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Dr. Gunnar Rätsch

Room number: FML 0.06a
Phone: +49 7071 601 820
Fax: +49 7071 601 801
E-Mail: gunnar.raetsch
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Gunnar Rätsch

Position: Research Scientist  Unit: Alumni Schölkopf

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Proceedings (1):

Bousquet O Person, von Luxburg U Person and Rätsch G Person: Advanced Lectures on Machine Learning, ML Summer Schools 2003, 240, Springer, Berlin, Germany, (2004).

978-3-540-23122-6

Articles (30):

Widmer C Person and Rätsch G Person (2012) Multitask Learning in Computational Biology JMLR W&CP. ICML 2011 Unsupervised and Transfer Learning Workshop 27 207--216.
Gan XC , Stegle O Person, Behr J Person, Steffen JG , Drewe P Person, Hildebrand KL , Lyngsoe R , Schultheiss SJ Person, Osborne EJ , Sreedharan VT Person, Kahles A Person, Bohnert R Person, Jean G Person, Derwent P , Kersey P , Belfield EJ , Harberd NP , Kemen E , Toomajian C , Kover PX , Clark RM , Rätsch G Person and Mott R (2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana Nature 477(7365) 419–423.
Stegle O Person, Drewe P Person, Bohnert R , Borgwardt K Person and Rätsch G Person (2010) Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts Nature Precedings 2010 1-11.
Widmer C Person, Toussaint NC Person, Altun Y Person and Rätsch G Person (2010) Inferring latent task structure for Multitask Learning by Multiple Kernel Learning BMC Bioinformatics 11 Suppl 8 S5.
Graf ABA Person, Bousquet O Person, Rätsch G Person and Schölkopf B Person (2009) Prototype Classification: Insights from Machine Learning Neural Computation 21(1) 272-300.
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Schweikert G Person, Zien A Person, Zeller G Person, Behr J Person, Dieterich C Person, Ong CS Person, Philips P Person, De Bona F Person, Hartmann L Person, Bohlen A Person, Krüger N , Sonnenburg S Person and Rätsch G Person (2009) mGene: accurate SVM-based gene finding with an application to nematode genomes Genome Research 19(11) 2133-43.
Schweikert G Person, Behr J Person, Zien A Person, Zeller G Person, Ong CS Person, Sonnenburg S Person and Rätsch G Person (2009) mGene.web: a web service for accurate computational gene finding Nucleic Acids Research 37 W312-6.
Ben-Hur A , Ong CS Person, Sonnenburg S Person, Schölkopf B Person and Rätsch G Person (2008) Support Vector Machines and Kernels for Computational Biology PLoS Computational Biology 4(10: e1000173) 1-10.
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Laubinger S , Zeller G , Henz SR , Sachsenberg T , Widmer CK , Naouar N , Vuylsteke M , Schölkopf B Person, Rätsch G Person and Weigel D (2008) At-TAX: A Whole Genome Tiling Array Resource for Developmental Expression Analysis and Transcript Identification in Arabidopsis thaliana Genome Biology 9(7: R112) 1-16.
Sonnenburg S Person, Schweikert G Person, Philips P , Behr J and Rätsch G Person (2007) Accurate Splice site Prediction Using Support Vector Machines BMC Bioinformatics 8(Supplement 10) 1-16.
Sonnenburg S Person, Braun ML , Ong CS Person, Bengio S , Bottou L , Holmes G , LeCun Y , Müller K-R Person, Pereira F , Rasmussen CE Person, Rätsch G Person, Schölkopf B Person, Smola A , Vincent P , Weston J Person and Williamson RC (2007) The Need for Open Source Software in Machine Learning Journal of Machine Learning Research 8 2443-2466.
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Clark RM , Schweikert G Person, Toomajian C , Ossowski S , Zeller G , Shinn P , Warthmann N , Hu TT , Fu G , Hinds DA , Chen H , Frazer KA , Huson DH , Schölkopf B Person, Nordborg M , Rätsch G Person, Ecker JR and Weigel D (2007) Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science 317(5836) 338-342.
