Publications

Z. Barutcuoglu, E. Airoldi, V. Dumeaux, R. E. Schapire, O. G. Troyanskaya,
"Aneuploidy Prediction and Tumor Classification with Heterogeneous Hidden Conditional Random Fields,"
Bioinformatics, 2008. [ Matlab code & data ]

L. Pena-Castillo, M. Tasan, C. L. Myers, H. Lee, T. Joshi, C. Zhang, Y. Guan, M. Leone, A. Pagnani, W. Kim, C. Krumpelman, W. Tian, G. Obozinski, Y. Qi, S. Mostafavi, G. N. Lin, G. Berriz, F. Gibbons, G. Lanckriet, J. Qiu, C. Grant, Z. Barutcuoglu, D. P. Hill, D. Warde-Farely, C. Grouios, D. Ray, J. A. Blake, M. Deng, M. Jordan, W. S. Noble, et al.
"A critical assessment of Mus musculus gene function prediction using integrated genomic evidence,"
Genome Biology, 2008, 9(Suppl 1):S2.

Y. Guan, C. L. Myers, D. Hess, Z. Barutcuoglu, A. Caudy and O. G. Troyanskaya,
"Predicting Gene Function in a Hierarchical Context with an Ensemble of Classifiers,"
Genome Biology, 2008, 9(Suppl 1):S3.

Z. Barutcuoglu, P. M. Long, R. A. Servedio,
"One-Pass Boosting,"
Neural Information Processing Systems (NIPS), 2007.

C. DeCoro, Z. Barutcuoglu, R. Fiebrink,
"Bayesian Aggregation for Hierarchical Genre Classification,"
8th International Conference on Music Information Retrieval (ISMIR), 2007.

Z. Barutcuoglu, C. DeCoro,
"Hierarchical Shape Classification Using Bayesian Aggregation,"
Shape Modeling International (SMI), 2006.

Z. Barutcuoglu, R. E. Schapire, O. G. Troyanskaya,
"Hierarchical Multi-label Prediction of Gene Function,"
Bioinformatics, 2006. [ Matlab code & data ]

Z. Barutcuoglu, E. Alpaydin,
"A Comparison of Model Aggregation Methods for Regression,"
Proceedings of the 13th International Conference on Artificial Neural Networks (ICANN), 2003.

Z. Barutcuoglu,
"A Neural Network Approach to the Crossword Puzzle Problem,"
Proceedings of the 8th Turkish Symposium on Artificial Intelligence and Neural Networks (TAINN), 1999.

Z. Barutcuoglu,
"Automated Generation of Unconstrained Crossword Puzzles and an Estimate of Their Solution Space",
Proceedings of the 12th International Symposium on Computer and Information Sciences (ISCIS), 1997.

Technical Report

Z. Barutcuoglu, C. DeCoro, R. E. Schapire, O. G. Troyanskaya,
"Bayesian Aggregation for Hierarchical Classification,"
Technical Report TR-785-07, Princeton University, Department of Computer Science, 2007.

Theses

"Using Structural Information in Machine Learning Applications,"
Ph.D. Thesis, supervised by R. E. Schapire, co-advisor O. G. Troyanskaya, Princeton University, 2008.

"Learning Rules and Exceptions for Regression: The REx Algorithm,"
M.S. Thesis, supervised by E. Alpaydin, Bogazici University, 2002.