~~NOTOC~~ {{ http://ls11-www.cs.tu-dortmund.de/people/kriege/kriege.jpg}} ==== Nils Kriege ==== I have moved to the \\ [[https://univie.ac.at|University of Vienna]] | Room: | 233 | | Phone: | +49 231 755-7737 | | Fax: | +49 231 755 7740 | | E-Mail: | nils.kriege{{:staff:at.gif|}}tu-dortmund.de| ===== Research Interests ===== * Combinatorial Optimization, Graph Algorithms * Data Mining, Machine Learning with Graphs * Information Visualization, Visual Analytics * Applications in Cheminformatics ===== Teaching (in German) ===== == Lehrveranstaltung == * **Wintersemester 2019/20** * Vorlesung [[teaching:aud-ws2019|Algorithmen und Datenstrukturen]] * Proseminar [[teaching:proseminar-ads-ws2019|Algorithmic Data Science]] * [[teaching:praesentationskurs-ws2019|Präsentationstechniken für Proseminare]] * **Sommersemester 2019** * [[teaching:dap2_ss19_praktikum|Programmierpraktikum]] zu [[http://ls2-www.cs.tu-dortmund.de/lehre/sommer2019/dap2/|Datenstrukturen, Algorithmen und Programmierung 2]] * Proseminar [[staff:mutzel:prosemgraphalg|Graphalgorithmen]] * **Wintersemester 2018/19** * Übung zu [[http://ls4-www.cs.tu-dortmund.de/cms/de/lehre/2018_ws/rvs/index.html|Rechnernetze und verteilte Systeme]] * **Sommersemester 2018** * [[teaching:dap2_ss18_praktikum|Programmierpraktikum]] zu [[http://ls2-www.cs.tu-dortmund.de/lehre/sommer2018/dap2/|Datenstrukturen, Algorithmen und Programmierung 2]] * Seminar [[teaching:seminarae-ss2018|Algorithm Engineering]] * **Wintersemester 2017/18** * Proseminar [[teaching:proseminar-gdm-ws2017|Grundlagen des Data-Minings für strukturierte Daten]] * **Sommersemester 2017** * [[teaching:dap2_ss17_praktikum|Programmierpraktikum]] zu [[http://ls2-www.cs.tu-dortmund.de/lehre/sommer2017/dap2/|Datenstrukturen, Algorithmen und Programmierung 2]] * Seminar [[teaching:seminarae-ss2017|Algorithm Engineering]] * **Wintersemester 2016/17** * Fachprojekt [[teaching:fp_ae-ws2016|Algorithm Engineering for Graph Data Mining]] * Proseminar [[staff:mutzel:prosemunplugged|Algorithms Unplugged]] * **Sommersemester 2016** * Proseminar [[teaching:proseminarklagra-ss2016|Klassische Probleme der Graphentheorie]] * Seminar [[teaching:seminar-gdm-ss2016|Graph Data Mining]] * Seminar [[teaching:seminarae-ss2016|Algorithm Engineering]] * **Wintersemester 2015/16** * Übung zu [[teaching:ep1516uebung|Einführung in die Programmierung]] * **Sommersemester 2015** * [[teaching:dap2_ss15_praktikum|Programmierpraktikum]] zu [[http://ls2-www.cs.tu-dortmund.de/lehre/sommer2015/dap2/|Datenstrukturen, Algorithmen und Programmierung 2]] * Seminar [[teaching:seminarae-ss2015|Algorithm Engineering]] * **Wintersemester 2014/15** * Übung zu [[http://ls5-www.cs.tu-dortmund.de/cms/de/lehre/lehrveranstaltungen/ws2014-15/Mathematik_f__r_Informatiker_1/index.shtml|Mathematik für Informatiker 1]] * Seminar [[teaching:seminarae-ws2014|Algorithm Engineering]] * **Sommersemester 2014** * [[teaching:dap2_ss14_praktikum|Programmierpraktikum]] zu [[http://ls2-www.cs.tu-dortmund.de/lehre/sommer2014/dap2/|Datenstrukturen, Algorithmen und Programmierung 2]] * **Wintersemester 2013/14** * Seminar [[teaching:seminarae-ws2013|Algorithm