Algorithmics and Computational Complexity

Prof. Dr. Mathias Weller

mathias

Organization name	Algorithmics and Computational Complexity
Office	TEL 5-1
Building	TEL
Room	TEL 509C

Curriculum Vitae

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

research interests

Parameterized Algorithmics

Genome Scaffolding

Phylogenetic Networks

Structural Parameterization

Preprocessing and permissive kernelization concepts

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.

DOI: 10.4230/LIPIcs.ESA.2022.69

L. Iersel, M. Jones and M. Weller, "Embedding phylogenetic trees in networks of low treewidth" , CoRR, vol. abs/2207.00574, 2022.

DOI: 10.48550/arXiv.2207.00574

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.

DOI: 10.1186/s13015-022-00223-x

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.

DOI: 10.1007/978-3-031-06220-9_9

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.

DOI: 10.1186/s13015-022-00216-w

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.

DOI: 10.1007/s00453-021-00819-6

M. Bentert and M. Weller, "Tree Containment With Soft Polytomies" , J. Graph Algorithms Appl., vol. 25, no. 1, pp. 417–436, 2021.

DOI: 10.7155/jgaa.00565

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.

DOI: 10.4230/LIPIcs.WABI.2021.6

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.

DOI: 10.1007/978-3-030-38919-2_42

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.

DOI: 10.4230/LIPIcs.MFCS.2020.71

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.

DOI: 10.1007/978-3-030-38919-2_41

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.

Weblink: http://arxiv.org/abs/1903.03003

M. Weller, "Listing Conflicting Triples in Optimal Time" , CoRR, vol. abs/1911.11048, 2019.

Weblink: http://arxiv.org/abs/1911.11048

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.

DOI: 10.1007/978-3-030-18174-1_2

L. Bulteau and M. Weller, "Parameterized Algorithms in Bioinformatics: An Overview" , Algorithms, vol. 12, no. 12, pp. 256, 2019.

DOI: 10.3390/a12120256

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.

DOI: 10.1007/978-3-030-25005-8_11

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.

DOI: 10.1007/s00453-018-0405-x

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.

Weblink: http://arxiv.org/abs/1811.09429

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.

DOI: 10.1007/978-3-319-98355-4_19

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.

DOI: 10.4230/LIPIcs.SWAT.2018.9

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.

DOI: 10.1007/978-3-030-00834-5_18

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.

DOI: 10.1007/978-3-030-00834-5_5

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.

DOI: 10.1007/s10878-017-0202-5

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.

DOI: 10.1007/978-3-030-04651-4_7

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.

DOI: 10.1016/j.jda.2018.11.006

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