| 2012 | KDD | 2D similarity kernels for biological sequence classification. | Pavel P. Kuksa |
| 2012 | KDD | Efficient evaluation of large sequence kernels. | Pavel P. Kuksa, Vladimir Pavlovic |
| 2012 | SDM | Generalized Similarity Kernels for Efficient Sequence Classification. | Pavel P. Kuksa, Imdadullah Khan, Vladimir Pavlovic |
| 2010 | ICPR | Spatial Representation for Efficient Sequence Classification. | Pavel P. Kuksa, Vladimir Pavlovic |
| 2010 | SDM | Semi-supervised Bio-named Entity Recognition with Word-Codebook Learning. | Pavel P. Kuksa, Yanjun Qi |
| 2009 | CIKM | Combining labeled and unlabeled data with word-class distribution learning. | Yanjun Qi, Ronan Collobert, Pavel P. Kuksa, Koray Kavukcuoglu, Jason Weston |
| 2009 | ICDM | Semi-Supervised Sequence Labeling with Self-Learned Features. | Yanjun Qi, Pavel P. Kuksa, Ronan Collobert, Kunihiko Sadamasa, Koray Kavukcuoglu, Jason Weston |
| 2008 | ICPR | Fast protein homology and fold detection with sparse spatial sample kernels. | Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic |
| 2007 | WABI | Fast Kernel Methods for SVM Sequence Classifiers. | Pavel P. Kuksa, Vladimir Pavlovic |