23 Search Results for "Johnson, Matthew"


Document
Complexity Framework for Forbidden Subgraphs III: When Problems Are Tractable on Subcubic Graphs

Authors: Matthew Johnson, Barnaby Martin, Sukanya Pandey, Daniël Paulusma, Siani Smith, and Erik Jan van Leeuwen

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


Abstract
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.

Cite as

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}
}
Document
Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks

Authors: Robert F. Johnson and Lulu Qian

Published in: LIPIcs, Volume 174, 26th International Conference on DNA Computing and Molecular Programming (DNA 26) (2020)


Abstract
In molecular programming, the Chemical Reaction Network model is often used to describe real or hypothetical systems. Often, an interesting computational task can be done with a known hypothetical Chemical Reaction Network, but often such networks have no known physical implementation. One of the important breakthroughs in the field was that any Chemical Reaction Network can be physically implemented, approximately, using DNA strand displacement mechanisms. This allows us to treat the Chemical Reaction Network model as a programming language and the implementation schemes as its compiler. This also suggests that it would be useful to optimize the result of such a compilation, and in general to find effective ways to design better DNA strand displacement systems. We discuss DNA strand displacement systems in terms of "motifs", short sequences of elementary DNA strand displacement reactions. We argue that describing such motifs in terms of their inputs and outputs, then building larger systems out of the abstracted motifs, can be an efficient way of designing DNA strand displacement systems. We discuss four previously studied motifs in this abstracted way, and present a new motif based on cooperative 4-way strand exchange. We then show how Chemical Reaction Network implementations can be built out of abstracted motifs, discussing existing implementations as well as presenting two new implementations based on 4-way strand exchange, one of which uses the new cooperative motif. The new implementations both have two desirable properties not found in existing implementations, namely both use only at most 2-stranded DNA complexes for signal and fuel complexes and both are physically reversible. There are reasons to believe that those properties may make them more robust and energy-efficient, but at the expense of using more fuel complexes than existing implementation schemes.

Cite as

Robert F. Johnson and Lulu Qian. Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks. In 26th International Conference on DNA Computing and Molecular Programming (DNA 26). Leibniz International Proceedings in Informatics (LIPIcs), Volume 174, pp. 2:1-2:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2020)


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@InProceedings{johnson_et_al:LIPIcs.DNA.2020.2,
  author =	{Johnson, Robert F. and Qian, Lulu},
  title =	{{Simplifying Chemical Reaction Network Implementations with Two-Stranded DNA Building Blocks}},
  booktitle =	{26th International Conference on DNA Computing and Molecular Programming (DNA 26)},
  pages =	{2:1--2:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-163-4},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{174},
  editor =	{Geary, Cody and Patitz, Matthew J.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.2020.2},
  URN =		{urn:nbn:de:0030-drops-129557},
  doi =		{10.4230/LIPIcs.DNA.2020.2},
  annote =	{Keywords: Molecular programming, DNA computing, Chemical Reaction Networks, DNA strand displacement}
}
Document
Track A: Algorithms, Complexity and Games
Approximate Nearest Neighbor for Curves - Simple, Efficient, and Deterministic

Authors: Arnold Filtser, Omrit Filtser, and Matthew J. Katz

Published in: LIPIcs, Volume 168, 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)


Abstract
In the (1+ε,r)-approximate near-neighbor problem for curves (ANNC) under some similarity measure δ, the goal is to construct a data structure for a given set 𝒞 of curves that supports approximate near-neighbor queries: Given a query curve Q, if there exists a curve C ∈ 𝒞 such that δ(Q,C)≤ r, then return a curve C' ∈ 𝒞 with δ(Q,C') ≤ (1+ε)r. There exists an efficient reduction from the (1+ε)-approximate nearest-neighbor problem to ANNC, where in the former problem the answer to a query is a curve C ∈ 𝒞 with δ(Q,C) ≤ (1+ε)⋅δ(Q,C^*), where C^* is the curve of 𝒞 most similar to Q. Given a set 𝒞 of n curves, each consisting of m points in d dimensions, we construct a data structure for ANNC that uses n⋅ O(1/ε)^{md} storage space and has O(md) query time (for a query curve of length m), where the similarity measure between two curves is their discrete Fréchet or dynamic time warping distance. Our method is simple to implement, deterministic, and results in an exponential improvement in both query time and storage space compared to all previous bounds. Further, we also consider the asymmetric version of ANNC, where the length of the query curves is k ≪ m, and obtain essentially the same storage and query bounds as above, except that m is replaced by k. Finally, we apply our method to a version of approximate range counting for curves and achieve similar bounds.

