Algorithmik und Komplexitätstheorie

Prof. Dr. Mathias Weller

 

 

 

Sekretariat TEL 5-1
Gebäude TEL
Raum TEL 509C

Curriculum Vitae

since 10/2022Chair of AKT group
2018 - 10/2022Full-Time Researcher, CNRS, LIGM, Paris, France.
2015 - 2017Post-doctoral position, IBC, LIRMM, Montpellier, France
2013-2014Post-doctoral position, AIGCo, LIRMM, Montpellier, France
2012PhD in Theoretical Computer Science, Technische Universität Berlin, Germany
2009Diploma in Computer Science, minor in Physics, Friedrich Schiller Universität, Jena, Germany

Forschungsinteressen

Parameterized Algorithmics
Genome Scaffolding
Phylogenetic Networks
Structural Parameterization
Preprocessing and permissive kernelization concepts

Publikationen

2022

L. Iersel, M. Jones and M. Weller, "Embedding Phylogenetic Trees in Networks of Low Treewidth" in 30th Annual European Symposium on Algorithms, ESA 2022, September 5-9, 2022, Berlin/Potsdam, Germany, Shiri Chechik and Gonzalo Navarro and Eva Rotenberg and Grzegorz Herman, Eds. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2022. pp. 69:1–69:14.
L. Iersel, M. Jones and M. Weller, "Embedding phylogenetic trees in networks of low treewidth" , CoRR, vol. abs/2207.00574, 2022.
T. Davot, A. Chateau, R. Fossé, R. Giroudeau and M. Weller, "On a greedy approach for genome scaffolding" , Algorithms Mol. Biol., vol. 17, no. 1, pp. 16, 2022.
K. M. Swenson, A. Elghraoui, F. Valafar, S. Mirarab and M. Weller, "Quantifying Hierarchical Conflicts in Homology Statements" in Comparative Genomics - 19th International Conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20-21, 2022, Proceedings, Lingling Jin and Dannie Durand, Eds. Springer, 2022. pp. 146–167.
C. Scornavacca and M. Weller, "Treewidth-based algorithms for the small parsimony problem on networks" , Algorithms Mol. Biol., vol. 17, no. 1, pp. 15, 2022.

2021

T. Davot, A. Chateau, R. Giroudeau, M. Weller and D. Tabary, "Producing Genomic Sequences after Genome Scaffolding with Ambiguous Paths: Complexity, Approximation and Lower Bounds" , Algorithmica, vol. 83, no. 7, pp. 2063–2095, 2021.
M. Bentert and M. Weller, "Tree Containment With Soft Polytomies" , J. Graph Algorithms Appl., vol. 25, no. 1, pp. 417–436, 2021.
C. Scornavacca and M. Weller, "Treewidth-Based Algorithms for the Small Parsimony Problem on Networks" in 21st International Workshop on Algorithms in Bioinformatics, WABI 2021, August 2-4, 2021, Virtual Conference, Alessandra Carbone and Mohammed El-Kebir, Eds. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. pp. 6:1–6:21.

2020

V. Berry, C. Scornavacca and M. Weller, "Scanning Phylogenetic Networks Is NP-hard" in SOFSEM 2020: Theory and Practice of Computer Science - 46th International Conference on Current Trends in Theory and Practice of Informatics, SOFSEM 2020, Limassol, Cyprus, January 20-24, 2020, Proceedings, Alexander Chatzigeorgiou and Riccardo Dondi and Herodotos Herodotou and Christos A. Kapoutsis and Yannis Manolopoulos and George A. Papadopoulos and Florian Sikora, Eds. Springer, 2020. pp. 519–530.
N. Morawietz, C. Rehs and M. Weller, "A Timecop's Work Is Harder Than You Think" in 45th International Symposium on Mathematical Foundations of Computer Science, MFCS 2020, August 24-28, 2020, Prague, Czech Republic, Javier Esparza and Daniel Král', Eds. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2020. pp. 71:1–71:14.
T. Davot, A. Chateau, R. Giroudeau and M. Weller, "Linearizing Genomes: Exact Methods and Local Search" in SOFSEM 2020: Theory and Practice of Computer Science - 46th International Conference on Current Trends in Theory and Practice of Informatics, SOFSEM 2020, Limassol, Cyprus, January 20-24, 2020, Proceedings, Alexander Chatzigeorgiou and Riccardo Dondi and Herodotos Herodotou and Christos A. Kapoutsis and Yannis Manolopoulos and George A. Papadopoulos and Florian Sikora, Eds. Springer, 2020. pp. 505–518.

