Large Scale Content-Based Audio Retrieval from Text Queries, Gal Chechik, Eugene Ie, Martin Rehn, Samy Bengio, Richard F. Lyon, ACM International Conference on Multimedia Information Retrieval (MIR), 2008.
Multi-class protein classification using adaptive codes, Iain Melvin, Eugene Ie, Jason Weston, William Stafford Noble, Christina Leslie, Journal of Machine Learning Research, vol. 8 (2007), pp. 1557-1581.
SVM-fold: a tool for discriminative multi-class protein fold and superfamily recognition, Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble, Christina Leslie, BMC Bioinformatics, vol. 8 (2007).
BioSpike: Efficient search for homologous proteins by indexing patterns, Eugene Ie, Yoav Freund, 2006.
Semi-supervised protein classification using cluster kernels, Jason Weston, Christina Leslie, Eugene Ie, William Stafford Noble, Semi-Supervised Learning, 2006, pp. 329-346.
Multi-class protein fold recognition using adaptive codes, Eugene Ie, Jason Weston, William Stafford Noble, Christina S. Leslie, Proceedings of the 22nd international conference on Machine learning, 2005, pp. 329-336.
Profile-based string kernels for remote homology detection and motif extraction, Rui Kuang, Eugene Ie, Ke Wang, Kai Wang, Mahira Siddiqi, Yoav Freund, Christina Leslie, Journal of Bioinformatics and Computational Biology, vol. 3 (2005), pp. 527-550.
Semi-supervised protein classification using cluster kernels, Jason Weston, Christina S. Leslie, Eugene Ie, Dengyong Zhou, Andr, William Stafford Noble, Bioinformatics, vol. 21 (2005), pp. 3241-3247.