Schulze U , Hepp B , Ong CS Person and Rätsch G Person (2007) PALMA: mRNA to Genome Alignments using Large Margin Algorithms Bioinformatics 23(15) 1892-1900.
Rätsch G Person, Sonnenburg S Person, Srinivasan J , Witte H , Müller K-R Person, Sommer R-J and Schölkopf B Person (2007) Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning PLoS Computational Biology 3(2, e20) 0313-0322.
Sonnenburg S Person, Zien A Person and Rätsch G Person (2006) ARTS: Accurate Recognition of Transcription Starts in Human Bioinformatics 22(14) e472-e480.
Sonnenburg S Person, Rätsch G Person, Schäfer C and Schölkopf B Person (2006) Large Scale Multiple Kernel Learning Journal of Machine Learning Research 7 1531-1565.
Tsuda K Person and Rätsch G Person (2005) Image Reconstruction by Linear Programming IEEE Transactions on Image Processing 14(6) 737-744.
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Tsuda K Person, Rätsch G Person and Warmuth M (2005) Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection Journal of Machine Learning Research 6 995-1018.
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Rätsch G Person, Sonnenburg S Person and Schölkopf B Person (2005) RASE: recognition of alternatively spliced exons in C.elegans Bioinformatics 21(Suppl. 1) i369-i377.
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Mika S , Rätsch G Person, Weston J Person, Schölkopf B Person, Smola AJ and Müller K-R Person (2003) Constructing Descriptive and Discriminative Non-linear Features: Rayleigh Coefficients in Kernel Feature Spaces IEEE Transactions on Pattern Analysis and Machine Intelligence 25(5) 623-628.
Warmuth MK , Liao J , Rätsch G Person, Mathieson M , Putta S and Lemmen C (2003) Active Learning with SVMs in the Drug Discovery Process Chemical Information and Computer Sciences 43(2) 667ß673-667ß673.
Tsuda K Person, Kawanabe M , Rätsch G Person, Sonnenburg S and Müller KR (2002) A New Discriminative Kernel from Probabilistic Models Neural Computation 14(10) 2397-2414.
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Rätsch G Person, Mika S , Schölkopf B Person and Müller K-R Person (2002) Constructing Boosting algorithms from SVMs: an application to one-class classification. IEEE Transactions on Pattern Analysis and Machine Intelligence 24(9) 1184-1199.
Rätsch G Person, Demiriz A and Bennett K (2002) Sparse Regression Ensembles in Infinite and Finite Hypothesis Spaces Machine Learning 48 193-221.
Müller K-R Person, Mika S , Rätsch G Person, Tsuda K Person and Schölkopf B Person (2001) An Introduction to Kernel-Based Learning Algorithms IEEE Transactions on Neural Networks 12(2) 181-201.
Onoda T , Rätsch G Person and Müller KR (2001) An Arcing algorithm with an intuitive learning control parameter Journal of the Japanese Society for AI 16(5C) 417-426.
Rätsch G Person, Onoda T and Müller KR (2001) Soft margins for AdaBoost Machine Learning 42 287-320.
Zien A Person, Rätsch G Person, Mika S , Schölkopf B Person, Lengauer T and Müller K-R Person (2000) Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites Bioinformatics 16(9) 799-807.
Onoda T , Rätsch G Person and Müller KR (2000) An asymptotical Analysis and Improvement of AdaBoost in the binary classification case Journal of the Japanese Society for AI 15(2) 287-296.
Schölkopf B Person, Mika S , Burges CJC , Knirsch P Person, Müller K-R , Rätsch G Person and Smola AJ (1999) Input space versus feature space in kernel-based methods IEEE Transactions On Neural Networks 10(5) 1000-1017.

