Falk Hüffner
פאלק הופנר

photo of Falk Hüffner

Since April 2016, I'm working in industry.
E-mail:

My research focus was on design, analysis, and experimental evaluation of algorithms for hard problems, in particular graph problems and discrete optimization problems, from various areas such as computational biology, VLSI design, and operations research.

Where I have been in former times:

Other things I do:

You might have met me here:
2014-09-30 Group of Prof. Roded Sharan, Tel Aviv University, Israel.
Talk: A graph modification approach for finding core–periphery structures in protein interaction networks
2014-03-17 – 2014-03-20 Towards the ground truth: Exact algorithms for bioinformatics research (NII Shonan Meeting Seminar 045), Shonan Village, Japan.
2013-09-28 – 2013-10-10 Research visit at the Laboratoire d'Informatique de Nantes Atlantique (LINA) at the Université de Nantes, France.
Talk: Optimally solving hard combinatorial problems in Computational Biology
2013-09-22 – 2013-09-27 Algorithm Engineering (Dagstuhl Seminar 13391), Dagstuhl, Germany.
Talk: Fixed-Parameter and Integer Programming Approaches for Clustering Problems
2013-06-05 – 2013-05-07 12th International Symposium on Experimental Algorithms (SEA 2013), Rome, Italy.
Talk: Evaluation of ILP-based approaches for partitioning into colorful components
2013-05-06 – 2013-05-11 Parameterized Complexity and the Understanding, Design and Analysis of Heuristics (NII Shonan Meeting Seminar 018), Shonan Village, Japan.
Talk: Implementing Fixed-Parameter Algorithms
2013-04-10 – 2013-04-12 5th Workshop on Kernelization (WorKer 2013), Warsaw, Poland.
2012-11-08 – 2012-11-12 3rd Brazilian-German Frontiers of Science and Technology Symposium (BRAGFOST 2012), Brasília, Brazil.
Poster: Partitioning networks into colorful components (or: How to fix Wikipedia interlanguage links)
2012-07-03 – 2012-07-05 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012), Helsinki, Finland.
2012-06-12 – 2012-06-15 Data Reduction and Problem Kernels (Dagstuhl Seminar 12241), Dagstuhl, Germany.
[more...]

