• O. İrsoy, E. Alpaydin (2022) “Distributed Decision Trees,” S+SSPR Workshop, ICPR 2022
• O. İrsoy, E. Alpaydin (2021) “Dropout Regularization in Hierarchical Mixture of Experts,” Neurocomputing, 419, 148-156.

2020

• A. Ahmetoğlu, E. Alpaydın (2020) “Hierarchical Mixtures of Generators for Adversarial Networks,” ICPR 2020.
• O. İrsoy, E. Alpaydın (2020) “Continuously Constructive Deep Neural Networks,” IEEE Transactions on Neural Networks and Learning Systems, 31(4), 1124-1133.
• U. Mutlu, E. Alpaydın (2020) “Training Bidirectional Generative Adversarial Networks with Hints,” Pattern Recognition, 103, 107320.
• A. Ahmetoğlu, O. İrsoy, E. Alpaydın (2018) “Convolutional Soft Decision Trees,” ICANN 2018.
• E. Alpaydın (2018) “Classifying Multimodal Data,” The Handbook of Multimodal-Multisensor Interfaces, 49-69.
• E. Emekligil, E. Alpaydın (2018) “What’s In A Game? The Effect of Game Complexity on Deep Reinforcement Learning,” Computer Games Workshop IJCAI 2018. 
• O. Irsoy, E. Alpaydin (2017) “Unsupervised Feature Extraction with Autoencoder Trees,” Neurocomputing, 258, 63-73.
• O. T. Yıldız, O. İrsoy, E. Alpaydın (2016) “Bagging Soft Decision Trees,” Machine Learning for Health Informatics, A. Holzinger (Ed.), Springer LNAI 9605, 25-36.
• C. Zor, B. Yanikoglu, E. Merdivan, T. Windeatt, J. Kittler, E. Alpaydin (2016) “Beam ECOC: A Local Search for the Optimization of the ECOC Matrix,” ICPR 2016.
• O. Irsoy, E. Alpaydin (2015) “Autoencoder Trees,” ACML 2015.
• E. Alpaydin, V. Cheplygina, M. Loog, D.M.J. Tax (2015) “Single- vs. Multiple-Instance Classification,” Pattern Recognition, 48(9), 2831-2838.
• O. T. Yildiz, E. Alpaydin (2014) “Multivariate Comparison of Classification Algorithms,” ArXiv:1409.4566.
• O. Irsoy, O. T. Yildiz, E. Alpaydin (2014) “Budding Trees,” ICPR 22.
• O. T. Yildiz, E. Alpaydin (2013) “Regularizing Soft Decision Trees,” ISCIS 28.
• M. Semerci, E. Alpaydin (2013) “Mixtures of Large Margin Nearest Neighbor Classifiers,” ECML 2013.
• M. Gonen, E. Alpaydin (2013) “Localized Algorithms for Multiple Kernel Learning,” Pattern Recognition, 46, 795-807.
• E. Dikici, M. Semerci, M. Saraclar, E. Alpaydin (2013) “ Classification and Ranking Approaches to Discriminative Language Modeling for ASR,” IEEE Transactions on Audio, Speech, and Language Processing, 21(2), 291-300.
• O. Irsoy, O. T. Yildiz, E. Alpaydin (2012) “Design and Analysis of Classifier Learning Experiments in Bioinformatics: Survey and Case Studies,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(6), 1663-1675.
• O. Irsoy, O. T. Yildiz, E. Alpaydin (2012) “Soft Decision Trees,” ICPR 21, Tsukuba, Japan.
• O. T. Yildiz, E. Alpaydin (2012) “ Statistical Tests using Hinge/Epsilon-Sensitive Loss,” ISCIS 27, Paris, France.
• A. Ulas, O. T. Yildiz, E. Alpaydin (2012) “ Eigenclassifiers for Combining Correlated Classifiers” Information Sciences, 187, 109-120.
• A. Ulas, O. T. Yildiz, E. Alpaydin (2012) “ Cost-Conscious Comparison of Supervised Learning Algorithms over Multiple Data Sets, ” Pattern Recognition, 45(4), 1772-1781.
• M. Gonen, E. Alpaydin (2011) “Multiple Kernel Learning Algorithms,” Journal of Machine Learning Research, 12, 2211-2268.
• E. Alpaydin (2011) “Machine Learning,” Wiley Interdisciplinary Reviews: Computational Statistics, 3(3), 195-203.
• O. T. Yildiz, O. Aslan, E. Alpaydin (2011) “Multivariate Statistical Tests for Comparing Classification Algorithms,“, LION5.
• O. Kursun, E. Alpaydin, O. Favorov (2011) “Canonical Correlation Analysis using Within-Class Coupling,” Pattern Recognition Letters, 32, 134-144.
• M. Gonen, E. Alpaydin (2011) “Regularizing Multiple Kernel Learning using Response Surface Methodology,” Pattern Recognition, 44, 159-171.