Conference papers (27):

Widmer C Person, Kloft M , Görnitz N and Rätsch G Person (2012) Efficient Training of Graph-Regularized Multitask SVMs In: Machine Learning and Knowledge Discovery in Databases - European Conference, ECML/PKDD 2012, LNCS Vol. 7523, (Ed) PA Flach, T De Bie and N Cristianini, ECML 2012, Springer, Berlin, Germany, 633-647.
Görnitz N , Widmer C Person, Zeller G Person, Kahles A Person, Sonnenburg S Person and Rätsch G Person (2011) Hierarchical Multitask Structured Output Learning for Large-scale Sequence Segmentation In: Advances in Neural Information Processing Systems 24, (Ed) J Shawe-Taylor, RS Zemel, P Bartlett, FCN Pereira and KQ Weinberger, Twenty-Fifth Annual Conference on Neural Information Processing Systems (NIPS 2011), Curran Associates, Inc., Red Hook, NY, USA, 2690--2698.
Widmer C Person, Leiva J Person, Altun Y Person and Rätsch G Person (2010) Leveraging Sequence Classification by Taxonomy-based Multitask Learning In: Research in Computational Molecular Biology, LNCS, Vol. 6044, (Ed) B Berger, 14th Annual International Conference, RECOMB 2010, Springer, Berlin, Germany, 522--534.
Widmer C Person, Toussaint NC Person, Altun Y Person, Kohlbacher O and Rätsch G Person (2010) Novel machine learning methods for MHC Class I binding prediction In: Pattern Recognition in Bioinformatics, (Ed) TMH Dijkstra, E Tsivtsivadze, E Marchiori and T Heskes, 5th IAPR International Conference, PRIB 2010, Springer, Berlin, Germany, 98--109.
Schweikert G Person, Widmer C , Schölkopf B Person and Rätsch G Person (2009) An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis In: Advances in neural information processing systems 21, (Ed) D Koller, D Schuurmans, Y Bengio and L Bottou, 22nd Annual Conference on Neural Information Processing Systems (NIPS 2008), Curran, Red Hook, NY, USA, 1433-1440.
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Shin H Person, Hill NJ Person and Rätsch G Person (2006) Graph Based Semi-Supervised Learning with Sharper Edges In: ECML 2006, (Ed) Fürnkranz, J. , T. Scheffer, M. Spiliopoulou, 17th European Conference on Machine Learning (ECML), Springer, Berlin, Germany, 401-412.
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Rätsch G Person, Hepp B , Schulze U and Ong CS Person (2006) PALMA: Perfect Alignments using Large Margin Algorithms In: GCB 2006, (Ed) Huson, D. , O. Kohlbacher, A. Lupas, K. Nieselt, A. Zell, German Conference on Bioinformatics 2006, Gesellschaft für Informatik, Bonn, Germany, 104-113.
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Tsuda K Person, Rätsch G Person and Warmuth MK (2005) Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection In: Advances in Neural Information Processing Systems 17, (Ed) Saul, L.K. , Y. Weiss, L. Bottou, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS 2004), MIT Press, Cambridge, MA, USA, 1425-1432.
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Sonnenburg S , Rätsch G Person and Schölkopf B Person (2005) Large Scale Genomic Sequence SVM Classifiers In: Proceedings of the 22nd International Conference on Machine Learning, (Ed) L De Raedt and S Wrobel, ICML 2005, ACM, New York, NY, USA, 849-856.
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Tsuda K Person and Rätsch G Person (2004) Image Construction by Linear Programming In: Advances in Neural Information Processing Systems 16, (Ed) Thrun, S., L.K. Saul, B. Schölkopf, Seventeenth Annual Conference on Neural Information Processing Systems (NIPS 2003), MIT Press, Cambridge, MA, USA, 57-64.
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Rätsch G Person, Smola A and Mika S (2003) Adapting Codes and Embeddings for Polychotomies In: Advances in Neural Information Processing Systems 15, (Ed) Becker, S. , S. Thrun, K. Obermayer, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS 2002), MIT Press, Cambridge, MA, USA, 513-520.
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Tsuda K Person, Kawanabe M , Rätsch G Person, Sonnenburg S and Müller K-R (2002) A new discriminative kernel from probabilistic models In: Advances in Neural Information Processing Systems 14, (Ed) Dietterich, T.G. , S. Becker, Z. Ghahramani, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 977-984.
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Warmuth MK , Rätsch G Person, Mathieson M , Liao J and Lemmen C (2002) Active Learning in the Drug Discovery Process In: Advances in Neural Information Processing Systems 14, (Ed) Dietterich, T.G. , S. Becker, Z. Ghahramani, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 1449-1456.
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Rätsch G Person, Mika S and Warmuth MK (2002) On the Convergence of Leveraging In: Advances in Neural Information Processing Systems 14, (Ed) Dietterich, T.G. , S. Becker, Z. Ghahramani, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 487-494.
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Rätsch G Person and Warmuth MK (2002) Maximizing the Margin with Boosting (Ed) Kivinen, J.; Sloan, R. H., Proceedings of the Annual Conference on Computational Learning Theory, 334-350.
Sonnenburg S , Rätsch G Person, Jagota A and Müller K-R (2002) New methods for Splice Site recognition Proceedings of the International Conference on Artificial Neural Networks.
Tsuda K Person, Rätsch G Person, Mika S and Müller K-R (2001) Learning to predict the leave-one-out error of kernel based classifiers (Ed) H. Bischof G. Dorffner and K. Hornik, International Conference on Artificial Neural Networks, ICANN'01, 331-338.
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Mika S , Rätsch G Person, Weston J Person, Schölkopf B Person, Smola AJ and Müller K-R (2000) Invariant feature extraction and classification in kernel spaces In: Advances in neural information processing systems 12, (Ed) SA Solla, TK Leen and K-R Müller, 13th Annual Neural Information Processing Systems Conference (NIPS 1999), MIT Press, Cambridge, MA, USA, 526-532.
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Rätsch G Person, Schölkopf B Person, Smola AJ , Müller K-R , Onoda T and Mika S (2000) v-Arc: Ensemble Learning in the Presence of Outliers In: Advances in Neural Information Processing Systems 12, (Ed) SA Solla, TK Leen and K-R Müller, 13th Annual Neural Information Processing Systems Conference (NIPS 1999), MIT Press, Cambridge, MA, USA, 561-567.
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