2019

V. Froese, B. J. Jain, M. Rymar and M. Weller, "Fast Exact Dynamic Time Warping on Run-Length Encoded Time Series" , CoRR, vol. abs/1903.03003, 2019.
M. Weller, "Listing Conflicting Triples in Optimal Time" , CoRR, vol. abs/1911.11048, 2019.
T. Davot, A. Chateau, R. Giroudeau and M. Weller, "New Polynomial-Time Algorithm Around the Scaffolding Problem" in Algorithms for Computational Biology - 6th International Conference, AlCoB 2019, Berkeley, CA, USA, May 28-30, 2019, Proceedings, Ian H. Holmes and Carlos Martín-Vide and Miguel A. Vega-Rodríguez, Eds. Springer, 2019. pp. 25–38.
L. Bulteau and M. Weller, "Parameterized Algorithms in Bioinformatics: An Overview" , Algorithms, vol. 12, no. 12, pp. 256, 2019.
P. Cazals, B. Darties, A. Chateau, R. Giroudeau and M. Weller, "Power Edge Set and Zero Forcing Set Remain Difficult in Cubic Graphs" in Combinatorial Algorithms - 30th International Workshop, IWOCA 2019, Pisa, Italy, July 23-25, 2019, Proceedings, Charles J. Colbourn and Roberto Grossi and Nadia Pisanti, Eds. Springer, 2019. pp. 122–135.

2018

M. Weller, A. Chateau, C. Dallard and R. Giroudeau, "Scaffolding Problems Revisited: Complexity, Approximation and Fixed Parameter Tractable Algorithms, and Some Special Cases" , Algorithmica, vol. 80, no. 6, pp. 1771–1803, 2018.
M. R. Fellows, L. Jaffke, A. I. Király, F. A. Rosamond and M. Weller, "What is known about Vertex Cover Kernelization?" , CoRR, vol. abs/1811.09429, 2018.
M. R. Fellows, L. Jaffke, A. I. Király, F. A. Rosamond and M. Weller, "What Is Known About Vertex Cover Kernelization?" in Adventures Between Lower Bounds and Higher Altitudes - Essays Dedicated to Juraj Hromkovič on the Occasion of His 60th Birthday, Hans-Joachim Böckenhauer and Dennis Komm and Walter Unger, Eds. Springer, 2018. pp. 330–356.
M. Bentert, J. Malík and M. Weller, "Tree Containment With Soft Polytomies" in 16th Scandinavian Symposium and Workshops on Algorithm Theory, SWAT 2018, June 18-20, 2018, Malmö, Sweden, David Eppstein, Eds. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. pp. 9:1–9:14.
M. Weller, "Linear-Time Tree Containment in Phylogenetic Networks" in Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings, Mathieu Blanchette and Aïda Ouangraoua, Eds. Springer, 2018. pp. 309–323.
T. Davot, A. Chateau, R. Giroudeau and M. Weller, "On the Hardness of Approximating Linearization of Scaffolds Sharing Repeated Contigs" in Comparative Genomics - 16th International Conference, RECOMB-CG 2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings, Mathieu Blanchette and Aïda Ouangraoua, Eds. Springer, 2018. pp. 91–107.
M. Weller, A. Chateau, R. Giroudeau, J. König and V. Pollet, "On residual approximation in solution extension problems" , J. Comb. Optim., vol. 36, no. 4, pp. 1195–1220, 2018.
D. Tabary, T. Davot, M. Weller, A. Chateau and R. Giroudeau, "New Results About the Linearization of Scaffolds Sharing Repeated Contigs" in Combinatorial Optimization and Applications - 12th International Conference, COCOA 2018, Atlanta, GA, USA, December 15-17, 2018, Proceedings, Donghyun Kim and R. N. Uma and Alexander Zelikovsky, Eds. Springer, 2018. pp. 94–107.
B. Darties, N. Champseix, A. Chateau, R. Giroudeau and M. Weller, "Complexity and lowers bounds for Power Edge Set Problem" , J. Discrete Algorithms, vol. 52-53, pp. 70–91, 2018.

