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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

Gunnar Rätsch

Position: Research Scientist Unit: Alumni Schölkopf

Publications

Proceedings (1):
•	Bousquet O , von Luxburg U and Rätsch G : Advanced Lectures on Machine Learning, ML Summer Schools 2003, 240, Springer, Berlin, Germany, (September-2004). 978-3-540-23122-6
Articles (26):
•	Gan XC , Stegle O , Behr J , Steffen JG , Drewe P , Hildebrand KL , Lyngsoe R , Schultheiss SJ , Osborne EJ , Sreedharan VT , Kahles A , Bohnert R , Jean G , Derwent P , Kersey P , Belfield EJ , Harberd NP , Kemen E , Toomajian C , Kover PX , Clark RM , Rätsch G and Mott R (September-2011) Multiple reference genomes and transcriptomes for Arabidopsis thaliana Nature 477(7365) 419–423.
•	Stegle O , Drewe P , Bohnert R , Borgwardt K and Rätsch G (May-2010) Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts Nature Precedings 2010 1-11.
•	Graf ABA , Bousquet O , Rätsch G and Schölkopf B (January-2009) Prototype Classification: Insights from Machine Learning Neural Computation 21(1) 272-300.
•	Ben-Hur A , Ong CS , Sonnenburg S , Schölkopf B and Rätsch G (October-2008) Support Vector Machines and Kernels for Computational Biology PLoS Computational Biology 4(10: e1000173) 1-10.
•	Laubinger S , Zeller G , Henz SR , Sachsenberg T , Widmer CK , Naouar N , Vuylsteke M , Schölkopf B , Rätsch G and Weigel D (July-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 , Schweikert G , Philips P , Behr J and Rätsch G (December-2007) Accurate Splice site Prediction Using Support Vector Machines BMC Bioinformatics 8(Supplement 10) 1-16.
•	Sonnenburg S , Braun ML , Ong CS , Bengio S , Bottou L , Holmes G , LeCun Y , Müller K-R , Pereira F , Rasmussen CE , Rätsch G , Schölkopf B , Smola A , Vincent P , Weston J and Williamson RC (October-2007) The Need for Open Source Software in Machine Learning Journal of Machine Learning Research 8 2443-2466.
•	Clark RM , Schweikert G , Toomajian C , Ossowski S , Zeller G , Shinn P , Warthmann N , Hu TT , Fu G , Hinds DA , Chen H , Frazer KA , Huson DH , Schölkopf B , Nordborg M , Rätsch G , Ecker JR and Weigel D (July-2007) Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana Science 317(5836) 338-342.
•	Schulze U , Hepp B , Ong CS and Rätsch G (May-2007) PALMA: mRNA to Genome Alignments using Large Margin Algorithms Bioinformatics 23(15) 1892-1900.
•	Rätsch G , Sonnenburg S , Srinivasan J , Witte H , Müller K-R , Sommer R-J and Schölkopf B (February-2007) Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning PLoS Computational Biology 3(2, e20) 0313-0322.
•	Sonnenburg S , Zien A and Rätsch G (July-2006) ARTS: Accurate Recognition of Transcription Starts in Human Bioinformatics 22(14) e472-e480.
•	Sonnenburg S , Rätsch G , Schäfer C and Schölkopf B (July-2006) Large Scale Multiple Kernel Learning Journal of Machine Learning Research 7 1531-1565.
•	Tsuda K and Rätsch G (June-2005) Image Reconstruction by Linear Programming IEEE Transactions on Image Processing 14(6) 737-744.
•	Tsuda K , Rätsch G and Warmuth M (June-2005) Matrix Exponentiated Gradient Updates for On-line Learning and Bregman Projection Journal of Machine Learning Research 6 995-1018.
•	Rätsch G , Sonnenburg S and Schölkopf B (June-2005) RASE: recognition of alternatively spliced exons in C.elegans Bioinformatics 21(Suppl. 1) i369-i377.
•	Mika S , Rätsch G , Weston J , Schölkopf B , Smola AJ and Müller K-R (May-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 , Mathieson M , Putta S and Lemmen C (March-2003) Active Learning with SVMs in the Drug Discovery Process Chemical Information and Computer Sciences 43(2) 667ß673-667ß673.
•	Tsuda K , Kawanabe M , Rätsch G , Sonnenburg S and Müller KR (October-2002) A New Discriminative Kernel from Probabilistic Models Neural Computation 14(10) 2397-2414.
•	Rätsch G , Mika S , Schölkopf B and Müller K-R (September-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 , Demiriz A and Bennett K (2002) Sparse Regression Ensembles in Infinite and Finite Hypothesis Spaces Machine Learning 48 193-221.
•	Müller K-R , Mika S , Rätsch G , Tsuda K and Schölkopf B (March-2001) An Introduction to Kernel-Based Learning Algorithms IEEE Transactions on Neural Networks 12(2) 181-201.
•	Onoda T , Rätsch G 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 , Onoda T and Müller KR (2001) Soft margins for AdaBoost Machine Learning 42 287-320.
•	Zien A , Rätsch G , Mika S , Schölkopf B , Lengauer T and Müller K-R (September-2000) Engineering Support Vector Machine Kernels That Recognize Translation Initiation Sites Bioinformatics 16(9) 799-807.
•	Onoda T , Rätsch G 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 , Mika S , Burges CJC , Knirsch P , Müller K-R , Rätsch G and Smola AJ (September-1999) Input space versus feature space in kernel-based methods IEEE Transactions On Neural Networks 10(5) 1000-1017.
Conference papers (23):
•	Schweikert G , Widmer C , Schölkopf B and Rätsch G (June-2009) An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis In: Advances in neural information processing systems 21, Twenty-Second Annual Conference on Neural Information Processing Systems (NIPS 2008), Curran, Red Hook, NY, USA, 1433-1440.