Cite as

Arnold Filtser, Omrit Filtser, and Matthew J. Katz. Approximate Nearest Neighbor for Curves - Simple, Efficient, and Deterministic. In 47th International Colloquium on Automata, Languages, and Programming (ICALP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 168, pp. 48:1-48:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)


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@InProceedings{filtser_et_al:LIPIcs.ICALP.2020.48,
  author =	{Filtser, Arnold and Filtser, Omrit and Katz, Matthew J.},
  title =	{{Approximate Nearest Neighbor for Curves - Simple, Efficient, and Deterministic}},
  booktitle =	{47th International Colloquium on Automata, Languages, and Programming (ICALP 2020)},
  pages =	{48:1--48:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-138-2},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{168},
  editor =	{Czumaj, Artur and Dawar, Anuj and Merelli, Emanuela},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2020.48},
  URN =		{urn:nbn:de:0030-drops-124555},
  doi =		{10.4230/LIPIcs.ICALP.2020.48},
  annote =	{Keywords: polygonal curves, Fr\'{e}chet distance, dynamic time warping, approximation algorithms, (asymmetric) approximate nearest neighbor, range counting}
}
Document
Validating Paired-End Read Alignments in Sequence Graphs

Authors: Chirag Jain, Haowen Zhang, Alexander Dilthey, and Srinivas Aluru

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Graph based non-linear reference structures such as variation graphs and colored de Bruijn graphs enable incorporation of full genomic diversity within a population. However, transitioning from a simple string-based reference to graphs requires addressing many computational challenges, one of which concerns accurately mapping sequencing read sets to graphs. Paired-end Illumina sequencing is a commonly used sequencing platform in genomics, where the paired-end distance constraints allow disambiguation of repeats. Many recent works have explored provably good index-based and alignment-based strategies for mapping individual reads to graphs. However, validating distance constraints efficiently over graphs is not trivial, and existing sequence to graph mappers rely on heuristics. We introduce a mathematical formulation of the problem, and provide a new algorithm to solve it exactly. We take advantage of the high sparsity of reference graphs, and use sparse matrix-matrix multiplications (SpGEMM) to build an index which can be queried efficiently by a mapping algorithm for validating the distance constraints. Effectiveness of the algorithm is demonstrated using real reference graphs, including a human MHC variation graph, and a pan-genome de-Bruijn graph built using genomes of 20 B. anthracis strains. While the one-time indexing time can vary from a few minutes to a few hours using our algorithm, answering a million distance queries takes less than a second.

Cite as

Chirag Jain, Haowen Zhang, Alexander Dilthey, and Srinivas Aluru. Validating Paired-End Read Alignments in Sequence Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 17:1-17:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{jain_et_al:LIPIcs.WABI.2019.17,
  author =	{Jain, Chirag and Zhang, Haowen and Dilthey, Alexander and Aluru, Srinivas},
  title =	{{Validating Paired-End Read Alignments in Sequence Graphs}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{17:1--17:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.17},
  URN =		{urn:nbn:de:0030-drops-110470},
  doi =		{10.4230/LIPIcs.WABI.2019.17},
  annote =	{Keywords: Sequence graphs, read mapping, index, sparse matrix-matrix multiplication}
}
Document
A Complexity Dichotomy for Critical Values of the b-Chromatic Number of Graphs