2017

N. Cohen, D. Gonçalves, E. J. Kim, C. Paul, I. Sau, D. M. Thilikos and M. Weller, "A polynomial-time algorithm for Outerplanar Diameter Improvement" , J. Comput. Syst. Sci., vol. 89, pp. 315–327, 2017.
C. Chauve, M. Jones, M. Lafond, C. Scornavacca and M. Weller, "Constructing a Consensus Phylogeny from a Leaf-Removal Distance" , CoRR, vol. abs/1705.05295, 2017.
C. Chauve, M. Jones, M. Lafond, C. Scornavacca and M. Weller, "Constructing a Consensus Phylogeny from a Leaf-Removal Distance (Extended Abstract)" in String Processing and Information Retrieval - 24th International Symposium, SPIRE 2017, Palermo, Italy, September 26-29, 2017, Proceedings, Gabriele Fici and Marinella Sciortino and Rossano Venturini, Eds. Springer, 2017. pp. 129–143.
B. Darties, A. Chateau, R. Giroudeau and M. Weller, "Improved Complexity for Power Edge Set Problem" in Combinatorial Algorithms - 28th International Workshop, IWOCA 2017, Newcastle, NSW, Australia, July 17-21, 2017, Revised Selected Papers, Ljiljana Brankovic and Joe Ryan and William F. Smyth, Eds. Springer, 2017. pp. 128–141.
M. Weller, "Linear-Time Tree Containment in Phylogenetic Networks" , CoRR, vol. abs/1702.06364, 2017.
B. Darties, A. Chateau, R. Giroudeau and M. Weller, "New Insights for Power Edge Set Problem" in Combinatorial Optimization and Applications - 11th International Conference, COCOA 2017, Shanghai, China, December 16-18, 2017, Proceedings, Part I, Xiaofeng Gao and Hongwei Du and Meng Han, Eds. Springer, 2017. pp. 180–194.
M. Weller, A. Chateau and R. Giroudeau, "On the Linearization of Scaffolds Sharing Repeated Contigs" in Combinatorial Optimization and Applications - 11th International Conference, COCOA 2017, Shanghai, China, December 16-18, 2017, Proceedings, Part II, Xiaofeng Gao and Hongwei Du and Meng Han, Eds. Springer, 2017. pp. 509–517.
E. Jacox, M. Weller, E. Tannier and C. Scornavacca, "Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses" , Bioinform., vol. 33, no. 7, pp. 980–987, 2017.
H. Dell, C. Komusiewicz, N. Talmon and M. Weller, "The PACE 2017 Parameterized Algorithms and Computational Experiments Challenge: The Second Iteration" in 12th International Symposium on Parameterized and Exact Computation, IPEC 2017, September 6-8, 2017, Vienna, Austria, Daniel Lokshtanov and Naomi Nishimura, Eds. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. pp. 30:1–30:12.

2016

S. Kelk, L. Iersel, C. Scornavacca and M. Weller, "Phylogenetic incongruence through the lens of Monadic Second Order logic" , J. Graph Algorithms Appl., vol. 20, no. 2, pp. 189–215, 2016.
M. Weller, A. Chateau, R. Giroudeau, J. König and V. Pollet, "On Residual Approximation in Solution Extension Problems" in Combinatorial Optimization and Applications - 10th International Conference, COCOA 2016, Hong Kong, China, December 16-18, 2016, Proceedings, T.-H. Hubert Chan and Minming Li and Lusheng Wang, Eds. Springer, 2016. pp. 463–476.
V. Garnero and M. Weller, "Parameterized certificate dispersal and its variants" , Theor. Comput. Sci., vol. 622, pp. 66–78, 2016.
C. Dallard, M. Weller, A. Chateau and R. Giroudeau, "Instance Guaranteed Ratio on Greedy Heuristic for Genome Scaffolding" in Combinatorial Optimization and Applications - 10th International Conference, COCOA 2016, Hong Kong, China, December 16-18, 2016, Proceedings, T.-H. Hubert Chan and Minming Li and Lusheng Wang, Eds. Springer, 2016. pp. 294–308.

2015

N. Cohen, D. Gonçalves, E. Kim, C. Paul, I. Sau, D. M. Thilikos and M. Weller, "A Polynomial-Time Algorithm for Outerplanar Diameter Improvement" in Computer Science - Theory and Applications - 10th International Computer Science Symposium in Russia, CSR 2015, Listvyanka, Russia, July 13-17, 2015, Proceedings, Lev D. Beklemishev and Daniil V. Musatov, Eds. Springer, 2015. pp. 123–142.
R. Bevern, M. Mnich, R. Niedermeier and M. Weller, "Interval scheduling and colorful independent sets" , J. Sched., vol. 18, no. 5, pp. 449–469, 2015.
M. A. Babenko, A. V. Goldberg, H. Kaplan, R. Savchenko and M. Weller, "On the Complexity of Hub Labeling" , CoRR, vol. abs/1501.02492, 2015.
M. A. Babenko, A. V. Goldberg, H. Kaplan, R. Savchenko and M. Weller, "On the Complexity of Hub Labeling (Extended Abstract)" in Mathematical Foundations of Computer Science 2015 - 40th International Symposium, MFCS 2015, Milan, Italy, August 24-28, 2015, Proceedings, Part II, Giuseppe F. Italiano and Giovanni Pighizzini and Donald Sannella, Eds. Springer, 2015. pp. 62–74.
M. Weller, A. Chateau and R. Giroudeau, "On the Complexity of Scaffolding Problems: From Cliques to Sparse Graphs" in Combinatorial Optimization and Applications - 9th International Conference, COCOA 2015, Houston, TX, USA, December 18-20, 2015, Proceedings, Zaixin Lu and Donghyun Kim and Weili Wu and Wei Li and Ding-Zhu Du, Eds. Springer, 2015. pp. 409–423.
J. Chen, C. Komusiewicz, R. Niedermeier, M. Sorge, O. Suchý and M. Weller, "Polynomial-Time Data Reduction for the Subset Interconnection Design Problem" , SIAM J. Discret. Math., vol. 29, no. 1, pp. 1–25, 2015.

