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**Published in:** LIPIcs, Volume 272, 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)

For any finite set ℋ = {H_1,…,H_p} of graphs, a graph is ℋ-subgraph-free if it does not contain any of H_1,…,H_p as a subgraph. In recent work, meta-classifications have been studied: these show that if graph problems satisfy certain prescribed conditions, their complexity can be classified on classes of ℋ-subgraph-free graphs. We continue this work and focus on problems that have polynomial-time solutions on classes that have bounded treewidth or maximum degree at most 3 and examine their complexity on H-subgraph-free graph classes where H is a connected graph. With this approach, we obtain comprehensive classifications for (Independent) Feedback Vertex Set, Connected Vertex Cover, Colouring and Matching Cut. This resolves a number of open problems.
We highlight that, to establish that Independent Feedback Vertex Set belongs to this collection of problems, we first show that it can be solved in polynomial time on graphs of maximum degree 3. We demonstrate that, with the exception of the complete graph on four vertices, each graph in this class has a minimum size feedback vertex set that is also an independent set.

Matthew Johnson, Barnaby Martin, Sukanya Pandey, Daniël Paulusma, Siani Smith, and Erik Jan van Leeuwen. Complexity Framework for Forbidden Subgraphs III: When Problems Are Tractable on Subcubic Graphs. In 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 272, pp. 57:1-57:15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)

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@InProceedings{johnson_et_al:LIPIcs.MFCS.2023.57, author = {Johnson, Matthew and Martin, Barnaby and Pandey, Sukanya and Paulusma, Dani\"{e}l and Smith, Siani and van Leeuwen, Erik Jan}, title = {{Complexity Framework for Forbidden Subgraphs III: When Problems Are Tractable on Subcubic Graphs}}, booktitle = {48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)}, pages = {57:1--57:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-292-1}, ISSN = {1868-8969}, year = {2023}, volume = {272}, editor = {Leroux, J\'{e}r\^{o}me and Lombardy, Sylvain and Peleg, David}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2023.57}, URN = {urn:nbn:de:0030-drops-185914}, doi = {10.4230/LIPIcs.MFCS.2023.57}, annote = {Keywords: forbidden subgraphs, independent feedback vertex set, treewidth} }

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**Published in:** LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)

A partition (V_1,...,V_k) of the vertex set of a graph G with a (not necessarily proper) colouring c is colourful if no two vertices in any V_i have the same colour and every set V_i induces a connected graph. The Colourful Partition problem, introduced by Adamaszek and Popa, is to decide whether a coloured graph (G,c) has a colourful partition of size at most k. This problem is related to the Colourful Components problem, introduced by He, Liu and Zhao, which is to decide whether a graph can be modified into a graph whose connected components form a colourful partition by deleting at most p edges.
Despite the similarities in their definitions, we show that Colourful Partition and Colourful Components may have different complexities for restricted instances. We tighten known NP-hardness results for both problems by closing a number of complexity gaps. In addition, we prove new hardness and tractability results for Colourful Partition. In particular, we prove that deciding whether a coloured graph (G,c) has a colourful partition of size 2 is NP-complete for coloured planar bipartite graphs of maximum degree 3 and path-width 3, but polynomial-time solvable for coloured graphs of treewidth 2.
Rather than performing an ad hoc study, we use our classical complexity results to guide us in undertaking a thorough parameterized study of Colourful Partition. We show that this leads to suitable parameters for obtaining FPT results and moreover prove that Colourful Components and Colourful Partition may have different parameterized complexities, depending on the chosen parameter.

Laurent Bulteau, Konrad K. Dabrowski, Guillaume Fertin, Matthew Johnson, Daniël Paulusma, and Stéphane Vialette. Finding a Small Number of Colourful Components. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 20:1-20:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2019)

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@InProceedings{bulteau_et_al:LIPIcs.CPM.2019.20, author = {Bulteau, Laurent and Dabrowski, Konrad K. and Fertin, Guillaume and Johnson, Matthew and Paulusma, Dani\"{e}l and Vialette, St\'{e}phane}, title = {{Finding a Small Number of Colourful Components}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {20:1--20:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-103-0}, ISSN = {1868-8969}, year = {2019}, volume = {128}, editor = {Pisanti, Nadia and P. Pissis, Solon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.20}, URN = {urn:nbn:de:0030-drops-104914}, doi = {10.4230/LIPIcs.CPM.2019.20}, annote = {Keywords: Colourful component, colourful partition, tree, treewidth, vertex cover} }