Authors: Lars Jaffke and Paloma T. Lima

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
A b-coloring of a graph G is a proper coloring of its vertices such that each color class contains a vertex that has at least one neighbor in all the other color classes. The b-Coloring problem asks whether a graph G has a b-coloring with k colors. The b-chromatic number of a graph G, denoted by chi_b(G), is the maximum number k such that G admits a b-coloring with k colors. We consider the complexity of the b-Coloring problem, whenever the value of k is close to one of two upper bounds on chi_b(G): The maximum degree Delta(G) plus one, and the m-degree, denoted by m(G), which is defined as the maximum number i such that G has i vertices of degree at least i-1. We obtain a dichotomy result for all fixed k in N when k is close to one of the two above mentioned upper bounds. Concretely, we show that if k in {Delta(G) + 1 - p, m(G) - p}, the problem is polynomial-time solvable whenever p in {0, 1} and, even when k = 3, it is NP-complete whenever p >= 2. We furthermore consider parameterizations of the b-Coloring problem that involve the maximum degree Delta(G) of the input graph G and give two FPT-algorithms. First, we show that deciding whether a graph G has a b-coloring with m(G) colors is FPT parameterized by Delta(G). Second, we show that b-Coloring{} is FPT parameterized by Delta(G) + l_k(G), where l_k(G) denotes the number of vertices of degree at least k.

Cite as

Lars Jaffke and Paloma T. Lima. A Complexity Dichotomy for Critical Values of the b-Chromatic Number of Graphs. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 34:1-34:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{jaffke_et_al:LIPIcs.MFCS.2019.34,
  author =	{Jaffke, Lars and Lima, Paloma T.},
  title =	{{A Complexity Dichotomy for Critical Values of the b-Chromatic Number of Graphs}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{34:1--34:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.34},
  URN =		{urn:nbn:de:0030-drops-109784},
  doi =		{10.4230/LIPIcs.MFCS.2019.34},
  annote =	{Keywords: b-Coloring, b-Chromatic Number}
}
Document
Colouring H-Free Graphs of Bounded Diameter

Authors: Barnaby Martin, Daniël Paulusma, and Siani Smith

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
The Colouring problem is to decide if the vertices of a graph can be coloured with at most k colours for an integer k, such that no two adjacent vertices are coloured alike. A graph G is H-free if G does not contain H as an induced subgraph. It is known that Colouring is NP-complete for H-free graphs if H contains a cycle or claw, even for fixed k >= 3. We examine to what extent the situation may change if in addition the input graph has bounded diameter.

Cite as

Barnaby Martin, Daniël Paulusma, and Siani Smith. Colouring H-Free Graphs of Bounded Diameter. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{martin_et_al:LIPIcs.MFCS.2019.14,
  author =	{Martin, Barnaby and Paulusma, Dani\"{e}l and Smith, Siani},
  title =	{{Colouring H-Free Graphs of Bounded Diameter}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{14:1--14:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.14},
  URN =		{urn:nbn:de:0030-drops-109584},
  doi =		{10.4230/LIPIcs.MFCS.2019.14},
  annote =	{Keywords: vertex colouring, H-free graph, diameter}
}
Document
A Golden Age of Hardware Description Languages: Applying Programming Language Techniques to Improve Design Productivity

Authors: Lenny Truong and Pat Hanrahan

Published in: LIPIcs, Volume 136, 3rd Summit on Advances in Programming Languages (SNAPL 2019)


Abstract
Leading experts have declared that there is an impending golden age of computer architecture. During this age, the rate at which architects will be able to innovate will be directly tied to the design and implementation of the hardware description languages they use. Thus, the programming languages community stands on the critical path to this new golden age. This implies that we are also on the cusp of a golden age of hardware description languages. In this paper, we discuss the intellectual challenges facing researchers interested in hardware description language design, compilers, and formal methods. The major theme will be identifying opportunities to apply programming language techniques to address issues in hardware design productivity. Then, we present a vision for a multi-language system that provides a framework for developing solutions to these intellectual problems. This vision is based on a meta-programmed host language combined with a core embedded hardware description language that is used as the basis for the research and development of a sea of domain-specific languages. Central to the design of this system is the core language which is based on an abstraction that provides a general mechanism for the composition of hardware components described in any language.

