat No: 7,183,905.
6. (2007) C. Yuan, C. Neubauer and Z. Cataltepe (Siemens Corporate Research), “Method and apparatus for detecting out-of-range conditions in power generation equipment operations,” US Pat No: 7,188,050.
7. (2006) Z. Cataltepe, M. Fang, C. Neubauer, C. Yuan (Siemens Corporate Research), “System and method for detecting and excluding outlier sensors in sensor-based monitoring,” US Pat No: 7,096,159.
8. (2006) C. Yuan, C. Neubauer, H.G. Brummel, M. Fang, Z. Cataltepe (Siemens Corporate Research), “Systems and methods for selecting training data and generating fault models for use in use sensor-based monitoring,” US Pat No: 7,035,763.

RESEARCH PROJECTS:

• (2009-2011) TUBITAK Research Project, " Multi-relational and Multi-view Collective Classification, Feature Selection and Generalization/Çoğul İlişkisel ve Çoğul Öznitelikli Kolektif Sınıflandırma, Öznitelik Seçimi ve Genelleme"", Zehra Cataltepe (PI), Ayse Erzan (Istanbul Technical Un.).
• (2009-2010) İTÜ Araştırma Fonu/İTÜ Research Fund, “Yüksek Boyutlu Öznitelik Uzaylarında Birlikte Öğrenme/Co-training in High Dimensional Input Spaces”, with Ph.D. Student, Yusuf Yaslan.
• (2006-2009) TUBITAK Research Project, "Makine Öğrenme ve Sinyal İşleme Teknikleri ile Protein Fonksiyon Öngörüsü/Protein Function Prediction Using Machine Learning and Function Prediction Techniques", Zehra Cataltepe (PI), Yucel Altunbasak (Sabanci Un&Georgia Inst of Technology), Ozlem Keskin (Koc University).
• (2006-2008) TUBITAK Research Project, "TR-Web: Daha Hızlı ve Doğru Bir Web Öneri Sistemi/TR-Web: A Faster and More Correct Recommendation System", Sule Gunduz-Oguducu (PI), Sima Etaner-Uyar, Zehra Cataltepe.

EXPERIENCE:

• 2009 (July) Visitor at Caltech, Learning Systems Group.
• 2009: Associate Professor at Istanbul Technical University, Computer Engineering Department.
• 2007-Now: Binghamton SUNY-ITU Information Systems Engineering Program Coordinator.
• 2005-2009: Assistant Professor at Istanbul Technical University, Computer Engineering Department.
• Got funding for two projects (on bioinformatics function prediction and web session recommendation) from The Scientific and Technological Research Council of Turkey (TUBITAK).
• Published one journal and many conference papers.
• Taught MS and PhD level Pattern Recognition/Machine Learning courses and a number of undergraduate courses (Project I and II, Advanced Data Structures, Analysis of Algorithms, Object Oriented Programming), graduated 2 MS students, is about to graduate 4 more, is advising PhD and M.Sc. students.
• 2002-2004: Siemens Corporate Research, Intelligent Vision and Reasoning Department, Princeton, NJ
• Designed and implemented machine learning algorithms and software for monitoring of power plants and AC motors and visualization of sensor data.
• Published three papers and eight patents.
• 2001-now: Honored to be mom of Irem.
• 2000-2001: Technical Team Member, Stream Center Inc. , Murray Hill, NJ
• Designed experiments to collect internet congestion data, to benchmark the company streaming software and also to understand the location and characteristics of internet congestion as seen by end users when streaming audio/video.
• Designed and implemented algorithms to analyze the internet congestion data.
• Participated in developing congestion signatures to identify the amount of congestion as seen by a streaming session and property based clustering to identify the location of congestion.
• Filed two US patents and published three papers.
• 1999-now: Honored to be mom of Ali.
• 1998-1999: Postdoctoral member of technical staff, Bell Labs Statistics and Data Mining Research, Murray Hill, NJ
• investigated modifications to discriminant analysis taking input information into account.
• 1992-1997: Research and teaching, California Institute of Technology, Computer Science Department, Pasadena, CA
• Showed that extra information, such as input information or expert knowledge (hints), about a machine-learning problem can be incorporated into learning from examples through augmented objective functions.
• Proved that early stopping can not improve the model, when no additional information is available.
• Investigated different aspects of learning from examples, such as objective functions, regularization methods, optimization methods.