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**Published in:** OASIcs, Volume 66, 2018 Imperial College Computing Student Workshop (ICCSW 2018)

Artificial Intelligence is increasingly being used to both augment existing fields of research and open up new avenues of discovery. From quality control for imaging flow cytometry to computational musicology, modern AI is an exciting new tool for research and thus knowing how to engineer AI systems in a research context is a vital new skill for RSEs to acquire. In this talk, I will outline four different areas of AI: supervised learning, unsupervised learning, interactive learning, and Bayesian learning. For each of these approaches, I will discuss how they typically map to different research problems and explore best practices for RSEs via specific use cases. At the end of the talk, you will have received a high-level overview of AI technologies and their use in research, have seen some cool examples of how AI has been used in a wide range of research areas, and have a good sense of where to go to learn more.

Matthew Johnson. Harnessing AI For Research. In 2018 Imperial College Computing Student Workshop (ICCSW 2018). Open Access Series in Informatics (OASIcs), Volume 66, p. 11:1, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2019)

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@InProceedings{johnson:OASIcs.ICCSW.2018.11, author = {Johnson, Matthew}, title = {{Harnessing AI For Research}}, booktitle = {2018 Imperial College Computing Student Workshop (ICCSW 2018)}, pages = {11:1--11:1}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-95977-097-2}, ISSN = {2190-6807}, year = {2019}, volume = {66}, editor = {Pirovano, Edoardo and Graversen, Eva}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.ICCSW.2018.11}, URN = {urn:nbn:de:0030-drops-101922}, doi = {10.4230/OASIcs.ICCSW.2018.11}, annote = {Keywords: Artificial intelligence} }

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**Published in:** LIPIcs, Volume 117, 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)

Let vc(G), fvs(G) and oct(G) denote, respectively, the size of a minimum vertex cover, minimum feedback vertex set and minimum odd cycle transversal in a graph G. One can ask, when looking for these sets in a graph, how much bigger might they be if we require that they are independent; that is, what is the price of independence? If G has a vertex cover, feedback vertex set or odd cycle transversal that is an independent set, then we let, respectively, ivc(G), ifvs(G) or ioct(G) denote the minimum size of such a set. We investigate for which graphs H the values of ivc(G), ifvs(G) and ioct(G) are bounded in terms of vc(G), fvs(G) and oct(G), respectively, when the graph G belongs to the class of H-free graphs. We find complete classifications for vertex cover and feedback vertex set and an almost complete classification for odd cycle transversal (subject to three non-equivalent open cases).

Konrad K. Dabrowski, Matthew Johnson, Giacomo Paesani, Daniël Paulusma, and Viktor Zamaraev. On the Price of Independence for Vertex Cover, Feedback Vertex Set and Odd Cycle Transversal. In 43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 117, pp. 63:1-63:15, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)

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@InProceedings{dabrowski_et_al:LIPIcs.MFCS.2018.63, author = {Dabrowski, Konrad K. and Johnson, Matthew and Paesani, Giacomo and Paulusma, Dani\"{e}l and Zamaraev, Viktor}, title = {{On the Price of Independence for Vertex Cover, Feedback Vertex Set and Odd Cycle Transversal}}, booktitle = {43rd International Symposium on Mathematical Foundations of Computer Science (MFCS 2018)}, pages = {63:1--63:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-086-6}, ISSN = {1868-8969}, year = {2018}, volume = {117}, editor = {Potapov, Igor and Spirakis, Paul and Worrell, James}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2018.63}, URN = {urn:nbn:de:0030-drops-96452}, doi = {10.4230/LIPIcs.MFCS.2018.63}, annote = {Keywords: vertex cover, feedback vertex set, odd cycle transversal, price of independence} }

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**Published in:** LIPIcs, Volume 92, 28th International Symposium on Algorithms and Computation (ISAAC 2017)

The NP-complete problem Feedback Vertex Set is to decide if it is possible, for a given integer k>=0, to delete at most k vertices from a given graph so that what remains is a forest. The variant in which the deleted vertices must form an independent set is called Independent Feedback Vertex Set and is also NP-complete. In fact, even deciding if an independent feedback vertex set exists is NP-complete and this problem is closely related to the 3-Colouring problem, or equivalently, to the problem of deciding if a graph has an independent odd cycle transversal, that is, an independent set of vertices whose deletion makes the graph bipartite. We initiate a systematic study of the complexity of Independent Feedback Vertex Set for H-free graphs. We prove that it is NP-complete if H contains a claw or cycle. Tamura, Ito and Zhou proved that it is polynomial-time solvable for P_4-free graphs. We show that it remains in P for P_5-free graphs. We prove analogous results for the Independent Odd Cycle Transversal problem, which asks if a graph has an independent odd cycle transversal of size at most k for a given integer k>=0.

