Scaffold Hunter - Interactive Exploration of Chemical Space. - Karsten Klein 001; Nils M. Kriege; Petra Mutzel; Herbert Waldmann; Stefan Wetzel (GD, 2009)

CT-index: Fingerprint-based graph indexing combining cycles and trees. - Karsten Klein 001; Nils M. Kriege; Petra Mutzel (ICDE, 2011)

Designing q-Unique DNA Sequences with Integer Linear Programs and Euler Tours in De Bruijn Graphs. - Marianna D'Addario; Nils M. Kriege; Sven Rahmann (GCB, 2012)

Scaffold Hunter - Visual Analysis of Chemical Compound Databases. - Karsten Klein 001; Nils M. Kriege; Petra Mutzel (GRAPP/IVAPP, 2012)

Subgraph Matching Kernels for Attributed Graphs. - Nils M. Kriege; Petra Mutzel (ICML, 2012)

Scaffold Hunter: Facilitating Drug Discovery by Visual Analysis of Chemical Space. - Karsten Klein 001; Nils M. Kriege; Petra Mutzel (VISIGRAPP (Selected Papers), 2012)

MolMap - Visualizing Molecule Libraries as Topographic Maps. - Martin Gronemann; Michael Jünger; Nils M. Kriege; Petra Mutzel (GRAPP/IVAPP, 2013)

The Landscape Metaphor for Visualization of Molecular Similarities. - Martin Gronemann; Michael Jünger; Nils M. Kriege; Petra Mutzel (VISIGRAPP (Selected Papers), 2013)

Explicit Versus Implicit Graph Feature Maps: A Computational Phase Transition for Walk Kernels. - Nils M. Kriege; Marion Neumann; Kristian Kersting; Petra Mutzel (ICDM, 2014)

Enumeration of Maximum Common Subtree Isomorphisms with Polynomial-Delay. - Andre Droschinsky; Bernhard Heinemann; Nils M. Kriege; Petra Mutzel (ISAAC, 2014)

Finding Maximum Common Biconnected Subgraphs in Series-Parallel Graphs. - Nils M. Kriege; Petra Mutzel (MFCS (2), 2014)

SAHN Clustering in Arbitrary Metric Spaces Using Heuristic Nearest Neighbor Search. - Nils M. Kriege; Petra Mutzel; Till Schäfer (WALCOM, 2014)

Scaffold hunter: visual analysis of biological activity data. - Karsten Klein 001; Oliver Koch; Nils M. Kriege; Petra Mutzel; Till Schäfer (J. Cheminformatics, 2014)

Practical SAHN Clustering for Very Large Data Sets and Expensive Distance Metrics. - Nils M. Kriege; Petra Mutzel; Till Schäfer (J. Graph Algorithms Appl., 2014)

Comparing graphs - Nils Morten Kriege (2015)

Faster Kernels for Graphs with Continuous Attributes via Hashing. - Christopher Morris 001; Nils M. Kriege; Kristian Kersting; Petra Mutzel (ICDM, 2016)

Faster Algorithms for the Maximum Common Subtree Isomorphism Problem. - Andre Droschinsky; Nils M. Kriege; Petra Mutzel (MFCS, 2016)

On Valid Optimal Assignment Kernels and Applications to Graph Classification. - Nils M. Kriege; Pierre-Louis Giscard; Richard C. Wilson 001 (NIPS, 2016)

Recent Advances in Kernel-Based Graph Classification. - Nils M. Kriege; Christopher Morris 001 (ECML/PKDD (3), 2017)

Finding Largest Common Substructures of Molecules in Quadratic Time. - Andre Droschinsky; Nils M. Kriege; Petra Mutzel (SOFSEM, 2017)

A Unifying View of Explicit and Implicit Feature Maps for Structured Data: Systematic Studies of Graph Kernels. - Nils M. Kriege; Marion Neumann; Christopher Morris 001; Kristian Kersting; Petra Mutzel (CoRR, 2017)

Scaffold Hunter: a comprehensive visual analytics framework for drug discovery. - Till Schäfer; Nils M. Kriege; Lina Humbeck; Karsten Klein 001; Oliver Koch; Petra Mutzel (J. Cheminformatics, 2017)

A Property Testing Framework for the Theoretical Expressivity of Graph Kernels. - Nils M. Kriege; Christopher Morris 001; Anja Rey; Christian Sohler (IJCAI, 2018)