Engineering]] * **Sommersemester 2013** * Seminar [[teaching:seminarae-ss2013|Algorithm Engineering]] * **Wintersemester 2012/13** * Seminar [[teaching:seminarae-ws2012|Algorithm Engineering]] * **Sommersemester 2012** * Seminar [[teaching:seminarae-ss2012|Algorithm Engineering]] mit Schwerpunkt //Graph Data Mining// * **Sommersemester 2011** * [[teaching:drughunting|PG 552: Drug Hunting]] - Navigation und visuelle Analyse im pharmakologischen Strukturraum * Fachprojekt [[teaching:fp_ae-2011|Algorithm Engineering]] * **Wintersemester 2010/11** * [[teaching:drughunting|PG 552: Drug Hunting]] - Navigation und visuelle Analyse im pharmakologischen Strukturraum * Seminar [[teaching:seminarae-2010|Algorithm Engineering]] * **Sommersemester 2010** * Seminar [[staff:wong:seminar2010|Graphenalgorithmen]] == Betreute studentische Arbeiten == * **Martin Rentz**: //Adaptive Color Refinement for Learning Graph Features//, Masterarbeit, 2020. * **Marvin Büsscher**: //Klassische und numerische Verfahren zur Lösung von Assignment-Problemen//, Masterarbeit, 2020. * **Franka Bause**: //Efficient Approximate k-Nearest-Neighbor-Search In Large Graph Databases//, Masterarbeit, 2020. * **Frederik Stehli**: //Approximation des Optimal Assignment Kernels durch explizite Merkmalsvektoren//, Bachelorarbeit, 2019. * **Dmytro Semenchenko**: //Approximating the Graph Edit Distance via Deep Learning//, Bachelorarbeit, 2019. * **Mohamad Reza Nirumand Alankesh**: //Extending SplineCNN by Structural Graph Features for Cheminformatics//, Bachelorarbeit, 2018. * **Robert Gehde**: //Erweiterung von Pharmakophor-basierten Fingerprints mittels Randomisierung//, Bachelorarbeit, 2018. * **[[staff:oettershagen|Lutz Oettershagen]]**: //On the Crossing Number of Almost Bishellable Drawings of Complete Graphs//, Masterarbeit, 2017. * **[[staff:dahn|Christine Dahn]]**: //Entwicklung eines Max-Cut-Algorithmus für fast-planare Graphen//, Masterarbeit, 2017 * **Franka Bause**: //Approximation der Editierdistanz für Graphen in linearer Zeit//, Bachelorarbeit, 2017 * **Martin Rentz**: //Approximative Algorithmen für das Assignment-Problem mit Hilfe von hierarchischem Clustering//, Bachelorarbeit, 2017 * **Jonas Ellert**: //Matchings in bipartiten Graphen im Semi-Streaming Modell//, Bachelorarbeit, 2016 * **Christopher Osthues**: //Experimenteller Vergleich von Labeling-Verfahren für Graphkerne//, Bachelorarbeit, 2016 * **David Schoen**: //Dynamische Layoutverfahren für semantische Molekülwolken//, Diplomarbeit, 2015 * **Markus Kloß**: //An output sensitive algorithm for enumerating all maximal common subgraphs//, Studienarbeit, 2014 * **[[https://www.fernuni-hagen.de/ak/team/andre.droschinsky.shtml|Andre Droschinsky]]**: //Effiziente Enumerationsalgorithmen für Common Subtree Probleme//, Diplomarbeit, 2014 * **[[staff:kurpicz|Florian Kurpicz]]**: //Efficient algorithms for the maximum common subgraph problem in partial 2-trees//, Masterarbeit 2014 * **Fabian Weißberg**: //Verfeinerung bitvektorbasierter Filterverfahren zur Substruktursuche in Molekülgraphdatenbanken//, Bachelorarbeit, 2013 * **Henning Garus**: //Interactive Visualization of Molecular Scaffold Networks//, Diplomarbeit, 