Dr. Matthias Rupp

Postdoc (machine learning in molecular sciences)

Publications

Articles

• John C. Snyder, Matthias Rupp, Katja Hansen, Klaus-Robert Müller, Kieron Burke: Finding Density Functionals with Machine Learning, Physical Review Letters, accepted, American Physical Society, 2012.
• Grigorios Skolidis, Katja Hansen, Guido Sanguinetti, Matthias Rupp: Multi-task learning for pKa prediction, Journal of Computer-Aided Molecular Design, accepted, Springer, 2012.
• Zachary D. Pozun, Katja Hansen, Daniel Sheppard, Matthias Rupp, Klaus-Robert Müller, Graeme Henkelman: Optimizing transition states via kernel-based machine learning, Journal of Chemical Physics, 136(17): 174101, American Institute of Physics, 2012. [doi]
• Markus Hartenfeller, Heiko Zettl, Miriam Walter, Matthias Rupp, Felix Reisen, Ewgenij Proschak, Sascha Weggen, Holger Stark, Gisbert Schneider: DOGS: Reaction-Driven De Novo Design of Bioactive Compounds, PLoS Computational Biology, 8(2): e1002380, Public Library of Science, 2012. [doi] [pdf]
• Matthias Rupp, Alexandre Tkatchenko, Klaus-Robert Müller, O. Anatole von Lilienfeld: Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning, Physical Review Letters, 108(5): 058301, American Physical Society, 2012. [doi] [pdf]
• Katja Hansen, David Baehrens, Timon Schroeter, Matthias Rupp, Klaus-Robert Müller: Visual Interpretation of Kernel-Based Prediction Models, Molecular Informatics, 30(9): 817–826, Wiley, 2011. [doi]
• Quan Wang, Kerstin Birod, Carlo Angioni, Sabine Grösch, Tim Geppert, Petra Schneider, Matthias Rupp, Gisbert Schneider: Spherical Harmonics Coefficients for Ligand-Based Virtual Screening of Cyclooxygenase Inhibitors, PLoS ONE, 6(7): e21554, Public Library of Science, 2011. [doi] [pdf]
• Iurii Sushko, Sergii Novotarskyi, Robert Körner, Anil Kumar Pandey, Matthias Rupp, Wolfram Teetz, Stefan Brandmaier, Ahmed Abdelaziz, Volodymyr V. Prokopenko, Vsevolod Y. Tanchuk, Roberto Todeschini, Alexandre Varnek, Gilles Marcou, Peter Ertl, Vladimir Potemkin, Maria Grishina, Johann Gasteiger, Christof Schwab, Igor I. Baskin, Vladimir A. Palyulin, Eugene V. Radchenko, William J. Welsh, Vladyslav Kholodovych, Dmitriy Chekmarev, Artem Cherkasov, Joao Aires-de-Sousa, Qing-You Zhang, Andreas Bender, Florian Nigsch, Luc Patiny, Antony Williams, Valery Tkachenko, Igor V. Tetko: Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information, Journal of Computer Aided Molecular Design, 25(6): 533–554, Springer, 2011. [doi]
• Matthias Rupp, Robert Körner, Igor V. Tetko: Predicting the pKa of small molecules, Combinatorial Chemistry & High Throughput Screening, 14(5): 307–327, Bentham, 2011. [link]
• Matthias Rupp, Robert Körner, Igor Tetko: Estimation of acid dissociation constants using graph kernels, Molecular Informatics, 29(10): 731–740, Wiley, 2010. [doi]
• Volker Hähnke, Matthias Rupp, Mireille Krier, Friedrich Rippmann, Gisbert Schneider: Pharmacophore alignment search tool (PhAST): Influence of Canonical Atom Labeling on Similarity Searching, Journal of Computational Chemistry, 31(15): 2810–2826, Wiley, 2010. [doi]
• Matthias Rupp, Gisbert Schneider: Graph kernels for molecular similarity, Molecular Informatics, 29(4): 266–273, Wiley, 2010. [doi]
• Ramona Steri, Petra Schneider, Alexander Klenner, Matthias Rupp, Manfred Schubert-Zsilavecz, Gisbert Schneider: Target profile prediction: Cross-activation of peroxisome proliferator-activated receptor (PPAR) and farnesoid X receptor (FXR), Molecular Informatics, 29(4): 287–292, Wiley, 2010. [doi]
• Ramona Steri, Matthias Rupp, Ewgenij Proschak, Timon Schroeter, Heiko Zettl, Katja Hansen, Oliver Schwarz, Lutz Müller-Kuhrt, Klaus-Robert Müller, Gisbert Schneider, Manfred Schubert-Zsilavecz: Truxillic acid derivatives act as peroxisome proliferator-activated receptor γ activators, Bioorganic & Medicinal Chemistry Letters, 20(9): 2920–2923, Elsevier, 2010. [doi]
• Matthias Rupp, Timon Schroeter, Ramona Steri, Heiko Zettl, Ewgenij Proschak, Katja Hansen, Oliver Rau, Oliver Schwarz, Lutz Müller-Kuhrt, Manfred Schubert-Zsilavecz, Klaus-Robert Müller, Gisbert Schneider: From machine learning to natural product derivatives selectively activating transcription factor PPARγ, ChemMedChem, 5(2): 191–194, Wiley, 2010. [doi]
• Matthias Rupp, Petra Schneider, Gisbert Schneider: Distance phenomena in high-dimensional chemical descriptor spaces: Consequences for similarity-based approaches, Journal of Computational Chemistry, 30(14): 2285–2296, Wiley, 2009. [doi]
• Ewgenij Proschak, Matthias Rupp, Swetlana Derksen, Gisbert Schneider: Shapelets: Possibilities and limitations of shape-based virtual screening, Journal of Computational Chemistry, 29(1): 108–114, Wiley, 2008. [doi]
• Matthias Rupp, Ewgenij Proschak, Gisbert Schneider: Kernel approach to molecular similarity based on iterative graph similarity, Journal of Chemical Information and Modeling, 47(6): 2280–2286, American Chemical Society, 2007. [doi]