2010

• C. Zor, B. Yanikoglu, T. Windeatt, E. Alpaydin (2010) “FLIP-ECOC: a greedy optimization of the ECOC matrix,” ISCIS 2010.
• M. Gonen, E. Alpaydin (2010) “Localized Multiple Kernel Regression,” ICPR 2010.
• O. Kursun, E. Alpaydin (2010) “Canonical Correlation Analysis for Multiview Semisupervised Feature Extraction,” ICAISC 2010.
• M. Gonen, E. Alpaydin (2010) “Supervised Learning of Local Projection Kernels,” Neurocomputing, 73 (10-12), 1694-1703.
• M. Gonen, E. Alpaydin (2010) “Cost-Conscious Multiple Kernel Learning,” Pattern Recognition Letters, 31(9), 959-965.
• A.Ulas, M. Semerci, O. T. Yildiz, E. Alpaydin (2009) “Incremental Construction of Classifier and Discriminant Ensembles,” Information Sciences, 179(9), 1298-1318.
• A.Ozen, M. Gonen, E. Alpaydin, T. Haliloglu (2009) “Machine Learning Integration for Predicting the Effect of Single Amino Acid Substitutions on Protein Stability,” BMC Structural Biology, 9(66).
• M. Gonen, E. Alpaydin (2009) “Multiple Kernel Machines Using Localized Kernels,” PRIB 2009.
• O. Aran, O. T. Yildiz, E. Alpaydin (2009) “An Incremental Framework Based on Cross-Validation for Estimating the Architecture of a Multilayer Perceptron,” International Journal of Pattern Recognition and Artificial Intelligence, 23(2), 159-190.
• M. Gonen, E. Alpaydin (2008) “Localized Multiple Kernel Learning,” ICML 2008.
• M. Gonen, A. G. Tanugur, E. Alpaydin (2008) “Multiclass Posterior Probability Support Vector Machines,” IEEE Transactions on Neural Networks, 19(1), 130-139.
• B. Gokberk, M. O. Irfanoglu, L. Akarun, E. Alpaydin (2007) “Learning the Best Subset of Local Features for Face Recognition,” Pattern Recognition, 40(5), 1520-1532.
• O. T. Yildiz, E. Alpaydin (2006) “Ordering and Finding the Best of K>2 Supervised Learning Algorithms,” IEEE Transactions on Pattern Analysis and Machine Intelligence, 28(3), 392-402.
• C. Demir, E. Alpaydin (2005) “Cost-Conscious Classifier Ensembles,” Pattern Recognition Letters, 26(14), 2206-2214.
• O. T. Yildiz, E. Alpaydin (2005) “Model Selection in Omnivariate Decision Trees,” ECML 2005.
• O. T. Yildiz, E. Alpaydin (2005) “Linear Discriminant Trees,” International Journal of Pattern Recognition and Artificial Intelligence, 19(3), 323-353.
• A. A. Salah, E. Alpaydin (2004) “Incremental Mixtures of Factor Analyzers,” ICPR 2004.
• B. Gokberk, M. O. Irfanoglu, L. Akarun, E. Alpaydin (2003) “Selection of Location, Frequency, and Orientation Parameters of 2D Gabor Wavelets for Face Recognition,” Summer School on Biometrics, Italy, June 2003.
• O. Aran, E. Alpaydin (2003) “An Incremental Neural Network Construction Algorithm for Training Multilayer Perceptrons,” ICANN 2003.
• Z. Barutcuoglu, E. Alpaydin (2003) “A Comparison of Model Aggregation Methods for Regression,” ICANN 2003.
• A. Baraldi, E. Alpaydin (2002) “Constructive Feedforward ART Clustering Network – Part I,” IEEE Transactions on Neural Networks, 13(3), 645-661.
• A. Baraldi, E. Alpaydin (2002) “Constructive Feedforward ART Clustering Network – Part II,” IEEE Transactions on Neural Networks, 13(3), 662-677.
• A. A. Salah, E. Alpaydin, L. Akarun (2002) “A Selective Attention-Based Method for Visual Pattern Recognition with Application to Handwritten Digit Recognition and Face Recognition,” IEEE Transactions on Pattern Analysis and Machine Intelligence, 24(3), 420-425 (Correct Fig 1).
• O. T. Yildiz, E. Alpaydin (2001) “Omnivariate Decision Trees,” IEEE Transactions on Neural Networks, 12(6), 1539-1546.
• F. Alimoglu, E. Alpaydin (2001) “Combining Multiple Representations for Pen-based Handwritten Digit Recognition,” ELEKTRIK: Turkish Journal of Electrical Engineering and Computer Sciences, 9(1), 1-12.
• F. Koksal, E. Alpaydin, G. Dundar (2001) “Weight Quantization for Multilayer Perceptrons using Soft Weight Sharing,” ICANN 2001.
• A. A. Salah, E. Alpaydin, L. Akarun (2001) “A Selective Attention Based Method for Visual Pattern Recognition,” 23rd Annual Conference of the Cognitive Science Society, Edinburgh, Scotland, August 2001.
• E. Alpaydin (2001) “Assessing and Comparing Classification Algorithms,” ISAS 2001.