2012 * **Patrick Baron**: //Integration ausgewählter Analyseverfahren für Affiliation-Netzwerke in Cytoscape//, Bachelorarbeit, 2012 * **[[staff:schaefer|Till Schäfer]]**: //Beschleunigung hierarchischer Clusterverfahren für allgemeine metrische Distanzmaße//, Diplomarbeit, 2012 * **[[staff:daddario|Marianna D'Addario]]**: //Entwurf von Oligonukleotid-Bibliotheken für die DNA-Nanotechnologie//, Diplomarbeit (Kooperation mit [[staff:rahmann|Prof. Rahmann]] und Prof. Niemeyer, Chemie), 2011 ===== Projects ===== * [[bwinf:2017:mol_class| Klassifikation pharmazeutischer Wirkstoffe]] -- [[https://www.bwinf.de|Bundeswettbewerb Informatik]] [[bwinf:2017|Workshop 2017]] * [[http://scaffoldhunter.sourceforge.net|Scaffold Hunter]] -- A tool for the analysis and exploration of chemical space * Google Summer of Code 2014: Mentoring project [[https://www.google-melange.com/gsoc/project/details/google/gsoc2014/anjenson/5657382461898752|Molecule Cloud]] * Google Summer of Code 2013: Mentoring project [[https://www.google-melange.com/gsoc/project/details/google/gsoc2013/lappie/5662278724616192|Tree Maps]] * [[http://graphkernels.cs.tu-dortmund.de|Benchmark Data Sets for Graph Kernels]] -- A collection of graph data sets with class labels for benchmarking purposes * [[http://sfb876.tu-dortmund.de/SPP/sfb876-a6.html|Resource efficient analysis of graphs]] -- Collaborative Research Center [[http://sfb876.tu-dortmund.de|Providing Information by Resource-Constrained Data Analysis]] (SFB 876) * [[http://www.big-data-spp.de/projects/graph-based-methods-for-rational-drug-design|Graph-Based Methods for Rational Drug Design]] -- DFG Priority Programme [[http://www.big-data-spp.de|Algorithms for Big Data]] (SPP 1736) * [[http://ls11-www.cs.tu-dortmund.de/people/wong/DFGWEB/start.html|Planarization Approaches in Automatic Graph Drawing]] -- DFG Priority Programme [[http://www.algorithm-engineering.de|Algorithm Engineering]] (SPP 1307) ===== Publications ===== === Preprints === * **[[https://arxiv.org/abs/1812.03074|Fixed-Parameter Algorithms for the Weighted Max-Cut Problem on Embedded 1-Planar Graphs]]** \\ Christine Dahn, Nils M. Kriege, Petra Mutzel, Julian Schilling, ''arXiv:1812.03074''. === Journal Articles === * **Classifying Dissemination Processes in Temporal Graphs**\\ Lutz Oettershagen, Nils M. Kriege, Christopher Morris, and Petra Mutzel \\ Big Data, 2020, accepted for publication. * **[[http://dx.doi.org/10.7155/jgaa.00523|Maximum Cut Parameterized by Crossing Number]]** (Preprint [[https://arxiv.org/abs/1903.06061|arXiv:1903.06061]]) \\ Markus Chimani, Christine Dahn, Martina Juhnke-Kubitzke, Nils M. Kriege, Petra Mutzel, Alexander Nover \\ Journal of Graph Algorithms and Applications (JGAA), vol. 24, no. 3, 155-170, 2020. * **[[https://doi.org/10.1007/s41109-019-0195-3|A Survey on Graph Kernels]]** (Preprint [[https://arxiv.org/abs/1903.11835|arXiv:1903.11835]]) \\ Nils M. Kriege, Fredrik D. Johansson, Christopher Morris \\ Applied Network Science, Machine learning with graphs, 5:6, 2020. * **[[https://doi.org/10.1007/s10618-019-00652-0|A unifying view of explicit and implicit feature maps of graph kernels]]** (Preprint [[https://arxiv.org/abs/1703.00676|arXiv:1703.00676]]) \\ Nils M. Kriege, Marion Neumann, Christopher Morris, Kristian Kersting, Petra Mutzel \\ Data Mining and Knowledge Discovery, 33, 1505-1547, 2019. * **[[https://doi.org/10.1007/s00453-019-00552-1|A general purpose algorithm for counting simple cycles and simple paths of any length]]** (Preprint [[https://arxiv.org/abs/1612.05531|arXiv:1612.05531]]) \\ Pierre-Louis Giscard, Nils Kriege, Richard C. Wilson \\ Algorithmica, vol. 81, no. 7, 2716-2737, 2019. * **[[http://dx.doi.org/10.7155/jgaa.00480|A note on block-and-bridge preserving maximum common subgraph algorithms for outerplanar graphs]]** (Preprint [[https://arxiv.org/abs/1805.10754|arXiv:1805.10754]]) \\ Nils M. Kriege, Andre Droschinsky, Petra Mutzel \\ Journal of Graph Algorithms and Applications (JGAA), vol. 22, no. 4, 607-616, 2018. * **[[https://doi.org/10.1016/j.ejc.2017.07.012|On Maximum Common Subgraph Problems in Series-Parallel Graphs]]** (Preprint [[http://arxiv.org/abs/1708.02772|arXiv:1708.02772]]) \\ Nils Kriege, Florian Kurpicz, Petra Mutzel \\ European Journal on Combinatorics (EJC), vol. 68, 79-95, 2018. * **[[http://dx.doi.org/10.1186/s13321-017-0213-3|Scaffold Hunter: A comprehensive visual analytics framework for drug discovery]]** \\ Till Schäfer, Nils Kriege, Lina Humbeck, Karsten Klein, Oliver Koch, Petra Mutzel \\ Journal of Cheminformatics, 9:28, 2017. * **[[http://dx.doi.org/10.7155/jgaa.00338|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. * **[[http://dx.doi.org/10.1002/minf.201300087|Visual Analysis of Biological Activity Data with Scaffold Hunter]]** \\ Karsten Klein, Oliver Koch, Nils Kriege, Petra Mutzel, Till Schäfer \\ Molecular Informatics, WILEY-VCH Verlag, 32, 964-975, 2013. === Refereed Conference Proceedings === * **[[https://grlplus.github.io/papers/79.pdf|TUDataset: A collection of benchmark datasets for learning with graphs]]** (Preprint [[https://arxiv.org/abs/2007.08663|arXiv:2007.08663]], [[https://github.com/chrsmrrs/tudataset|Source code]]) \\ Christopher Morris, Nils M. Kriege, Franka Bause, Kristian Kersting, Petra Mutzel, Marion Neumann \\ ICML 2020 Workshop on Graph Representation Learning and Beyond (GRL+), 2020 * **[[https://openreview.net/forum?id=HyeJf1HKvS|Deep Graph Matching Consensus]]** (Preprint [[https://arxiv.org/abs/2001.09621|arXiv:2001.09621]], [[https://github.com/rusty1s/deep-graph-matching-consensus|Source code]]) \\ Matthias Fey, Jan E. Lenssen, Christopher Morris, Jonathan Masci, Nils M. Kriege \\ International Conference on Learning Representations (ICLR) 2020, accepted for publication. * **[[https://doi.org/10.1137/1.9781611976236.56|Temporal Graph Kernels for Classifying Dissemination Processes]]** (Preprint [[https://arxiv.org/abs/1911.05496|arXiv:1911.05496]])\\ Lutz Oettershagen, Nils M. Kriege, Christopher Morris, Petra Mutzel \\ SIAM International Conference on Data Mining (SDM) 2020, accepted for publication. * **[[https://doi.org/10.1109/ICDM.2019.00045|Computing Optimal Assignments in Linear Time for Approximate Graph Matching]]** (Preprint [[https://arxiv.org/abs/1901.10356|arXiv:1901.10356]], [[https://github.com/nlskrg/linear_time_assignments_for_graph_matching|Source code]]) \\ Nils M. Kriege, Pierre-Louis Giscard, Franka Bause, Richard C. Wilson \\ International Conference on Data Mining (ICDM) 2019, 349-358. * **[[https://doi.org/10.1007/978-3-030-32047-8_27|Protein Complex Similarity based on Weisfeiler-Lehman labeling]]** ([[https://doi.org/10.7287/peerj.preprints.26612v1|PeerJ Preprints, vol. 6, e26612v1]]) \\ Bianca K. Stöcker, Till Schäfer, Petra Mutzel, Johannes Köster, Nils Kriege, Sven Rahmann \\ International Conference on Similarity Search and Applications (SISAP) 2019, 308-322. * **[[https://www.elen.ucl.ac.be/Proceedings/esann/esannpdf/es2019-60.pdf|Deep Weisfeiler-Lehman Assignment Kernels via Multiple Kernel Learning]]** (Preprint [[https://arxiv.org/abs/1908.06661|arXiv:1908.06661]]) \\ Nils M. Kriege \\ European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN) 2019. * **[[http://dx.doi.org/10.4230/LIPIcs.MFCS.2018.54|Largest Weight Common Subtree Embeddings with Distance Penalties]]** (Preprint [[https://arxiv.org/abs/1805.00821|arXiv:1805.00821]]) \\ Andre Droschinsky, Nils M. Kriege, Petra Mutzel \\ International Symposium on Mathematical Foundations of Computer Science (MFCS) 2018, 54:1-54:15. * **[[https://doi.org/10.24963/ijcai.2018/325|A Property Testing Framework for the Theoretical Expressivity of Graph Kernels]]** \\ Nils M. Kriege, Christopher Morris, Anja Rey, Christian Sohler \\ International Joint Conference on Artificial Intelligence and European Conference on Artificial Intelligence (IJCAI-ECAI) 2018, 2348-2354. * **[[https://doi.org/10.1007/978-3-319-94667-2_12|A Fixed-Parameter Algorithm for the Max-Cut Problem on Embedded 1-Planar Graphs]]** (Preprint [[https://arxiv.org/abs/1803.10983|arXiv:1803.10983]]) \\ Christine Dahn, Nils M. Kriege, Petra Mutzel \\ International Workshop on Combinatorial Algorithms (IWOCA) 2018, 141-152. * **[[http://proceedings.mlr.press/v88/kriege18a.html|Recognizing Cuneiform Signs Using Graph Based Methods]]** (Preprint [[https://arxiv.org/abs/1802.05908|arXiv:1802.05908]]) \\ Nils M. Kriege, Matthias Fey, Denis Fisseler, Petra Mutzel, Frank Weichert \\ International Workshop on Cost-Sensitive Learning (COST), SIAM International Conference on Data Mining (SDM) 2018, 31-44. * **[[https://doi.org/10.1007/978-3-319-71273-4_37|Recent Advances in Kernel-Based Graph Classification]]** \\ Nils M. Kriege, Christopher Morris \\ European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD) 2017, 388-392. * **[[http://dx.doi.org/10.1007/978-3-319-51963-0_24|Finding Largest Common Substructures of Molecules in Quadratic Time]]** (Preprint [[https://arxiv.org/abs/1610.08739|arXiv:1610.08739]]) \\ Andre Droschinsky, Nils Kriege, Petra Mutzel \\ 43rd International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM-FOCS) 2017, 309-321. * **[[https://doi.org/10.1109/ICDM.2016.0142|Faster Kernels for Graphs with Continuous Attributes via Hashing]]** (Preprint [[http://arxiv.org/abs/1610.00064|arXiv:1610.00064]], [[https://github.com/chrsmrrs/hashgraphkernel|Source code]]) \\ Christopher Morris, Nils M. Kriege, Kristian Kersting, Petra Mutzel \\ IEEE