A Fixed-Parameter Algorithm for the Max-Cut Problem on Embedded 1-Planar Graphs. - Christine Dahn; Nils M. Kriege; Petra Mutzel (IWOCA, 2018)

Largest Weight Common Subtree Embeddings with Distance Penalties. - Andre Droschinsky; Nils M. Kriege; Petra Mutzel (MFCS, 2018)

Recognizing Cuneiform Signs Using Graph Based Methods. - Nils M. Kriege; Matthias Fey; Denis Fisseler; Petra Mutzel; Frank Weichert (COST@SDM, 2018)

On maximum common subgraph problems in series-parallel graphs. - Nils M. Kriege; Florian Kurpicz; Petra Mutzel (Eur. J. Comb., 2018)

A note on block-and-bridge preserving maximum common subgraph algorithms for outerplanar graphs. - Nils M. Kriege; Andre Droschinsky; Petra Mutzel (J. Graph Algorithms Appl., 2018)

Deep Weisfeiler-Lehman assignment kernels via multiple kernel learning. - Nils M. Kriege (ESANN, 2019)

Computing Optimal Assignments in Linear Time for Approximate Graph Matching. - Nils M. Kriege; Pierre-Louis Giscard; Franka Bause; Richard C. Wilson 001 (ICDM, 2019)

Protein Complex Similarity Based on Weisfeiler-Lehman Labeling. - Bianca K. Stöcker; Till Schäfer; Petra Mutzel; Johannes Köster; Nils M. Kriege; Sven Rahmann (SISAP, 2019)

A General Purpose Algorithm for Counting Simple Cycles and Simple Paths of Any Length. - Pierre-Louis Giscard; Nils M. Kriege; Richard C. Wilson 001 (Algorithmica, 2019)

Computing Optimal Assignments in Linear Time for Graph Matching. - Nils M. Kriege; Pierre-Louis Giscard; Franka Bause; Richard C. Wilson 001 (CoRR, 2019)

A unifying view of explicit and implicit feature maps of graph kernels. - Nils M. Kriege; Marion Neumann; Christopher Morris 001; Kristian Kersting; Petra Mutzel (Data Min. Knowl. Discov., 2019)

Chemical Similarity and Substructure Searches. - Oliver Koch; Nils M. Kriege; Lina Humbeck (Encyclopedia of Bioinformatics and Computational Biology (2), 2019)

Deep Graph Matching Consensus. - Matthias Fey; Jan Eric Lenssen; Christopher Morris 001; Jonathan Masci; Nils M. Kriege (ICLR, 2020)

Temporal Graph Kernels for Classifying Dissemination Processes. - Lutz Oettershagen; Nils M. Kriege; Christopher Morris 001; Petra Mutzel (SDM, 2020)

A survey on graph kernels. - Nils M. Kriege; Fredrik D. Johansson; Christopher Morris 001 (Appl. Netw. Sci., 2020)

Classifying Dissemination Processes in Temporal Graphs. - Lutz Oettershagen; Nils M. Kriege; Christopher Morris 001; Petra Mutzel (Big Data, 2020)

TUDataset: A collection of benchmark datasets for learning with graphs. - Christopher Morris 001; Nils M. Kriege; Franka Bause; Kristian Kersting; Petra Mutzel; Marion Neumann (CoRR, 2020)

Maximum Cut Parameterized by Crossing Number. - Markus Chimani; Christine Dahn; Martina Juhnke-Kubitzke; Nils M. Kriege; Petra Mutzel; Alexander Nover (J. Graph Algorithms Appl., 2020)

The Power of the Weisfeiler-Leman Algorithm for Machine Learning with Graphs. - Christopher Morris 001; Matthias Fey; Nils M. Kriege (IJCAI, 2021)

Metric Indexing for Graph Similarity Search. - Franka Bause; David B. Blumenthal; Erich Schubert; Nils M. Kriege (SISAP, 2021)

Fixed-parameter algorithms for the weighted Max-Cut problem on embedded 1-planar graphs. - Christine Dahn; Nils M. Kriege; Petra Mutzel; Julian Schilling (Theor. Comput. Sci., 2021)

The Weisfeiler-Leman Method for Machine Learning with Graphs. - Nils M. Kriege; Christopher Morris 001 (Mach. Learn. under Resour. Constraints Vol. 1 (1), 2022)

Protein Complex Similarity. - Bianca K. Stöcker; Till Schäfer; Petra Mutzel; Johannes Köster; Nils M. Kriege; Sven Rahmann (Mach. Learn. under Resour. Constraints Vol. 3 (3), 2022)