Publications

See also:
2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001
2015
Conference articles
  • Falk Hüffner, Christian Komusiewicz, and André Nichterlein:
    Editing graphs into few cliques: complexity, approximation, and kernelization schemes.
    In Proceedings of the 14th Algorithms and Data Structures Symposium (WADS ’15), Victoria, Canada. August 2015.
    Volume 9214 in Lecture Notes in Computer Science, pages 410–421, Springer, 2015 (original publication). [show abstract]
  • Falk Hüffner, Christian Komusiewicz, and Manuel Sorge:
    Finding highly connected subgraphs.
    In Proceedings of the 41st International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM ’15), Pec pod Sněžkou, Czech Republic. January 2015.
    Volume 8939 in Lecture Notes in Computer Science, pages 254–265, Springer, 2015 (original publication). [show abstract]
Journal articles
Book chapters (to appear)
  • Falk Hüffner, Christian Komusiewicz, Rolf Niedermeier, and Sebastian Wernicke:
    Parameterized algorithmics for finding exact solutions of NP-hard biological problems.
    In: Bioinformatics, Volume II: Structure, Function and Applications. Series: Methods in Molecular Biology, Springer. [show abstract]
2014
Conference articles
  • Sharon Bruckner, Falk Hüffner, and Christian Komusiewicz:
    A graph modification approach for finding core–periphery structures in protein interaction networks.
    In Proceedings of the 14th Workshop on Algorithms in Bioinformatics (WABI ’14), Wrocław, Poland. September 2014.
    Volume 8701 in Lecture Notes in Bioinformatics, pages 340–351, Springer, 2014 (original publication). Journal version available. [show abstract]
  • Falk Hüffner, Christian Komusiewicz, Rolf Niedermeier, and Martin Rötzschke:
    The parameterized complexity of the rainbow subgraph problem.
    In Proceedings of the 40th International Workshop on Graph-Theoretic Concepts in Computer Science (WG ’14), Le Domaine de Chalès, France, June 2014.
    Volume 8747 in Lecture Notes in Computer Science, pages 287–298, Springer, 2014 (original publication). Journal version available. [show abstract]
Journal articles
  • Laurent Bulteau, Falk Hüffner, Christian Komusiewicz, and Rolf Niedermeier:
    Multivariate algorithmics for NP-hard string problems.
    Bulletin of the EATCS 114:31–73, 2014 (original publication).
    Note: Compared to the published version, this version fixes typos in Figure 1 and in Challenge 13.
    [show abstract]
  • Falk Hüffner, Christian Komusiewicz, Adrian Liebtrau, and Rolf Niedermeier:
    Partitioning biological networks into highly connected clusters with maximum edge coverage.
    IEEE/ACM Transactions on Computational Biology and Bioinformatics 11(3):455–467, 2014 (original publication). [show abstract]
2013
Conference articles
  • René van Bevern, Robert Bredereck, Morgan Chopin, Sepp Hartung, Falk Hüffner, André Nichterlein, and Ondřej Suchý:
    Parameterized complexity of DAG partitioning.
    In Proceedings of the 8th International Conference on Algorithms and Complexity (CIAC ’13), Barcelona, Spain. May 2013.
    Volume 7878 in Lecture Notes in Computer Science, pages 49–60, Springer, 2013 (original publication). [show abstract]
  • Sharon Bruckner, Falk Hüffner, Christian Komusiewicz, and Rolf Niedermeier:
    Evaluation of ILP-based approaches for partitioning into colorful components.
    In Proceedings of the 12th International Symposium on Experimental Algorithms (SEA ’13), Rome, Italy. June 2013.
    Volume 7933 in Lecture Notes in Computer Science, pages 176–187, Springer, 2013 (original publication). [show abstract]
  • Falk Hüffner, Christian Komusiewicz, Adrian Liebtrau, and Rolf Niedermeier:
    Partitioning biological networks into highly connected clusters with maximum edge coverage.
    In Proceedings of the 9th International Symposium on Bioinformatics Research and Applications (ISBRA ’13), Charlotte, North Carolina. May 2013.
    Volume 7875 in Lecture Notes in Computer Science, pages 99–111, Springer, 2013 (original publication). Journal version available. [show abstract]
Journal articles
  • Hartmut Ehrig, Claudia Ermel, Falk Hüffner, Rolf Niedermeier, and Olga Runge:
    Confluence in data reduction: bridging graph transformation and kernelization.
    Computability 2(1):31–49, 2013 (original publication). [show abstract]
2012
Conference articles
  • Sharon Bruckner, Falk Hüffner, Christian Komusiewicz, Rolf Niedermeier, Sven Thiel, and Johannes Uhlmann:
    Partitioning into colorful components by minimum edge deletions.
    In Proceedings of the 23rd Annual Symposium on Combinatorial Pattern Matching (CPM ’12), Helsinki, Finland. July 2012.
    Volume 7354 in Lecture Notes in Computer Science, pages 56–69, Springer, 2012 (original publication). [show abstract]
  • Hartmut Ehrig, Claudia Ermel, Falk Hüffner, Rolf Niedermeier, and Olga Runge:
    Confluence in data reduction: bridging graph transformation and kernelization.