Book chapters

• Matthias Rupp: Graph kernels. In Matthias Dehmer, Subhash Basak (editors): Machine Learning Approach for Network Analysis: Novel Graph Classes for Classification Techniques, Wiley, accepted.

Conferences

• Matthias Rupp: Modeling of molecular atomization energies using machine learning, 7th German Conference on Chemoinformatics, Goslar, Germany, November 6–8, 2011. [pdf]
• Katja Hansen, David Baehrens, Timon Schroeter, Matthias Rupp, Klaus-Robert Müller: Interpretation and explanation of kernel-based prediction models, 242nd Annual Meeting of the American Chemical Society, Denver, Colorado, USA, August 28–September 1, 2011.
• Matthias Rupp: From machine learning to novel agonists of the peroxisome proliferator-activated receptor, 24th Annual Conference on Neural Information Processing Systems (NIPS 2010) Workshop on Charting Chemical Space: Challenges and Opportunities for AI and Machine Learning, Whistler, Canada, December 10–11, 2010. [pdf]
• Matthias Rupp: Graph kernels for chemoinformatics. A critical discussion, 6th German Conference on Chemoinformatics, Goslar, Germany, November 7–9, 2010. [pdf]
• Matthias Rupp, Timon Schroeter, Ramona Steri, Ewgenij Proschak, Katja Hansen, Heiko Zettl, Oliver Rau, Manfred Schubert-Zsilavecz, Klaus-Robert Müller, Gisbert Schneider: Kernel learning for virtual screening: Discovery of a new PPARγ agonist, 5th German Conference on Chemoinformatics, Goslar, Germany, November 8–10, 2009. [pdf]
• Igor Tetko, Iurii Sushko, Sergeii Novotarsky, Robert Körner, Anil Kumar Pandey, Matthias Rupp: Online chemical modeling environment, 1st World Conference on Physico-Chemical Methods in Drug Discovery and Development, Rovinj, Croatia, September 27–October 1, 2009. [pdf]
• Matthias Rupp, Petra Schneider, Gisbert Schneider: Distance phenomena in chemical spaces: Consequences for similarity approaches, 4th German Conference on Chemoinformatics, Goslar, Germany, November 9–11, 2008. [pdf]
• Timon Schroeter, Matthias Rupp, Katja Hansen, Klaus-Robert Müller, Gisbert Schneider: Virtual screening for PPAR-gamma ligands using the ISOAK molecular graph kernel and Gaussian processes, 4th German Conference on Chemoinformatics, Goslar, Germany, November 9–11, 2008. [pdf]
• Matthias Rupp, Ewgenij Proschak, Gisbert Schneider: Molecular similarity for machine learning in drug development, 3rd German Conference on Chemoinformatics, Goslar, Germany, November 11–13, 2007. [pdf]
• Matthias Rupp, Wolfgang Mergenthaler, Bernhard Mauersberg, Jens Feller: Markov mills, reliable rolls and Monte-Carlo mines: Minimizing the operating costs of grinding mills, Proceedings of the 2005 International Conference on Numerical Analysis and Applied Mathematics (ICNAAM 2005), Rhodes, Greece, September 26–20, 2005. [pdf]

Theses

• Matthias Rupp: Kernel methods for virtual screening, PhD dissertation, University of Frankfurt, Germany, 2009. [pdf]
• Matthias Rupp: Zeitoptimale Bearbeitungsreihenfolgen für mehrere Schweißroboter: Modelle und Algorithmen, degree dissertation, University of Frankfurt, Germany, 2004. [pdf]

Software

• Grigorios Skolidis: Multi-task Gaussian process regression, Matlab code, version 2012-05-10. [zip]
• Matthias Rupp: Iterative similarity optimal assignment kernel (ISOAK), Java implementation, version 2008-01-15. [mloss] [zip]

Other

• Matthias Rupp: Floating point comparisons, 2007. [pdf]
• Matthias Rupp: Roots of cubic equations, 2007. [pdf]
• Matthias Rupp: Review checklist, 2006. [pdf]

Intra-European fellowship

EU 7th framework programme
Marie Curie actions
Grant 273039 "SymPati"

Best poster award

3rd German Conference
on Chemoinformatics,
Goslar, Germany, 2 007

FIRST scholarship

Frankfurt International
Research Graduate School
for Translational Biomedicine

Photos

• Costa Rica 2007: Four weeks in Costa Rica.
• Australia 2005: Five weeks in Australia and New Zealand.
• Spain 2004: Two weeks in the language school Academia pradoventura in Andalusia.