Combinatorial Optimization, Graph Algorithms

Data Mining, Machine Learning with Graphs

Information Visualization, Visual Analytics

Applications in Cheminformatics

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.

Lutz Oettershagen: On the Crossing Number of Almost Bishellable Drawings of Complete Graphs, Masterarbeit, 2017.

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

Andre Droschinsky: Effiziente Enumerationsalgorithmen für Common Subtree Probleme, Diplomarbeit, 2014

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

Till Schäfer: Beschleunigung hierarchischer Clusterverfahren für allgemeine metrische Distanzmaße, Diplomarbeit, 2012

Marianna D'Addario: Entwurf von Oligonukleotid-Bibliotheken für die DNA-Nanotechnologie, Diplomarbeit (Kooperation mit Prof. Rahmann und Prof. Niemeyer, Chemie), 2011

Klassifikation pharmazeutischer Wirkstoffe – Bundeswettbewerb Informatik Workshop 2017

Benchmark Data Sets for Graph Kernels – A collection of graph data sets with class labels for benchmarking purposes

Resource efficient analysis of graphs – Collaborative Research Center Providing Information by Resource-Constrained Data Analysis (SFB 876)

Graph-Based Methods for Rational Drug Design – DFG Priority Programme Algorithms for Big Data (SPP 1736)

Planarization Approaches in Automatic Graph Drawing – DFG Priority Programme Algorithm Engineering (SPP 1307)

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.

Classifying Dissemination Processes in Temporal Graphs
Lutz Oettershagen, Nils M. Kriege, Christopher Morris, and Petra Mutzel
Big Data, 2020, accepted for publication.

Maximum Cut Parameterized by Crossing Number (Preprint 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.

A Survey on Graph Kernels (Preprint arXiv:1903.11835)
Nils M. Kriege, Fredrik D. Johansson, Christopher Morris
Applied Network Science, Machine learning with graphs, 5:6, 2020.

A unifying view of explicit and implicit feature maps of graph kernels (Preprint arXiv:1703.00676)
Nils M. Kriege, Marion Neumann, Christopher Morris, Kristian Kersting, Petra Mutzel
Data Mining and Knowledge Discovery, 33, 1505-1547, 2019.

A general purpose algorithm for counting simple cycles and simple paths of any length (Preprint arXiv:1612.05531)
Pierre-Louis Giscard, Nils Kriege, Richard C. Wilson
Algorithmica, vol. 81, no. 7, 2716-2737, 2019.

A note on block-and-bridge preserving maximum common subgraph algorithms for outerplanar graphs (Preprint arXiv:1805.10754)
Nils M. Kriege, Andre Droschinsky, Petra Mutzel
Journal of Graph Algorithms and Applications (JGAA), vol. 22, no. 4, 607-616, 2018.

On Maximum Common Subgraph Problems in Series-Parallel Graphs (Preprint arXiv:1708.02772)
Nils Kriege, Florian Kurpicz, Petra Mutzel
European Journal on Combinatorics (EJC), vol. 68, 79-95, 2018.

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.

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.

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.

TUDataset: A collection of benchmark datasets for learning with graphs (Preprint arXiv:2007.08663, 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

Deep Graph Matching Consensus (Preprint arXiv:2001.09621, Source code)
Matthias Fey, Jan E. Lenssen, Christopher Morris, Jonathan Masci, Nils M. Kriege
International Conference on Learning Representations (ICLR) 2020, accepted for publication.

Temporal Graph Kernels for Classifying Dissemination Processes (Preprint arXiv:1911.05496)
Lutz Oettershagen, Nils M. Kriege, Christopher Morris, Petra Mutzel
SIAM International Conference on Data Mining (SDM) 2020, accepted for publication.

Computing Optimal Assignments in Linear Time for Approximate Graph Matching (Preprint arXiv:1901.10356, Source code)
Nils M. Kriege, Pierre-Louis Giscard, Franka Bause, Richard C. Wilson
International Conference on Data Mining (ICDM) 2019, 349-358.

Protein Complex Similarity based on Weisfeiler-Lehman labeling (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.

Deep Weisfeiler-Lehman Assignment Kernels via Multiple Kernel Learning (Preprint arXiv:1908.06661)
Nils M. Kriege
European Symposium on Artificial Neural Networks, Computational Intelligence and Machine Learning (ESANN) 2019.

Largest Weight Common Subtree Embeddings with Distance Penalties (Preprint arXiv:1805.00821)
Andre Droschinsky, Nils M. Kriege, Petra Mutzel
International Symposium on Mathematical Foundations of Computer Science (MFCS) 2018, 54:1-54:15.

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.

A Fixed-Parameter Algorithm for the Max-Cut Problem on Embedded 1-Planar Graphs (Preprint arXiv:1803.10983)
Christine Dahn, Nils M. Kriege, Petra Mutzel
International Workshop on Combinatorial Algorithms (IWOCA) 2018, 141-152.

Recognizing Cuneiform Signs Using Graph Based Methods (Preprint 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.

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.

Finding Largest Common Substructures of Molecules in Quadratic Time (Preprint 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.

Faster Kernels for Graphs with Continuous Attributes via Hashing (Preprint arXiv:1610.00064, Source code)
Christopher Morris, Nils M. Kriege, Kristian Kersting, Petra Mutzel
IEEE International Conference on Data Mining (ICDM) 2016, 1095-1100.

On Valid Optimal Assignment Kernels and Applications to Graph Classification (Preprint arXiv:1606.01141, Source code)
Nils M. Kriege, Pierre-Louis Giscard, Richard C. Wilson
Advances in Neural Information Processing Systems (NIPS) 2016, 1615-1623.

Faster Algorithms for the Maximum Common Subtree Isomorphism Problem (Preprint arXiv:1602.07210)
Andre Droschinsky, Nils M. Kriege, Petra Mutzel
International Symposium on Mathematical Foundations of Computer Science (MFCS) 2016, 33:1-33:14.

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.

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, 200-212.

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
Nils Kriege, Petra Mutzel, Till Schäfer
International Workshop on Algorithms and Computation (WALCOM) 2014, 90-101.

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
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 (arXiv.org, Source code)
Nils Kriege, Petra Mutzel
International Conference on Machine Learning (ICML) 2012.

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.

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

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.

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.

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.

Algorithm Engineering für Probleme aus der Chemieinformatik
Nils M. Kriege
Informatik Ruhr: Doktorandenkolleg, Valbert, Germany, 2011.

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.

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.

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.

Comparing Graphs: Algorithms & Applications (Erratum)
Nils Morten Kriege
PhD Thesis, TU Dortmund, 2015.

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.

Using Scaffold Hunter for the Visual Analysis of Chemical Datasets
Nils Kriege, Till Schäfer, Hands-on Workshops, OpenTox Euro 2013, Mainz, Best Software Award

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)