    In Proceedings of the 8th Conference on Computability in Europe (CiE ’12), Cambridge, UK. June 2012.
    Volume 7318 in Lecture Notes in Computer Science, pages 193–202, Springer, 2012 (original publication). Journal version available. [show abstract]
2011
Conference articles
  • Antonios Antoniadis, Falk Hüffner, Pascal Lenzner, Carsten Moldenhauer, and Alexander Souza:
    Balanced interval coloring.
    In Proceedings of the 28th Symposium on Theoretical Aspects of Computer Science (STACS ’11), Dortmund, Germany. March 2011.
    Volume 9 in Leibniz International Proceedings in Informatics (LIPIcs), pages 531–542, Schloss Dagstuhl–Leibniz-Zentrum für Informatik (original publication). [show abstract]
  • Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier, and Johannes Uhlmann:
    Exploiting bounded signal flow for graph orientation based on cause–effect pairs.
    In Proceedings of the 1st International ICST Conference on Theory and Practice of Algorithms in (Computer) Systems (TAPAS ’11), Rome, Italy. April 2011.
    Volume 6595 in Lecture Notes in Computer Science, pages 104–115, Springer (original publication). Journal version available. [show abstract]
Journal articles
  • Britta Dorn, Falk Hüffner, Dominikus Krüger, Rolf Niedermeier, and Johannes Uhlmann:
    Exploiting bounded signal flow for graph orientation based on cause–effect pairs.
    Algorithms for Molecular Biology 6(1):21, 2011 (original publication). [show abstract]
Book chapters
2010
Journal articles
  • Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, and Roded Sharan:
    Topology-free querying of protein interaction networks.
    Journal of Computational Biology 17(3):237–252, 2010 (original publication). [show abstract]
  • Michael Dom, Jiong Guo, Falk Hüffner, Rolf Niedermeier, and Anke Truss:
    Fixed-parameter tractability results for feedback set problems in tournaments.
    Journal of Discrete Algorithms 8(1):76–86, 2010 (original publication). [show abstract]
  • Falk Hüffner, Christian Komusiewicz, Hannes Moser, and Rolf Niedermeier:
    Fixed-parameter algorithms for cluster vertex deletion.
    Theory of Computing Systems 47(1):196–217, 2010 (original publication). [show abstract]
  • Falk Hüffner, Nadja Betzler, and Rolf Niedermeier:
    Separator-based data reduction for signed graph balancing.
    Journal of Combinatorial Optimization 20(4):335–360, 2010 (original publication). [show abstract]
Book chapters
2009
Conference articles
  • Sebastian Böcker, Falk Hüffner, Anke Truss, and Magnus Wahlström:
    A faster fixed-parameter approach to drawing binary tanglegrams.
    In Proceedings of the 4th International Workshop on Parameterized and Exact Computation (IWPEC ’09), Copenhagen, Denmark. September 2009.
    Volume 5917 in Lecture Notes in Computer Science, pages 38–49, Springer (original publication). [show abstract]
  • Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, and Roded Sharan:
    Topology-free querying of protein interaction networks.
    In Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB ’09), Tucson, Arizona, USA. May 2009.
    Volume 5541 in Lecture Notes in Bioinformatics, pages 74–89, Springer (original publication). Journal version available. [show abstract]
Journal articles
  • Sharon Bruckner, Falk Hüffner, Richard M. Karp, Ron Shamir, and Roded Sharan:
    Torque: Topology-free querying of protein interaction networks.
    Nucleic Acids Research 37(Web Server issue):W106–W108, 2009 (original publication). [show abstract]
  • Falk Hüffner:
    Algorithm engineering for optimal graph bipartization.
    Journal of Graph Algorithms and Applications, 13(2):77–98, 2009 (original publication). [show abstract]
  • Falk Hüffner:
    Parametrisierte Ansätze für schwere Graphprobleme: Algorithmen und Experimente.
    it – Information Technology, 51(3):171–174, 2009 (original publication).
  • Falk Hüffner, Christian Komusiewicz, Hannes Moser, and Rolf Niedermeier:
    Isolation concepts for clique enumeration: comparison and computational experiments.
    Theoretical Computer Science, 410(52):5384–5397, 2009 (original publication). [show abstract]
  • Christian Komusiewicz, Falk Hüffner, Hannes Moser, and Rolf Niedermeier:
    Isolation concepts for efficiently enumerating dense subgraphs.
    Theoretical Computer Science, 410(38–40):3640–3654, 2009 (original publication). [show abstract]
Book chapters
2008
Conference articles
  • Jiong Guo, Falk Hüffner, Christian Komusiewicz, and Yong Zhang:
    Improved algorithms for bicluster editing.
    In Proceedings of the 5th Annual Conference on Theory and Applications of Models of Computation (TAMC ’08), Xian, China. April 2008.
    Volume 4978 in Lecture Notes in Computer Science, pages 445–456, Springer (original publication).