Marthe Bonamy, Konrad K. Dabrowski, Carl Feghali, Matthew Johnson, and Daniël Paulusma. Independent Feedback Vertex Set for P_5-free Graphs. In 28th International Symposium on Algorithms and Computation (ISAAC 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 92, pp. 16:1-16:12, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)

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@InProceedings{bonamy_et_al:LIPIcs.ISAAC.2017.16, author = {Bonamy, Marthe and Dabrowski, Konrad K. and Feghali, Carl and Johnson, Matthew and Paulusma, Dani\"{e}l}, title = {{Independent Feedback Vertex Set for P\underline5-free Graphs}}, booktitle = {28th International Symposium on Algorithms and Computation (ISAAC 2017)}, pages = {16:1--16:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-054-5}, ISSN = {1868-8969}, year = {2017}, volume = {92}, editor = {Okamoto, Yoshio and Tokuyama, Takeshi}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2017.16}, URN = {urn:nbn:de:0030-drops-82308}, doi = {10.4230/LIPIcs.ISAAC.2017.16}, annote = {Keywords: feedback vertex set, odd cycle transversal, independent set, H-free graph} }

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**Published in:** LIPIcs, Volume 83, 42nd International Symposium on Mathematical Foundations of Computer Science (MFCS 2017)

We continue research into a well-studied family of problems that ask if the vertices of a graph can be partitioned into sets A and B, where A is an independent set and B induces a graph from some specified graph class G. We let G be the class of k-degenerate graphs. The problem is known to be polynomial-time solvable if k=0 (bipartite graphs) and NP-complete if k=1 (near-bipartite graphs) even for graphs of diameter 4, as shown by Yang and Yuan, who also proved polynomial-time solvability for graphs of diameter 2. We show that recognizing near-bipartite graphs of diameter 3 is NP-complete resolving their open problem. To answer another open problem, we consider graphs of maximum degree D on n vertices. We show how to find A and B in O(n) time for k=1 and D=3, and in O(n^2) time for k >= 2 and D >= 4. These results also provide an algorithmic version of a result of Catlin [JCTB, 1979] and enable us to complete the complexity classification of another problem: finding a path in the vertex colouring reconfiguration graph between two given k-colourings of a graph of bounded maximum degree.

Marthe Bonamy, Konrad K. Dabrowski, Carl Feghali, Matthew Johnson, and Daniël Paulusma. Recognizing Graphs Close to Bipartite Graphs. In 42nd International Symposium on Mathematical Foundations of Computer Science (MFCS 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 83, pp. 70:1-70:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)

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@InProceedings{bonamy_et_al:LIPIcs.MFCS.2017.70, author = {Bonamy, Marthe and Dabrowski, Konrad K. and Feghali, Carl and Johnson, Matthew and Paulusma, Dani\"{e}l}, title = {{Recognizing Graphs Close to Bipartite Graphs}}, booktitle = {42nd International Symposium on Mathematical Foundations of Computer Science (MFCS 2017)}, pages = {70:1--70:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-046-0}, ISSN = {1868-8969}, year = {2017}, volume = {83}, editor = {Larsen, Kim G. and Bodlaender, Hans L. and Raskin, Jean-Francois}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2017.70}, URN = {urn:nbn:de:0030-drops-80740}, doi = {10.4230/LIPIcs.MFCS.2017.70}, annote = {Keywords: degenerate graphs, near-bipartite graphs, reconfiguration graphs} }

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**Published in:** LIPIcs, Volume 83, 42nd International Symposium on Mathematical Foundations of Computer Science (MFCS 2017)