International Conference on Data Mining (ICDM) 2016, 1095-1100. * **[[http://papers.nips.cc/paper/6166-on-valid-optimal-assignment-kernels-and-applications-to-graph-classification|On Valid Optimal Assignment Kernels and Applications to Graph Classification]]** (Preprint [[http://arxiv.org/abs/1606.01141|arXiv:1606.01141]], [[https://github.com/nlskrg/optimal_assignment_kernels|Source code]]) \\ Nils M. Kriege, Pierre-Louis Giscard, Richard C. Wilson \\ Advances in Neural Information Processing Systems (NIPS) 2016, 1615-1623. * **[[http://dx.doi.org/10.4230/LIPIcs.MFCS.2016.33|Faster Algorithms for the Maximum Common Subtree Isomorphism Problem]]** (Preprint [[http://arxiv.org/abs/1602.07210|arXiv:1602.07210]])\\ Andre Droschinsky, Nils M. Kriege, Petra Mutzel \\ International Symposium on Mathematical Foundations of Computer Science (MFCS) 2016, 33:1-33:14. * **[[http://dx.doi.org/10.1109/ICDM.2014.129|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, 881-886. * **[[http://dx.doi.org/10.1007/978-3-319-13075-0_7|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. * **[[http://dx.doi.org/10.1007/978-3-319-19315-1_18|On Maximum Common Subgraph Problems in Series-Parallel Graphs]]** \\ Nils Kriege, Florian Kurpicz, Petra Mutzel \\ International Workshop on Combinatorial Algorithms (IWOCA) 2014, 200-212. * **[[http://dx.doi.org/10.1007/978-3-662-44465-8_43|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. * **[[http://dx.doi.org/10.1007/978-3-662-44911-0_6|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. * **[[http://dx.doi.org/10.1007/978-3-319-04657-0_11|SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search]]** \\ Nils Kriege, Petra Mutzel, Till Schäfer \\ International Workshop on Algorithms and Computation (WALCOM) 2014, 90-101. * **[[http://dx.doi.org/10.1007/978-3-642-38241-3_12|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. * **[[http://dx.doi.org/10.5220/0004267205150524|MolMap - Visualizing Molecule Libraries as Topographic Maps]]** \\ Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel \\ International Conference on Information Visualization Theory and Applications (IVAPP) 2013, 537-541, **Best Paper Award**. * **[[http://dx.doi.org/10.4230/OASIcs.GCB.2012.82|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. * **[[http://icml.cc/2012/papers/542.pdf|Subgraph Matching Kernels for Attributed Graphs]]** ([[http://arxiv.org/abs/1206.6483|arXiv.org]], [[https://ls11-www.cs.uni-dortmund.de/people/kriege/software/smkernel.zip|Source code]]) \\ Nils Kriege, Petra Mutzel \\ International Conference on Machine Learning (ICML) 2012. * **[[http://dx.doi.org/10.5220/0003836806260635|Scaffold Hunter - Visual Analysis of Chemical Compound Databases]]** \\ Karsten Klein, Nils Kriege, Petra Mutzel \\ International Conference on Information Visualization Theory and Applications (IVAPP) 2012, 626-635, **Best Paper Award**. * **[[http://dx.doi.org/10.1109/ICDE.2011.5767909|CT-Index: Fingerprint-based Graph Indexing Combining Cycles and Trees]]** ([[https://ls11-www.cs.tu-dortmund.de/people/kriege/software/ctindex.zip|Software]])\\ Karsten Klein, Nils Kriege, Petra Mutzel \\ in: Proceedings