Cite as

Lenny Truong and Pat Hanrahan. A Golden Age of Hardware Description Languages: Applying Programming Language Techniques to Improve Design Productivity. In 3rd Summit on Advances in Programming Languages (SNAPL 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 136, pp. 7:1-7:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{truong_et_al:LIPIcs.SNAPL.2019.7,
  author =	{Truong, Lenny and Hanrahan, Pat},
  title =	{{A Golden Age of Hardware Description Languages: Applying Programming Language Techniques to Improve Design Productivity}},
  booktitle =	{3rd Summit on Advances in Programming Languages (SNAPL 2019)},
  pages =	{7:1--7:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-113-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{136},
  editor =	{Lerner, Benjamin S. and Bod{\'\i}k, Rastislav and Krishnamurthi, Shriram},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2019.7},
  URN =		{urn:nbn:de:0030-drops-105508},
  doi =		{10.4230/LIPIcs.SNAPL.2019.7},
  annote =	{Keywords: Hardware Description Languages}
}
Document
Blame Tracking and Type Error Debugging

Authors: Sheng Chen and John Peter Campora III

Published in: LIPIcs, Volume 136, 3rd Summit on Advances in Programming Languages (SNAPL 2019)


Abstract
In this work, we present an unexpected connection between gradual typing and type error debugging. Namely, we illustrate that gradual typing provides a natural way to defer type errors in statically ill-typed programs, providing more feedback than traditional approaches to deferring type errors. When evaluating expressions that lead to runtime type errors, the usefulness of the feedback depends on blame tracking, the defacto approach to locating the cause of such runtime type errors. Unfortunately, blame tracking suffers from the bias problem for type error localization in languages with type inference. We illustrate and formalize the bias problem for blame tracking, present ideas for adapting existing type error debugging techniques to combat this bias, and outline further challenges.

Cite as

Sheng Chen and John Peter Campora III. Blame Tracking and Type Error Debugging. In 3rd Summit on Advances in Programming Languages (SNAPL 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 136, pp. 2:1-2:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{chen_et_al:LIPIcs.SNAPL.2019.2,
  author =	{Chen, Sheng and Campora III, John Peter},
  title =	{{Blame Tracking and Type Error Debugging}},
  booktitle =	{3rd Summit on Advances in Programming Languages (SNAPL 2019)},
  pages =	{2:1--2:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-113-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{136},
  editor =	{Lerner, Benjamin S. and Bod{\'\i}k, Rastislav and Krishnamurthi, Shriram},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SNAPL.2019.2},
  URN =		{urn:nbn:de:0030-drops-105451},
  doi =		{10.4230/LIPIcs.SNAPL.2019.2},
  annote =	{Keywords: Blame tracking, type error debugging, gradual typing, type inference}
}
Document
Pearl
Finally, a Polymorphic Linear Algebra Language (Pearl)

Authors: Amir Shaikhha and Lionel Parreaux

Published in: LIPIcs, Volume 134, 33rd European Conference on Object-Oriented Programming (ECOOP 2019)


Abstract
Many different data analytics tasks boil down to linear algebra primitives. In practice, for each different type of workload, data scientists use a particular specialised library. In this paper, we present Pilatus, a polymorphic iterative linear algebra language, applicable to various types of data analytics workloads. The design of this domain-specific language (DSL) is inspired by both mathematics and programming languages: its basic constructs are borrowed from abstract algebra, whereas the key technology behind its polymorphic design uses the tagless final approach (a.k.a. polymorphic embedding/object algebras). This design enables us to change the behaviour of arithmetic operations to express matrix algebra, graph algorithms, logical probabilistic programs, and differentiable programs. Crucially, the polymorphic design of Pilatus allows us to use multi-stage programming and rewrite-based optimisation to recover the performance of specialised code, supporting fixed sized matrices, algebraic optimisations, and fusion.

Cite as

Amir Shaikhha and Lionel Parreaux. Finally, a Polymorphic Linear Algebra Language (Pearl). In 33rd European Conference on Object-Oriented Programming (ECOOP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 134, pp. 25:1-25:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{shaikhha_et_al:LIPIcs.ECOOP.2019.25,
  author =	{Shaikhha, Amir and Parreaux, Lionel},
  title =	{{Finally, a Polymorphic Linear Algebra Language}},
  booktitle =	{33rd European Conference on Object-Oriented Programming (ECOOP 2019)},
  pages =	{25:1--25:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-111-5},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{134},
  editor =	{Donaldson, Alastair F.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2019.25},
  URN =		{urn:nbn:de:0030-drops-108172},
  doi =		{10.4230/LIPIcs.ECOOP.2019.25},
  annote =	{Keywords: Linear Algebra, Domain-Specific Languages, Tagless Final, Polymorphic Embedding, Object Algebra, Multi-Stage Programming, Graph Processing, Probabilistic Programming, Automatic Differentiation}
}
Document
Garbage-Free Abstract Interpretation Through Abstract Reference Counting