Graph-Based Methods for Rational Drug Design. - Andre Droschinsky; Lina Humbeck; Oliver Koch; Nils M. Kriege; Petra Mutzel; Till Schäfer (Algorithms for Big Data, 2022)

Gradual Weisfeiler-Leman: Slow and Steady Wins the Race. - Franka Bause; Nils Morten Kriege (LoG, 2022)

Weisfeiler and Leman Go Walking: Random Walk Kernels Revisited. - Nils M. Kriege (NeurIPS, 2022)

Temporal Walk Centrality: Ranking Nodes in Evolving Networks. - Lutz Oettershagen; Petra Mutzel; Nils M. Kriege (WWW, 2022)

EmbAssi: embedding assignment costs for similarity search in large graph databases. - Franka Bause; Erich Schubert; Nils M. Kriege (Data Min. Knowl. Discov., 2022)

A Higher-Order Temporal H-Index for Evolving Networks. - Lutz Oettershagen; Nils M. Kriege; Petra Mutzel (KDD, 2023)

A Temporal Graphlet Kernel For Classifying Dissemination in Evolving Networks. - Lutz Oettershagen; Nils M. Kriege; Claude Jordan; Petra Mutzel (SDM, 2023)

Improved Exact and Heuristic Algorithms for Maximum Weight Clique. - Roman Erhardt; Kathrin Hanauer; Nils M. Kriege; Christian Schulz 003; Darren Strash (CoRR, 2023)

Non-Redundant Graph Neural Networks with Improved Expressiveness. - Franka Bause; Samir Moustafa; Johannes Langguth; Wilfried N. Gansterer; Nils M. Kriege (CoRR, 2023)

Attacking Graph Neural Networks with Bit Flips: Weisfeiler and Lehman Go Indifferent. - Lorenz Kummer; Samir Moustafa; Nils M. Kriege; Wilfried N. Gansterer (CoRR, 2023)

Weisfeiler and Leman go Machine Learning: The Story so far. - Christopher Morris 001; Yaron Lipman; Haggai Maron; Bastian Rieck; Nils M. Kriege; Martin Grohe; Matthias Fey; Karsten M. Borgwardt (J. Mach. Learn. Res., 2023)

Attacking Graph Neural Networks with Bit Flips: Weisfeiler and Leman Go Indifferent. - Lorenz Kummer; Samir Moustafa; Sebastian Schrittwieser; Wilfried N. Gansterer; Nils M. Kriege (KDD, 2024)

Preventing Representational Rank Collapse in MPNNs by Splitting the Computational Graph. - Andreas Roth; Franka Bause; Nils Morten Kriege; Thomas Liebig (LoG, 2024)

On the Two Sides of Redundancy in Graph Neural Networks. - Franka Bause; Samir Moustafa; Johannes Langguth; Wilfried N. Gansterer; Nils M. Kriege (ECML/PKDD (6), 2024)

Approximating the Graph Edit Distance with Compact Neighborhood Representations. - Franka Bause; Christian Permann; Nils M. Kriege (ECML/PKDD (5), 2024)

Enhanced Expressivity in Graph Neural Networks with Lanczos-Based Linear Constraints. - Niloofar Azizi; Nils M. Kriege; Horst Bischof (CoRR, 2024)

Crossfire: An Elastic Defense Framework for Graph Neural Networks Under Bit Flip Attacks. - Lorenz Kummer; Samir Moustafa; Wilfried N. Gansterer; Nils Morten Kriege (AAAI, 2025)

On the Relationship Between Robustness and Expressivity of Graph Neural Networks. - Lorenz Kummer; Wilfried N. Gansterer; Nils Morten Kriege (AISTATS, 2025)

Efficient Mixed Precision Quantization in Graph Neural Networks. - Samir Moustafa; Nils M. Kriege; Wilfried N. Gansterer (ICDE, 2025)

Maximally Expressive GNNs for Outerplanar Graphs. - Franka Bause; Fabian Jogl; Patrick Indri; Tamara Drucks; David Penz; Nils Morten Kriege; Thomas Gärtner 001; Pascal Welke; Maximilian Thiessen (Trans. Mach. Learn. Res., 2025)

Weisfeiler and Leman Go Gambling: Why Expressive Lottery Tickets Win. - Lorenz Kummer; Samir Moustafa; Anatol Ehrlich; Franka Bause; Nikolaus Süss; Wilfried N. Gansterer; Nils M. Kriege (CoRR, 2025)