    Note: After publication, we have been notified of a problem in the proof of Theorem 4 (the factor-4 approximation). Thus, we retract the results in Section 4. A correct factor-4 approximation algorithm was given by Nir Ailon, Noa Avigdor-Elgrabli, Edo Liberty, and Anke van Zuylen: Improved Approximation Algorithms for Bipartite Correlation Clustering.
    [show abstract]
  • Falk Hüffner, Christian Komusiewicz, Hannes Moser, and Rolf Niedermeier:
    Enumerating isolated cliques in synthetic and financial networks.
    In Proceedings of the 2nd Annual International Conference on Combinatorial Optimization and Applications (COCOA ’08), St. John’s, Newfoundland, Canada. August 2008.
    Volume 5165 in Lecture Notes in Computer Science, pages 405–416, Springer (original publication). Journal version available. [show abstract]
  • Falk Hüffner, Christian Komusiewicz, Hannes Moser, and Rolf Niedermeier:
    Fixed-parameter algorithms for cluster vertex deletion.
    In Proceedings of the 8th Latin American Theoretical Informatics Symposium (LATIN ’08), Búzios, Brazil. April 2008.
    Volume 4957 in Lecture Notes in Computer Science, pages 711–722, Springer (original publication). Journal version available. [show abstract]
  • Oriana Ponta, Falk Hüffner, and Rolf Niedermeier:
    Speeding up dynamic programming for some NP-hard graph recoloring problems.
    In Proceedings of the 5th Annual Conference on Theory and Applications of Models of Computation (TAMC ’08), Xian, China. April 2008.
    Volume 4978 in Lecture Notes in Computer Science, pages 490–501, Springer (original publication). [show abstract]
Journal articles
  • Michael Dom, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Closest 4-leaf power is fixed-parameter tractable.
    Discrete Applied Mathematics, 156(18):3345–3361, 2008 (original publication). [show abstract]
  • Jens Gramm, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Data reduction and exact algorithms for clique cover.
    ACM Journal of Experimental Algorithmics, 13, Article 2.2, 15 pages, 2008 (original publication). [show abstract]
  • Jiong Guo, Falk Hüffner, Erhan Kenar, Rolf Niedermeier, and Johannes Uhlmann:
    Complexity and exact algorithms for vertex multicut in interval and bounded treewidth graphs.
    European Journal of Operational Research, 186(2):542–553, 2008 (original publication). [show abstract]
  • Falk Hüffner, Rolf Niedermeier, and Sebastian Wernicke:
    Techniques for Practical Fixed-Parameter Algorithms.
    The Computer Journal, 51(1):7–25, 2008 (original publication). [show abstract]
  • Falk Hüffner, Sebastian Wernicke, and Thomas Zichner:
    Algorithm engineering for color-coding with applications to signaling pathway detection.
    Algorithmica, 52(2):114–132, 2008 (original publication). [show abstract]
Book chapters
2007
Conference articles
  • Falk Hüffner, Nadja Betzler, and Rolf Niedermeier:
    Optimal edge deletions for signed graph balancing.
    In Proceedings of the 6th Workshop on Experimental Algorithms (WEA ’07), Rome, Italy. June 2007.
    Volume 4525 in Lecture Notes in Computer Science, pages 297–310, Springer (original publication). Journal version available. [show abstract]
  • Falk Hüffner, Sebastian Wernicke, and Thomas Zichner:
    Algorithm engineering for color-coding to facilitate signaling pathway detection.
    In Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC ’07), Hong Kong. January 2007.
    Volume 5 in Advances in Bioinformatics and Computational Biology, pages 277–286, Imperial College Press (original publication). Journal version available. [show abstract]
  • Christian Komusiewicz, Falk Hüffner, Hannes Moser, and Rolf Niedermeier:
    Isolation concepts for enumerating dense subgraphs.
    In Proceedings of the 13th International Computing and Combinatorics Conference (COCOON ’07), Banff, Canada. July 2007.
    Volume 4598 in Lecture Notes in Computer Science, pages 140–150, Springer (original publication). Journal version available. [show abstract]
Journal articles
  • Jens Gramm, Jiong Guo, Falk Hüffner, Rolf Niedermeier, Hans-Peter Piepho, and Ramona Schmid:
    Algorithms for compact letter displays: comparison and evaluation.
    Computational Statistics & Data Analysis, 52(2):725–736, 2007 (original publication). [show abstract]
  • Jiong Guo, Falk Hüffner, and Hannes Moser:
    Feedback arc set in bipartite tournaments is NP-complete.
    Information Processing Letters, 102(2–3): 62–65, 2007 (original publication). [show abstract]
  • Falk Hüffner, Sebastian Wernicke, and Thomas Zichner:
    FASPAD: fast signaling pathway detection.
    Bioinformatics Applications Note, 23(13): 1708–1709, 2007 (original publication). [show abstract]
    • FASPAD for Linux (i386) or Windows (i386) and as source code
Theses
  • Falk Hüffner:
    Algorithms and Experiments for Parameterized Approaches to Hard Graph Problems.
    PhD thesis, Institut für Informatik, Friedrich-Schiller-Universität Jena, 2007. [show abstract]
2006
Conference articles
  • Matthias Brosemann, Jochen Alber, Falk Hüffner, and Rolf Niedermeier:
    Matrix robustness, with an application to power system observability.
    In Proceedings of the 2nd Algorithms and Complexity in Durham (ACiD ’06), Durham, England. September 2006.
    Volume 7 in Texts in Algorithmics, pages 37–48, College Publications. [show abstract]
  • Michael Dom, Jiong Guo, Falk Hüffner, Rolf Niedermeier, and Anke Truß:
    Fixed-parameter tractability results for feedback set problems in tournaments.
    In Proceedings of the 6th Conference on Algorithms and Complexity (CIAC ’06), Rome, Italy. May 2006.
    Volume 3998 in Lecture Notes in Computer Science, pages 320–331, Springer (original publication). Journal version available. [show abstract]
  • Jens Gramm, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Data reduction, exact, and heuristic algorithms for clique cover.
    In Proceedings of the 8th Workshop on Algorithm Engineering and Experiments (ALENEX ’06), Miami, USA. January 2006.
    Pages 86–94, SIAM (original publication). Journal version available. [show abstract]
  • Jiong Guo, Falk Hüffner, Erhan Kenar, Rolf Niedermeier, and Johannes Uhlmann:
    Complexity and exact algorithms for multicut.
    In Proceedings of the 32nd International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM ’06), Merin, Czech Republic. January 2006.
    Volume 3831 in Lecture Notes in Computer Science, pages 303–312, Springer (original publication). Journal version available.
Journal articles
  • Michael Dom, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Error compensation in leaf power problems.
    Algorithmica, 44(4): 363–381, 2006 (original publication). [show abstract]
  • Jiong Guo, Jens Gramm, Falk Hüffner, Rolf Niedermeier, and Sebastian Wernicke:
    Compression-based fixed-parameter algorithms for Feedback Vertex Set and Edge Bipartization.
    Journal of Computer and System Sciences, 72(8): 1386–1396, 2006 (original publication). [show abstract]
2005
Conference articles
  • Michael Dom, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Extending the tractability border for closest leaf powers.
    In Proceedings of the 31st International Workshop on Graph-Theoretic Concepts in Computer Science (WG ’05), Metz, France. June 2005.
    Volume 3787 in Lecture Notes in Computer Science, pages 397–408, Springer (original publication). Journal version available. [show abstract]
  • Jiong Guo, Jens Gramm, Falk Hüffner, Rolf Niedermeier, and Sebastian Wernicke:
    Improved fixed-parameter algorithms for two feedback set problems.
    In Proceedings of the 9th Workshop on Algorithms and Data Structures (WADS ’05), Waterloo, Canada. August 2005.
    Volume 3608 in Lecture Notes in Computer Science, pages 158–168, Springer (original publication). Journal version available.
  • Falk Hüffner:
    Algorithm engineering for optimal graph bipartization.
    In Proceedings of the 4th International Workshop on Efficient and Experimental Algorithms (WEA ’05), Santorini Island, Greece. May 2005.
    Volume 3503 in Lecture Notes in Computer Science, pages 240–252, Springer (original publication). Journal version available. [show abstract]
Journal articles
  • Jens Gramm, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Graph-modeled data clustering: Exact algorithms for clique generation.
    Theory of Computing Systems, 38(4):373–392, 2005 (original publication). [show abstract]
2004
Conference articles
  • Michael Dom, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Error compensation in leaf root problems.
    In Proceedings of the 15th Annual International Symposium on Algorithms and Computation (ISAAC ’04), Hong Kong, China. December 2004.
    Volume 3341 in Lecture Notes in Computer Science, pages 389–401, Springer (original publication). Journal version available.
  • Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    A structural view on parameterizing problems: distance from triviality.
    In Proceedings of the International Workshop on Parameterized and Exact Computation (IWPEC ’04), Bergen, Norway. September 2004.
    Volume 3162 in Lecture Notes in Computer Science, pages 162–173, Springer (original publication). [show abstract]
Journal articles
  • Jens Gramm, Jiong Guo, Falk Hüffner, and Rolf Niedermeier:
    Automated generation of search tree algorithms for hard graph modification problems.
    Algorithmica, 39(4):321–347, 2004 (original publication). [show abstract]
2003
Conference articles
Theses
  • Falk Hüffner:
    Graph Modification Problems and Automated Search Tree Generation.
    Diplomarbeit, Wilhelm-Schickard-Institut für Informatik, Universität Tübingen, October 2003. [show abstract]
2002
Posters
Theses
  • Falk Hüffner:
    Finding Optimal Solutions to Atomix.
    Studienarbeit, Wilhelm-Schickard-Institut für Informatik, University of Tübingen, December 2002. [show abstract]

2001
Conference articles

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Last modified: Saturday, 7 May 2016 at 16:04 UTC.