2014

N. Cohen, D. Gonçalves, E. J. Kim, C. Paul, I. Sau, D. M. Thilikos and M. Weller, "A Polynomial-time Algorithm for Outerplanar Diameter Improvement" , CoRR, vol. abs/1403.5702, 2014.
M. Chopin, A. Nichterlein, R. Niedermeier and M. Weller, "Constant Thresholds Can Make Target Set Selection Tractable" , Theory Comput. Syst., vol. 55, no. 1, pp. 61–83, 2014.
M. Sorge, H. Moser, R. Niedermeier and M. Weller, "Exploiting a hypergraph model for finding Golomb rulers" , Acta Informatica, vol. 51, no. 7, pp. 449–471, 2014.
R. Bevern, M. Mnich, R. Niedermeier and M. Weller, "Interval scheduling and colorful independent sets" , CoRR, vol. abs/1402.0851, 2014.
M. Dörnfelder, J. Guo, C. Komusiewicz and M. Weller, "On the parameterized complexity of consensus clustering" , Theor. Comput. Sci., vol. 542, pp. 71–82, 2014.
M. Weller, "Optimal Hub Labeling is NP-complete" , CoRR, vol. abs/1407.8373, 2014.

2013

J. Uhlmann and M. Weller, "Two-Layer Planarization parameterized by feedback edge set" , Theor. Comput. Sci., vol. 494, pp. 99–111, 2013.
A. Nichterlein, R. Niedermeier, J. Uhlmann and M. Weller, "On tractable cases of Target Set Selection" , Soc. Netw. Anal. Min., vol. 3, no. 2, pp. 233–256, 2013.
F. Dorn, H. Moser, R. Niedermeier and M. Weller, "Efficient Algorithms for Eulerian Extension and Rural Postman" , SIAM J. Discret. Math., vol. 27, no. 1, pp. 75–94, 2013.
J. Chen, C. Komusiewicz, R. Niedermeier, M. Sorge, O. Suchý and M. Weller, "Effective and Efficient Data Reduction for the Subset Interconnection Design Problem" in Algorithms and Computation - 24th International Symposium, ISAAC 2013, Hong Kong, China, December 16-18, 2013, Proceedings, Leizhen Cai and Siu-Wing Cheng and Tak Wah Lam, Eds. Springer, 2013. pp. 361–371.
M. Weller, "An Improved Branching Algorithm for Two-Layer Planarization Parameterized by the Feedback Edge Set Number" in Experimental Algorithms, 12th International Symposium, SEA 2013, Rome, Italy, June 5-7, 2013. Proceedings, Vincenzo Bonifaci and Camil Demetrescu and Alberto Marchetti-Spaccamela, Eds. Springer, 2013. pp. 337–353.
M. Weller, "Aspects of preprocessing applied to combinatorial graph problems", Berlin Institute of Technology, 2013.
ISBN
978-3-7983-2508-1

