Cheminformatics

The challenging task in Cheminformatics is to support the drug discovery process by adequate computational methods including largely automated data mining algorithms as well as visual analysis tools. Our research includes algorithms to compare graphs, which are a prerequisite to apply data mining algorithms to structured objects like chemical compounds. Moreover, we develop methods for searching graph databases as well as visual analysis approaches for chemical space.

We develop Scaffold Hunter, a tool for the analysis and exploration of chemical space aiming at an intuitive access to large and complex data sets. The tool offers a variety of views, e.g. graph, dendrogram, and plot view, as well as analysis methods, e.g., for clustering and classification.

• Practical SAHN Clustering for Very Large Data Sets and Expensive Distance Metrics
  Nils Kriege, Petra Mutzel, Till Schäfer
  Journal of Graph Algorithms and Applications (JGAA), vol. 18, no. 4, 577-602, 2014.

• Explicit versus Implicit Graph Feature Maps: A Computational Phase Transition for Walk Kernels
  Nils Kriege, Marion Neumann, Kristian Kersting, Petra Mutzel
  International Conference on Data Mining (ICDM) 2014, to appear.

• Enumeration of Maximum Common Subtree Isomorphisms with Polynomial-Delay
  Andre Droschinsky, Bernhard Heinemann, Nils Kriege, Petra Mutzel
  International Symposium on Algorithms and Computation (ISAAC) 2014, 81-93.

• On Maximum Common Subgraph Problems in Series-Parallel Graphs
  Nils Kriege, Florian Kurpicz, Petra Mutzel
  International Workshop on Combinatorial Algorithms (IWOCA) 2014, to appear.

• Finding Maximum Common Biconnected Subgraphs in Series-Parallel Graphs
  Nils Kriege, Petra Mutzel
  International Symposium on Mathematical Foundations of Computer Science (MFCS) 2014, 505-516.

• The Landscape Metaphor for Visualization of Molecular Similarities
  Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel
  in: Battiato, S.; Coquillart, S.; Laramee, R. S.; Kerren, A. & Braz, J. (Eds.), Computer Vision, Imaging and Computer Graphics. Theory and Application; Communications in Computer and Information Science, 2014, 458, 85-100.

• SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search
  Till Schäfer, Petra Mutzel, Nils Kriege
  International Workshop on Algorithms and Computation (WALCOM) 2014, 90-101

• Scaffold Hunter: Visual Analysis of Biological Activity Data
  Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer
  German Conference on Chemoinformatics, Fulda, Germany, 2013.

• SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search [Kriege/etal/2013]
  Nils Kriege, Petra Mutzel, Till Schäfer
  in: Algorithm Engineering Reports, TR13-1-003, TU Dortmund, 2013

• Visual Analysis of Biological Activity Data with Scaffold Hunter
  Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer
  Molecular Informatics, WILEY-VCH Verlag, 2013, 32, 964-975

• Scaffold Hunter: Facilitating Drug Discovery by Visual Analysis of Chemical Space
  Karsten Klein, Nils Kriege, Petra Mutzel
  in: G. Csurka, M. Kraus, R. Laramee, P. Richard, J. Braz (Eds.), Computer Vision, Imaging and Computer Graphics. Theory and Application; Communications in Computer and Information Science, 2013, 359, 176-192

• MolMap - Visualizing Molecule Libraries as Topographic Maps [Gronemann/etal/2013]
  Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel
  International Conference on Information Visualization Theory and Applications (IVAPP) 2013, 537-541, Best Paper Award.

• Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs
  Marianna D'Addario, Nils Kriege, Sven Rahmann
  German Conference on Bioinformatics (GCB) 2012, Jena, Germany, 82-92.

• Subgraph Matching Kernels for Attributed Graphs [Kriege/etal/2012]
  Nils Kriege, Petra Mutzel
  International Conference on Machine Learning (ICML) 2012.

• Scaffold Hunter - Visual Analysis of Chemical Compound Databases [Klein/etal/2012]
  Karsten Klein, Nils Kriege, Petra Mutzel
  International Conference on Information Visualization Theory and Applications (IVAPP) 2012, 626-635, Best Paper Award.

• CT-Index: Fingerprint-based Graph Indexing Combining Cycles and Trees [Klein/etal/2011]
  Karsten Klein, Nils Kriege, Petra Mutzel
  in: Proceedings of the 27th International Conference on Data Engineering (ICDE) 2011, Hannover, Germany, 1115-1126

• Scaffold Hunter - Interactive Exploration of Chemical Space
  Karsten Klein, Nils Kriege, Petra Mutzel, Herbert Waldmann, Stefan Wetzel
  in: D. Eppstein, E. Gansner (Eds.), 17th Symposium on Graph Drawing 2009, Chicago
  Lecture Notes in Computer Science 5849, 2010, 426-427

• Interactive Exploration of Chemical Space with Scaffold Hunter [Wetzel/etal/2009a]
  Stefan Wetzel, Karsten Klein, Steffen Renner, Daniel Rauh, Tudor I. Oprea, Petra Mutzel, Herbert Waldmann
  Nature Chemical Biology 5, 2009, 581-583

• Effiziente Enumerationsalgorithmen für Common Subtree Probleme
  Andre Droschinsky, Diploma Thesis, 2014

• Efficient algorithms for the maximum common subgraph problem in partial 2-trees
  Florian Kurpicz, Master Thesis, 2014

• Verfeinerung bitvektorbasierter Filterverfahren zur Substruktursuche in Molekülgraphdatenbanken
  Fabian Weißberg, Bachelor Thesis, 2013

• Beschleunigung hierarchischer Clusterverfahren für allgemeine metrische Distanzmaße
  Till Schäfer, Diploma Thesis, 2012

• Entwurf von Oligonukleotid-Bibliotheken für die DNA-Nanotechnologie
  Marianna D'Addario, Diploma Thesis, 2011 (Collaboration with Prof. Rahmann and Prof. Niemeyer, Chemistry)

• Erweiterte Substruktursuche in Moleküldatenbanken und ihre Integration in Scaffold Hunter
  Nils Kriege
  in: TR10-1-001, Algorithm Engineering Report, Fakultät für Informatik, TU Dortmund, 2010.
  Diploma Thesis, TU Dortmund, December 2009.