Authors: Noah Van Es, Quentin Stiévenart, and Coen De Roover

Published in: LIPIcs, Volume 134, 33rd European Conference on Object-Oriented Programming (ECOOP 2019)


Abstract
Abstract garbage collection is the application of garbage collection to an abstract interpreter. Existing work has shown that abstract garbage collection can improve both the interpreter’s precision and performance. Current approaches rely on heuristics to decide when to apply abstract garbage collection. Garbage will build up and impact precision and performance when the collection is applied infrequently, while too frequent applications will bring about their own performance overhead. A balance between these tradeoffs is often difficult to strike. We propose a new approach to cope with the buildup of garbage in the results of an abstract interpreter. Our approach is able to eliminate all garbage, therefore obtaining the maximum precision and performance benefits of abstract garbage collection. At the same time, our approach does not require frequent heap traversals, and therefore adds little to the interpreters’s running time. The core of our approach uses reference counting to detect and eliminate garbage as soon as it arises. However, reference counting cannot deal with cycles, and we show that cycles are much more common in an abstract interpreter than in its concrete counterpart. To alleviate this problem, our approach detects cycles and employs reference counting at the level of strongly connected components. While this technique in general works for any system that uses reference counting, we argue that it works particularly well for an abstract interpreter. In fact, we show formally that for the continuation store, where most of the cycles occur, the cycle detection technique only requires O(1) amortized operations per continuation push. We present our approach formally, and provide a proof-of-concept implementation in the Scala-AM framework. We empirically show our approach achieves both the optimal precision and significantly better performance compared to existing approaches to abstract garbage collection.

Cite as

Noah Van Es, Quentin Stiévenart, and Coen De Roover. Garbage-Free Abstract Interpretation Through Abstract Reference Counting. In 33rd European Conference on Object-Oriented Programming (ECOOP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 134, pp. 10:1-10:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{vanes_et_al:LIPIcs.ECOOP.2019.10,
  author =	{Van Es, Noah and Sti\'{e}venart, Quentin and De Roover, Coen},
  title =	{{Garbage-Free Abstract Interpretation Through Abstract Reference Counting}},
  booktitle =	{33rd European Conference on Object-Oriented Programming (ECOOP 2019)},
  pages =	{10:1--10:33},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-111-5},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{134},
  editor =	{Donaldson, Alastair F.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2019.10},
  URN =		{urn:nbn:de:0030-drops-108022},
  doi =		{10.4230/LIPIcs.ECOOP.2019.10},
  annote =	{Keywords: abstract interpretation, abstract garbage collection, reference counting}
}
Document
Finding a Small Number of Colourful Components

Authors: Laurent Bulteau, Konrad K. Dabrowski, Guillaume Fertin, Matthew Johnson, Daniël Paulusma, and Stéphane Vialette

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


Abstract
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.

Cite as

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}
}
Document
Harnessing AI For Research

Authors: Matthew Johnson

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


Abstract
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.

Cite as

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}
}
Document
Deciding the Closure of Inconsistent Rooted Triples Is NP-Complete

Authors: Matthew P. Johnson

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


Abstract
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.

Cite as

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}
}
Document
On the Price of Independence for Vertex Cover, Feedback Vertex Set and Odd Cycle Transversal

Authors: Konrad K. Dabrowski, Matthew Johnson, Giacomo Paesani, Daniël Paulusma, and Viktor Zamaraev

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


Abstract
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).

Cite as

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}
}
Document
Independent Feedback Vertex Set for P_5-free Graphs

Authors: Marthe Bonamy, Konrad K. Dabrowski, Carl Feghali, Matthew Johnson, and Daniël Paulusma

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


Abstract
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.

Cite as

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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