Publications of Alexander Zien

2010	Sonnenburg, S, Rätsch, G, Henschel, S, Widmer, C, Behr, J, Zien, A, de Bona, F, Binder, A, Gehl, C, and Franc, V (2010). The SHOGUN Machine Learning Toolbox Journal of Machine Learning Research, 11:1799-1802. Printable file

Kloft, M, Brefeld, U, Sonnenburg, S, and Zien, A (2010). Non-Sparse Regularization and Efficient Training with Multiple Kernels University of California, Berkeley. Printable file

2009	Schweikert, G, Behr, J, Zien, A, Zeller, G, Ong, CS, Sonnenburg, S, and Rätsch, G (2009). mGene.web: a web service for accurate computational gene finding Nucleic Acids Research, 37(Web Server issue):W312–W316. Online access Printable file

Zien, A, Krämer, N, Sonnenburg, S, and Rätsch, G (2009). The Feature Importance Ranking Measure In: Proc. ECML PKDD, ed. by W. Buntine, M. Grobelnik, D. Mladenic, J. Shawe-Taylor, vol. 5782/2009, pp. 694-709, Springer Berlin / Heidelberg, Springer, XXIX ed.. Lecture Notes in Artificial Intelligence. Printable file

Schweikert, G, Zien, A, Zeller, G, Behr, J, Dieterich, C, Ong, CS, Philips, P, De Bona, F, Hartmann, L, Bohlen, A, Krüger, N, Sonnenburg, S, and Rätsch, G (2009). mGene: Accurate SVM-Based Gene Finding with an Application to Nematode Genomes Genome Research, 19:2133-2143. Online access Supplementary website Printable file

Kloft, M, Brefeld, U, Sonnenburg, S, Laskow, P, Mueller, K, and Zien, A (2009). Efficient and Accurate Lp-Norm MKL In: Advances in Neural Information Processing Systems 21, ed. by Y. Bengio and D. Schuurmans and J. Lafferty and C. K. I. Williams and A. Culotta, pp. 997--1005, Cambridge, MA, MIT Press.

Jenssen, R, Kloft, M, Zien, A, Sonnenburg, S, and Müller, K (2009). A Multi-Class Support Vector Machine Based on Scatter Criteria Technical University Berlin, Technical Report(014-2009). Online access Printable file

2008	Sonnenburg, S, Zien, A, Philips, P, and Rätsch, G (2008). POIMs: Positional Oligomer Importance Matrices - Understanding Support Vector Machine Based Signal Detectors In: Bioinformatics/Proc. ISMB 2008, vol. 24(13), pp. i6, Oxford University Press. Online access Printable file

Ong, CS and Zien, A (2008). An Automated Combination of Kernels for Predicting Protein Subcellular Localization In: Proceedings of the 8th Workshop on Algorithms in Bioinformatics (WABI), pp. 186-179, Springer. Lecture Notes in Bioinformatics. Online access Printable file

2007	Zien, A, Sonnenburg, S, and Philips, P (2007). Computing Positional Oligomer Importance Matrices (POIMs) Fraunhofer Institute FIRST, technical report(2). Online access Printable file

Zien, A, De Bona, F, and Ong, CS (2007). Training and Approximation of a Primal Multiclass Support Vector Machine In: 12th International Conference on Applied Stochastic Models and Data Analysis (ASMDA). Online access Printable file

Zien, A and Ong, CS (2007). Multiclass Multiple Kernel Learning In: Proceedings of the 24th International Conference on Machine Learning (ICML), pp. 1191-1198, New York, NY, USA, ACM Press. Online access

Zien, A, Brefeld, U, and Scheffer, T (2007). Transductive Support Vector Machines for Structured Variables In: Proceedings of the 24th International Conference on Machine Learning (ICML), pp. 1183-1190, New York, NY, USA, ACM Press. Online access Printable file

Zien, A, Gebhard, PM, Fundel, K, and Aigner, T (2007). Phenotyping of Chondrocytic Cells Using the cDNA Array Technology Clinical Orthopaedics and Related Research, 460:226-233.

2006	Sonnenburg, S, Zien, A, and Rätsch, G (2006). ARTS: Accurate Recognition of Transcription Starts in Human Bioinformatics, 22(14):e472-e480. Online access

Zien, A, Ong, CS, and Rätsch, G (2006). Towards the Inference of Graphs on Ordered Vertices Max Planck Institute for biological Cybernetics, Research Note(150), Tübingen, Germany. Online access Printable file

Chapelle, O, Schölkopf, B, and Zien, A (2006). Semi-Supervised Learning The MIT Press, Cambridge, MA, USA. (ISBN: 978-0-262-03358-9). Online access

Chapelle, O, Chi, M, and Zien, A (2006). A Continuation Method for Semi-Supervised SVMs In: Proceedings of the 23rd International Conference on Machine Learning (ICML), pp. 185-192, New York, NY, USA, ACM Press. Online access Printable file

Aigner, T, Fundel, K, Saas, J, Gebhard, PM, Haag, J, Weiss, T, Zien, A, Obermayr, F, Zimmer, R, and Bartnik, E (2006). Large-Scale Gene Expression Profiling Reveals Major Pathogenetic Pathways of Cartilage Degeneration in Osteoarthritis Arthritis and Rheumatism, 54(11):3533-3544. Online access

2000	Zien, A, Rätsch, G, Mika, S, Schölkopf, B, Lengauer, T, and Müller, K (2000). Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites in DNA Bioinformatics, 16(9):799-807.

1999	Zien, A, Rätsch, G, Mika, S, Schölkopf, CL, Smola, AJ, Lengauer, T, and Mueller, K (1999). Engineering Support Vector Machine Kernel That Recognize Translation Initiation Sites in DNA In: Proceedings GCB'99.