TEACHING:

• Machine Learning and Pattern Recognition (M.S. and Ph.D. Level classes).
• Advanced Data Structures
• Analysis of Algorithms
• Object Oriented Programming
• Java Programming
• Project 1 and 2.

STUDENTS:

Current Students:

• Ph.D. Students: Yusuf Yaslan, Eser Aygün, Abdullah Sönmez, , Ismail Gunes.
• M.S. Students: Baris Senliol, Kenan Kule, Ozgur Macit.

Graduated

1. (2009) G. Gülgezen, M.Sc. in Computer Engineering, Istanbul Technical University,
2. Thesis title: " Stable and Accurate Feature Selection”
3. (2009) E. Aygün, M.Sc. in Computer Engineering, Istanbul Technical University,
4. 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”
5. (2008) Asli Filiz, M.Sc. in Information Sciences, Istanbul Technical University,
   Thesis title: " Alignment and Compression-Based Protein Function Prediction Using Secondary Structure”
6. (2008) Caner Kömürlü, M.Sc. in Information Sciences, Istanbul Technical University,
   Thesis title: " Protein Function Prediction Using Hidden Markov Models”
7. (2008) U. Ulkem Yildirim, M.Sc. in Computer Engineering, Istanbul Technical University,
   Thesis title: " Short Time Traffic Speed Prediction Using Pattern Recognition and Feature Selection/Örüntü Tanıma ve Öznitelik Seçme Yöntemleri Kullanarak Kısa Zaman Sonraki Yol Trafik Hız Öngörüsü”
8. (2007) Berna Altinel, M.Sc. in Computer Engineering, Istanbul Technical University,
   Thesis title: "A Hybrid Music Recommender System Based on Different Features of Music and User".
9. (2005) Abdullah Sonmez, M.Sc. in Computer Engineering, Istanbul Technical University,
   Thesis title: "Music Genre and Composer Identification by Using Kolmogorov Distance" (co-advisor with Prof. E. Adali).

COLLABORATORS:

• Ayse Erzan (Istanbul Technical University)
• Lei Yu (Binghamton Un.)
• B. John Oommen (Carleton Un.)
• Yucel Altunbasak (Georgia Inst. Of Technology)
• Cenk Saninalp (Simon Fraser Un.)
• Yaser S. Abu-Mostafa (Caltech)
• Malik Magdon-Ismail (RPI)
• Ozlem Keskin (Koc University)
• Mustafa Kamasak (Istanbul Technical University)
• Enis Cetin (Bilkent Un.)
• Thomas Pearson (USDA)

HONORS AND AWARDS:

• 1992: Earle C. Anthony Graduate Fellowship at Caltech
• 1991: Bilkent University, graduated first in class of Computer Engineering and Information Sciences Department.
• 1986: Ranked 25. at OSS and 35 at OYS, nationwide university entrance exams and got a full scholarship at Bilkent University.
• 1987: Physics and Chemistry awards of Turkish Science Foundation (TUBITAK)

PROFESSIONAL ACTIVITIES:

Conferences:

• ICPR 2010, Contest co-chair
• ISCIS 2008, Conference co-chair.
• HIBIT 2008, Organizing and Program Committee.
• HIBIT 2007, Reviewer Committee.
• ISCIS 2007, Program Committee.
• ISCIS 2006, Review Committee.
• PRIB 2007, Program Committee.
• BioSignals 2008, Program Committee.
• ICDE 2007, Organization Committee.
• DBMI 2007, Program Committee.

Editorial board member of Turkish Journal of Electrical Engineering and Computer Sciences.

Reviewer for Computer Journal, Machine Vision and Applications, Neurocomputing, Journal of Intelligent Information Systems journals.

Project reviewer, Turkish Technology Development Foundation (TTGV), TÜBİTAK: Elektrik Elektronik ve Enformatik Araştırma Grubu (EEEAG), TEYDEB.

SKILLS:

Java, Matlab, C, C++, Pascal, SQL, Mathematica, Linux/Unix, Windows.

REFERENCES:
Available upon request.