of the 27th International Conference on Data Engineering (ICDE) 2011, Hannover, Germany, 1115-1126. === Book Chapters === * **[[https://doi.org/10.1016/B978-0-12-809633-8.20195-7|Chemical similarity and substructure searches]]** \\ Nils M. Kriege, Lina Humbeck, and Oliver Koch \\ Encyclopedia of Bioinformatics and Computational Biology, Academic Press, Oxford, 2019, 640-649. === Posters === * **Evaluation and Application of a Graph-based Method for Rational Drug Design** \\ Lina Humbeck, Andre Droschinsky, Till Schäfer, Nils Kriege, Petra Mutzel, Oliver Koch \\ German Conference on Chemoinformatics, 2017. * **Chemogenomics analysis of small molecule bioactivity data: Privileged scaffolds and conserved structural elements in proteins** \\ Lina Humbeck, Till Schäfer, Nils Kriege, Petra Mutzel, Oliver Koch \\ International Conference on Chemical Structures / German Conference on Chemoinformatics, Noordwijkerhout, The Netherlands, 2014. * **[[http://dx.doi.org/10.1186/1758-2946-6-S1-P33|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 \\ Journal of Cheminformatics 2014, 6(Suppl 1):P33. * **[[http://doko2011.cs.tu-dortmund.de/files/DoKo2011-Abstracts.pdf|Algorithm Engineering für Probleme aus der Chemieinformatik]]** \\ Nils M. Kriege \\ Informatik Ruhr: Doktorandenkolleg, Valbert, Germany, 2011. * **[[http://dx.doi.org/10.1007/978-3-642-11805-0_47|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. === Technical Reports === * **[[http://ls11-www.cs.tu-dortmund.de/_media/techreports/tr13-03.pdf|SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search]]** \\ Nils Kriege, Petra Mutzel, Till Schäfer \\ Algorithm Engineering Reports, TR13-1-003, Fakultät für Informatik, TU Dortmund, 2013. * **[[http://dx.doi.org/10.17877/DE290R-8897|ChemBioSpace Explorer: PG504 Endbericht]]** \\ Adalbert Gorecki, Anke Arndt, Arbia Ben Ahmed, Andre Wiesniewski, Cengizhan Yücel, Gebhard Schrader, Henning Wagner, Michael Rex, Nils Kriege, Philipp Büderbender, Sergej Rakov, Vanessa Bembenek \\ Fakultät für Informatik, TU Dortmund, 2008. === Theses === * **[[http://hdl.handle.net/2003/34281|Comparing Graphs: Algorithms & Applications]]** ({{:staff:kriege:comparing_graphs_erratum.pdf|Erratum}}) \\ Nils Morten Kriege \\ PhD Thesis, TU Dortmund, 2015. * **[[http://ls11-www.cs.tu-dortmund.de/_media/techreports/tr10-01.pdf|Erweiterte Substruktursuche in Moleküldatenbanken und ihre Integration in Scaffold Hunter]]** \\ Nils Kriege \\ in: Algorithm Engineering Reports, TR10-1-001, Fakultät für Informatik, TU Dortmund, 2010.\\ Diploma Thesis, TU Dortmund, December 2009. ===== Tutorials & Invited Talks ===== === Tutorials === * **[[staff:kriege:opentox2013workshop|Using Scaffold Hunter for the Visual Analysis of Chemical Datasets]]** \\ Nils Kriege, Till Schäfer, Hands-on Workshops, OpenTox Euro 2013, Mainz, **Best Software Award** === Invited Talks === * **Visual Analysis of Chemical Space with Scaffold Hunter** \\ Nils Kriege, OpenTox Euro 2013, Mainz * **Engineering Graph Algorithms for Cheminformatics** \\ Martin Gronemann, Michael Jünger, Nils Kriege, Petra Mutzel \\ SPP Algorithm Engineering Annual Meeting 2012, Frankfurt (Main)