2000

• E. Alpaydin, C. Kaynak, F. Alimoglu (2000) “Cascading Multiple Classifiers and Representations for Optical and Pen-Based Handwritten Digit Recognition,” IWFHR 2000.
• C. Kaynak, E. Alpaydin (2000) “MultiStage Cascading of Multiple Classifiers: One Man’s Noise is Another Man’s Data,” ICML 2000.
• O. T. Yildiz, E. Alpaydin (2000) “Linear Discriminant Trees, ICML 2000.
• E. Alpaydin (1999) “Combined 5x2cv F Test for Comparing Supervised Classification Learning Algorithms,” Neural Computation, 11(8), 1885-1892.
• I. Bayraktaroglu, A. S. Ogrenci, G. Dundar, S. Balkir, E. Alpaydin (1999) “ANNSyS: An Analog Neural Network Synthesis System,” Neural Networks, 12(2), 325-338.
• E. Alpaydin, Ed. (1999) Special Issue on Engineering of Intelligent Systems, Artificial Intelligence in Engineering, ” Guest Editorial,” 13(4).
• E. Alpaydin, E. Mayoraz (1999) “Learning Error-Correcting Output Codes from Data,” ICANN 1999.
• E. Mayoraz, E. Alpaydin (1999) “Support Vector Machines for Multi-Class Classification,” IWANN 1999.
• E. Alpaydin, C. Kaynak (1998) “Cascading Classifiers,” Kybernetika, 34(4), 369-374.
• E. Alpaydin (1998) “Soft Vector Quantization and the EM Algorithm,” Neural Networks, 11(3), 467-477.
• E. Alpaydin (1998) “Techniques for Combining Multiple Learners, Engineering of Intelligent Systems EIS 1998.
• E. Alpaydin, F. Gurgen (1998) “Comparison of Statistical and Neural Classifiers and Their Applications to Optical Character Recognition and Speech Classification,” Neural Network Systems Techniques and Applications, vol 5, Image Processing and Pattern Recognition, C.T. Leondes (Ed.) Academic Press, 61-88.
• E. Alpaydin (1997) “Voting over Multiple Condensed Nearest Neighbors,” Artificial Intelligence Review, 11, 115-132.
• F. Alimoglu, E. Alpaydin (1997) “Combining Multiple Representations and Classifiers for Pen-based Handwritten Digit Recognition,” ICDAR 1997.
• E. Alpaydin, I. K. Altinel, N. Aras (1996) “Parametric Distance Functions vs Nonparametric Neural Networks for Estimating Road Travel Distances,” European Journal on Operational Research , 93(2), 230-243.
• E. Alpaydin, M. I. Jordan (1996) “Local Linear Perceptrons for Classification,” IEEE Transactions on Neural Networks, 7(3), 788-792.
• E. Alpaydin (1996) “Selective Attention for Handwritten Digit Recognition,” Advances in Neural Information Processing Systems 8, D.S. Touretzky, M.C. Mozer, M.E. Hasselmo (Eds.) MIT Press, 771-777.
• E. Alpaydin, F. Gurgen (1995) “Comparison of Kernel Estimators, Perceptrons, and Radial-Basis Functions for OCR and Speech Classification,” Neural Computing and Applications, 3, 38-49.
• F. Gurgen, R. Alpaydin, U. Unluakin, E. Alpaydin (1994) “Distributed and Local Neural Classifiers for Phoneme Recognition,” Pattern Recognition Letters, 15, 1111-1118.
• E. Alpaydin, S. Aratma, M. Yagci (1994) “Recognition of Handwritten Digits using Neural Networks,” ELEKTRIK: Turkish Journal of Electrical Engineering and Computer Sciences, 2, 20-31.
• E. Alpaydin (1994) “GAL: Networks that Grow when they Learn and Shrink when they Forget,” International Journal of Pattern Recognition and Artificial Intelligence 8, 391-414.
• E. Alpaydin (1993) “Multiple Networks for Function Learning,” IEEE ICNN 1993.
• E. Alpaydin (1992) “Multiple Neural Networks and Weighted Voting,” IAPR 1992.