2012

M. Sorge, R. Bevern, R. Niedermeier and M. Weller, "A new view on Rural Postman based on Eulerian Extension and Matching" , J. Discrete Algorithms, vol. 16, pp. 12–33, 2012.
M. Chopin, A. Nichterlein, R. Niedermeier and M. Weller, "Constant Thresholds Can Make Target Set Selection Tractable" in Design and Analysis of Algorithms - First Mediterranean Conference on Algorithms, MedAlg 2012, Kibbutz Ein Gedi, Israel, December 3-5, 2012. Proceedings, Guy Even and Dror Rawitz, Eds. Springer, 2012. pp. 120–133.
M. Sorge, H. Moser, R. Niedermeier and M. Weller, "Exploiting a Hypergraph Model for Finding Golomb Rulers" in Combinatorial Optimization - Second International Symposium, ISCO 2012, Athens, Greece, April 19-21, 2012, Revised Selected Papers, Ali Ridha Mahjoub and Vangelis Markakis and Ioannis Milis and Vangelis Th. Paschos, Eds. Springer, 2012. pp. 368–379.
R. Bevern, M. Mnich, R. Niedermeier and M. Weller, "Interval Scheduling and Colorful Independent Sets" in Algorithms and Computation - 23rd International Symposium, ISAAC 2012, Taipei, Taiwan, December 19-21, 2012. Proceedings, Kun-Mao Chao and Tsan-sheng Hsu and Der-Tsai Lee, Eds. Springer, 2012. pp. 247–256.
M. Weller, C. Komusiewicz, R. Niedermeier and J. Uhlmann, "On making directed graphs transitive" , J. Comput. Syst. Sci., vol. 78, no. 2, pp. 559–574, 2012.

2011

M. Dörnfelder, J. Guo, C. Komusiewicz and M. Weller, "On the Parameterized Complexity of Consensus Clustering" in Algorithms and Computation - 22nd International Symposium, ISAAC 2011, Yokohama, Japan, December 5-8, 2011. Proceedings, Takao Asano and Shin-Ichi Nakano and Yoshio Okamoto and Osamu Watanabe, Eds. Springer, 2011. pp. 624–633.
M. Sorge, R. Bevern, R. Niedermeier and M. Weller, "A New View on Rural Postman Based on Eulerian Extension and Matching" in Combinatorial Algorithms - 22nd International Workshop, IWOCA 2011, Victoria, BC, Canada, July 20-22, 2011, Revised Selected Papers, Costas S. Iliopoulos and William F. Smyth, Eds. Springer, 2011. pp. 310–323.
R. Bevern, S. Hartung, F. Kammer, R. Niedermeier and M. Weller, "Linear-Time Computation of a Linear Problem Kernel for Dominating Set on Planar Graphs" in Parameterized and Exact Computation - 6th International Symposium, IPEC 2011, Saarbrücken, Germany, September 6-8, 2011. Revised Selected Papers, Dániel Marx and Peter Rossmanith, Eds. Springer, 2011. pp. 194–206.
M. Sorge, R. Bevern, R. Niedermeier and M. Weller, "From Few Components to an Eulerian Graph by Adding Arcs" in Graph-Theoretic Concepts in Computer Science - 37th International Workshop, WG 2011, Teplá Monastery, Czech Republic, June 21-24, 2011. Revised Papers, Petr Kolman and Jan Kratochvíl, Eds. Springer, 2011. pp. 307–318.

2010

F. Dorn, H. Moser, R. Niedermeier and M. Weller, "Efficient Algorithms for Eulerian Extension" in Graph Theoretic Concepts in Computer Science - 36th International Workshop, WG 2010, Zarós, Crete, Greece, June 28-30, 2010 Revised Papers, Dimitrios M. Thilikos, Eds. 2010. pp. 100–111.
R. Fleischer, J. Guo, R. Niedermeier, J. Uhlmann, Y. Wang, M. Weller and X. Wu, "Extended Islands of Tractability for Parsimony Haplotyping" in Combinatorial Pattern Matching, 21st Annual Symposium, CPM 2010, New York, NY, USA, June 21-23, 2010. Proceedings, Amihood Amir and Laxmi Parida, Eds. Springer, 2010. pp. 214–226.
A. Nichterlein, R. Niedermeier, J. Uhlmann and M. Weller, "On Tractable Cases of Target Set Selection" in Algorithms and Computation - 21st International Symposium, ISAAC 2010, Jeju Island, Korea, December 15-17, 2010, Proceedings, Part I, Otfried Cheong and Kyung-Yong Chwa and Kunsoo Park, Eds. Springer, 2010. pp. 378–389.
J. Uhlmann and M. Weller, "Two-Layer Planarization Parameterized by Feedback Edge Set" in Theory and Applications of Models of Computation, 7th Annual Conference, TAMC 2010, Prague, Czech Republic, June 7-11, 2010. Proceedings, Jan Kratochvíl and Angsheng Li and Jirí Fiala and Petr Kolman, Eds. Springer, 2010. pp. 431–442.

2009

M. Weller, C. Komusiewicz, R. Niedermeier and J. Uhlmann, "On Making Directed Graphs Transitive" in Algorithms and Data Structures, 11th International Symposium, WADS 2009, Banff, Canada, August 21-23, 2009. Proceedings, Frank K. H. A. Dehne and Marina L. Gavrilova and Jörg-Rüdiger Sack and Csaba D. Tóth, Eds. Springer, 2009. pp. 542–553.