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, accepted, American Physical Society, 2012. [link][pdf]
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]
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, 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]
Invited talks
Matthias Rupp: New Uses of Pattern Recognition in Quantum Chemistry and Drug Design, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland, 2011.
Matthias Rupp: Kernels for kernel-based machine learning, Institute for Pure and Applied Mathematics, University of California at Los Angeles, Los Angeles, California, USA, 2011. [pdf]
Matthias Rupp, Robert Körner, Igor Tetko: Prediction of ionization constants with graph kernels, Eidgenössische Technische Hochschule Zürich, Switzerland, 2010. [pdf]
Matthias Rupp: Kernel-based machine learning for virtual screening, Helmholtz Research Center for Environmental Health, Munich, Germany, 2008. [pdf]
Matthias Rupp: Virtual screening for novel ligands, Summer School on Roles of Eicosanoids in Biology and Medicine, Aigen, Austria, 2007. [pdf]
Matthias Rupp: A kernel approach to molecular similarity based on iterative graph similarity, University of Frankfurt, Germany, 2007. [pdf]
Matthias Rupp: Optimierung in der Industrie, Technical University of Darmstadt, Germany, 2006. [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]