•	Shin H , Hill NJ and Rätsch G (September-2006) Graph Based Semi-Supervised Learning with Sharper Edges In: ECML 2006, 17th European Conference on Machine Learning (ECML), Springer, Berlin, Germany, 401-412.
•	Rätsch G , Hepp B , Schulze U and Ong CS (September-2006) PALMA: Perfect Alignments using Large Margin Algorithms In: GCB 2006, German Conference on Bioinformatics 2006, Gesellschaft für Informatik, Bonn, Germany, 104-113.
•	Tsuda K , Rätsch G and Warmuth MK (July-2005) Matrix Exponential Gradient Updates for On-line Learning and Bregman Projection In: Advances in Neural Information Processing Systems 17, Eighteenth Annual Conference on Neural Information Processing Systems (NIPS 2004), MIT Press, Cambridge, MA, USA, 1425-1432.
•	Sonnenburg S , Rätsch G and Schölkopf B (2005) Large Scale Genomic Sequence SVM Classifiers ICML Bonn, USA, 849.
•	Tsuda K and Rätsch G (June-2004) Image Construction by Linear Programming In: Advances in Neural Information Processing Systems 16, Seventeenth Annual Conference on Neural Information Processing Systems (NIPS 2003), MIT Press, Cambridge, MA, USA, 57-64.
•	Rätsch G , Smola A and Mika S (October-2003) Adapting Codes and Embeddings for Polychotomies In: Advances in Neural Information Processing Systems 15, Sixteenth Annual Conference on Neural Information Processing Systems (NIPS 2002), MIT Press, Cambridge, MA, USA, 513-520.
•	Tsuda K , Kawanabe M , Rätsch G , Sonnenburg S and Müller K-R (September-2002) A new discriminative kernel from probabilistic models In: Advances in Neural Information Processing Systems 14, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 977-984.
•	Warmuth MK , Rätsch G , Mathieson M , Liao J and Lemmen C (September-2002) Active Learning in the Drug Discovery Process In: Advances in Neural Information Processing Systems 14, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 1449-1456.
•	Rätsch G , Mika S and Warmuth MK (September-2002) On the Convergence of Leveraging In: Advances in Neural Information Processing Systems 14, Fifteenth Annual Neural Information Processing Systems Conference (NIPS 2001), MIT Press, Cambridge, MA, USA, 487-494.
•	Rätsch G and Warmuth MK (2002) Maximizing the Margin with Boosting Proceedings of the Annual Conference on Computational Learning Theory, 334-350.
•	Sonnenburg S , Rätsch G , Jagota A and Müller K-R (2002) New methods for Splice Site recognition Proceedings of the International Conference on Artificial Neural Networks.
•	Tsuda K , Rätsch G , Mika S and Müller K-R (2001) Learning to predict the leave-one-out error of kernel based classifiers International Conference on Artificial Neural Networks, ICANN'01, 331-338.
•	Mika S , Rätsch G , Weston J , Schölkopf B , Smola AJ and Müller K-R (June-2000) Invariant feature extraction and classification in kernel spaces In: Advances in neural information processing systems 12, Thirteenth Annual Neural Information Processing Systems Conference (NIPS 1999), MIT Press, Cambridge, MA, USA, 526-532.
•	Rätsch G , Schölkopf B , Smola AJ , Müller K-R , Onoda T and Mika S (June-2000) v-Arc: Ensemble Learning in the Presence of Outliers In: Advances in Neural Information Processing Systems 12, Thirteenth Annual Neural Information Processing Systems Conference (NIPS 1999), MIT Press, Cambridge, MA, USA, 561-567.
•	Rätsch G , Warmuth MK , Mika S , Onoda T , Lemm S and Müller K-R (2000) Barrier Boosting Proceedings of the Annual Conference on Computational Learning Theory, 170-179.
•	Rätsch G , Schölkopf B , Smola AJ , Mika S , Onoda T and Müller K-R (2000) Robust Ensemble Learning for Data Mining Fourth Pacific-Asia Conference on Knowledge Discovery and Data Mining, 1805, 341-341.
•	Mika S , Schölkopf B , Smola AJ , Müller K-R , Scholz M and Rätsch G (June-1999) Kernel PCA and De-noising in feature spaces In: Advances in Neural Information Processing Systems 11, Twelfth Annual Conference on Neural Information Processing Systems (NIPS 1998), MIT Press, Cambridge, MA, USA, 536-542.
•	Rätsch G , Onoda T and Müller KR (June-1999) Regularizing AdaBoost In: Advances in Neural Information Processing Systems 11, Twelfth Annual Conference on Neural Information Processing Systems (NIPS 1998), MIT Press, Cambridge, MA, USA, 564-570.
•	Mika S , Rätsch G , Weston J , Schölkopf B and Müller K-R (1999) Fisher discriminant analysis with kernels. Neural Networks for Signal Processing, 9, 41-48.
•	Smola AJ , Schölkopf B and Rätsch G (1999) Linear programs for automatic accuracy control in regression. Ninth International Conference on Artificial Neural Networks, 470, 575.
•	Schölkopf B , Mika S , Smola AJ , Rätsch G and Müller K-R (1998) Kernel PCA pattern reconstruction via approximate pre-images. 8th International Conference on Artificial Neural Networks, 147-152.
•	Müller K-R , Smola AJ , Rätsch G , Schölkopf B , Kohlmorgen J and Vapnik V (October-1997) Predicting time series with support vectur machines In: Artificial neural networks: ICANN '97, 7th International Conference on Artificial Neural Networks, Springer, Berlin, Germany, 999-1004.