Clique-width is an important graph parameter due to its algorithmic and structural properties. A graph class is hereditary if it can be characterized by a (not necessarily finite) set H of forbidden induced subgraphs. We initiate a systematic study into the boundedness of clique-width of hereditary graph classes closed under complementation. First, we extend the known classification for the |H|=1 case by classifying the boundedness of clique-width for every set H of self-complementary graphs. We then completely settle the |H|=2 case. In particular, we determine one new class of (H1, complement of H1)-free graphs of bounded clique-width (as a side effect, this leaves only six classes of (H1, H2)-free graphs, for which it is not known whether their clique-width is bounded).
Once we have obtained the classification of the |H|=2 case, we research the effect of forbidding self-complementary graphs on the boundedness of clique-width. Surprisingly, we show that for a set F of self-complementary graphs on at least five vertices, the classification of the boundedness of clique-width for ({H1, complement of H1} + F)-free graphs coincides with the one for the |H|=2 case if and only if F does not include the bull (the only non-empty self-complementary graphs on fewer than five vertices are P_1 and P_4, and P_4-free graphs have clique-width at most 2).
Finally, we discuss the consequences of our results for COLOURING.

Alexandre Blanché, Konrad K. Dabrowski, Matthew Johnson, Vadim V. Lozin, Daniël Paulusma, and Viktor Zamaraev. Clique-Width for Graph Classes Closed under Complementation. In 42nd International Symposium on Mathematical Foundations of Computer Science (MFCS 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 83, pp. 73:1-73:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2017)

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@InProceedings{blanche_et_al:LIPIcs.MFCS.2017.73, author = {Blanch\'{e}, Alexandre and Dabrowski, Konrad K. and Johnson, Matthew and Lozin, Vadim V. and Paulusma, Dani\"{e}l and Zamaraev, Viktor}, title = {{Clique-Width for Graph Classes Closed under Complementation}}, booktitle = {42nd International Symposium on Mathematical Foundations of Computer Science (MFCS 2017)}, pages = {73:1--73:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-046-0}, ISSN = {1868-8969}, year = {2017}, volume = {83}, editor = {Larsen, Kim G. and Bodlaender, Hans L. and Raskin, Jean-Francois}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2017.73}, URN = {urn:nbn:de:0030-drops-80756}, doi = {10.4230/LIPIcs.MFCS.2017.73}, annote = {Keywords: clique-width, self-complementary graph, forbidden induced subgraph} }

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**Published in:** LIPIcs, Volume 123, 29th International Symposium on Algorithms and Computation (ISAAC 2018)

Interpreting three-leaf binary trees or rooted triples as constraints yields an entailment relation, whereby binary trees satisfying some rooted triples must also thus satisfy others, and thence a closure operator, which is known to be polynomial-time computable. This is extended to inconsistent triple sets by defining that a triple is entailed by such a set if it is entailed by any consistent subset of it.
Determining whether the closure of an inconsistent rooted triple set can be computed in polynomial time was posed as an open problem in the Isaac Newton Institute's "Phylogenetics" program in 2007. It appears (as NC4) in a collection of such open problems maintained by Mike Steel, and it is the last of that collection's five problems concerning computational complexity to have remained open. We resolve the complexity of computing this closure, proving that its decision version is NP-Complete.
In the process, we also prove that detecting the existence of any acyclic B-hyperpath (from specified source to destination) is NP-Complete, in a significantly narrower special case than the version whose minimization problem was recently proven NP-hard by Ritz et al. This implies it is NP-hard to approximate (our special case of) their minimization problem to within any factor.

Matthew P. Johnson. Deciding the Closure of Inconsistent Rooted Triples Is NP-Complete. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 12:1-12:13, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)

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@InProceedings{johnson:LIPIcs.ISAAC.2018.12, author = {Johnson, Matthew P.}, title = {{Deciding the Closure of Inconsistent Rooted Triples Is NP-Complete}}, booktitle = {29th International Symposium on Algorithms and Computation (ISAAC 2018)}, pages = {12:1--12:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-094-1}, ISSN = {1868-8969}, year = {2018}, volume = {123}, editor = {Hsu, Wen-Lian and Lee, Der-Tsai and Liao, Chung-Shou}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2018.12}, URN = {urn:nbn:de:0030-drops-99600}, doi = {10.4230/LIPIcs.ISAAC.2018.12}, annote = {Keywords: phylogenetic trees, rooted triple entailment, NP-Completeness, directed hypergraphs, acyclic induced subgraphs, computational complexity} }

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