18 Search Results for "Jones, Mark"

Document
Short Paper
DOI: 10.4230/OASIcs.DX.2024.25
FLEX: Fault Localization and Explanation Using Open-Source Large Language Models in Powertrain Systems (Short Paper)

Authors: Herbert Muehlburger and Franz Wotawa

Published in: OASIcs, Volume 125, 35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024)

Abstract
Cyber-physical systems (CPS) are critical to modern infrastructure, but are vulnerable to faults and anomalies that threaten their operational safety. In this work, we evaluate the use of open-source Large Language Models (LLMs), such as Mistral 7B, Llama3.1:8b-instruct-fp16, and others to detect anomalies in two distinct datasets: battery management and powertrain systems. Our methodology utilises retrieval-augmented generation (RAG) techniques, incorporating a novel two-step process where LLMs first infer operational rules from normal behavior before applying these rules for fault detection. During the experiments, we found that the original prompt design yielded strong results for the battery dataset but required modification for the powertrain dataset to improve performance. The adjusted prompt, which emphasises rule inference, significantly improved anomaly detection for the powertrain dataset. Experimental results show that models like Mistral 7B achieved F1-scores up to 0.99, while Llama3.1:8b-instruct-fp16 and Gemma 2 reached perfect F1-scores of 1.0 in complex scenarios. These findings demonstrate the impact of effective prompt design and rule inference in improving LLM-based fault detection for CPS, contributing to increased operational resilience.
Cite as

Herbert Muehlburger and Franz Wotawa. FLEX: Fault Localization and Explanation Using Open-Source Large Language Models in Powertrain Systems (Short Paper). In 35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024). Open Access Series in Informatics (OASIcs), Volume 125, pp. 25:1-25:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{muehlburger_et_al:OASIcs.DX.2024.25,
  author =	{Muehlburger, Herbert and Wotawa, Franz},
  title =	{{FLEX: Fault Localization and Explanation Using Open-Source Large Language Models in Powertrain Systems}},
  booktitle =	{35th International Conference on Principles of Diagnosis and Resilient Systems (DX 2024)},
  pages =	{25:1--25:14},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-356-0},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{125},
  editor =	{Pill, Ingo and Natan, Avraham and Wotawa, Franz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.DX.2024.25},
  URN =		{urn:nbn:de:0030-drops-221170},
  doi =		{10.4230/OASIcs.DX.2024.25},
  annote =	{Keywords: Fault detection, anomaly detection, powertrain systems, large language models, open-source LLMs}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.33
Compiling with Arrays

Authors: David Richter, Timon Böhler, Pascal Weisenburger, and Mira Mezini

Published in: LIPIcs, Volume 313, 38th European Conference on Object-Oriented Programming (ECOOP 2024)

Abstract
Linear algebra computations are foundational for neural networks and machine learning, often handled through arrays. While many functional programming languages feature lists and recursion, arrays in linear algebra demand constant-time access and bulk operations. To bridge this gap, some languages represent arrays as (eager) functions instead of lists. In this paper, we connect this idea to a formal logical foundation by interpreting functions as the usual negative types from polarized type theory, and arrays as the corresponding dual positive version of the function type. Positive types are defined to have a single elimination form whose computational interpretation is pattern matching. Just like (positive) product types bind two variables during pattern matching, (positive) array types bind variables with multiplicity during pattern matching. We follow a similar approach for Booleans by introducing conditionally-defined variables. The positive formulation for the array type enables us to combine typed partial evaluation and common subexpression elimination into an elegant algorithm whose result enjoys a property we call maximal fission, which we argue can be beneficial for further optimizations. For this purpose, we present the novel intermediate representation indexed administrative normal form (A_{i}NF), which relies on the formal logical foundation of the positive formulation for the array type to facilitate maximal loop fission and subsequent optimizations. A_{i}NF is normal with regard to commuting conversion for both let-bindings and for-loops, leading to flat and maximally fissioned terms. We mechanize the translation and normalization from a simple surface language to A_{i}NF, establishing that the process terminates, preserves types, and produces maximally fissioned terms.
Cite as

David Richter, Timon Böhler, Pascal Weisenburger, and Mira Mezini. Compiling with Arrays. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 33:1-33:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{richter_et_al:LIPIcs.ECOOP.2024.33,
  author =	{Richter, David and B\"{o}hler, Timon and Weisenburger, Pascal and Mezini, Mira},
  title =	{{Compiling with Arrays}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{33:1--33:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-341-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{313},
  editor =	{Aldrich, Jonathan and Salvaneschi, Guido},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2024.33},
  URN =		{urn:nbn:de:0030-drops-208823},
  doi =		{10.4230/LIPIcs.ECOOP.2024.33},
  annote =	{Keywords: array languages, functional programming, domain-specific languages, normalization by evaluation, common subexpression elimination, polarity, positive function type, intrinsic types}
}
Document
DOI: 10.4230/LIPIcs.CP.2024.20
Constraint Modelling with LLMs Using In-Context Learning

Authors: Kostis Michailidis, Dimos Tsouros, and Tias Guns

Published in: LIPIcs, Volume 307, 30th International Conference on Principles and Practice of Constraint Programming (CP 2024)

Abstract
Constraint Programming (CP) allows for the modelling and solving of a wide range of combinatorial problems. However, modelling such problems using constraints over decision variables still requires significant expertise, both in conceptual thinking and syntactic use of modelling languages. In this work, we explore the potential of using pre-trained Large Language Models (LLMs) as coding assistants, to transform textual problem descriptions into concrete and executable CP specifications. We present different transformation pipelines with explicit intermediate representations, and we investigate the potential benefit of various retrieval-augmented example selection strategies for in-context learning. We evaluate our approach on 2 datasets from the literature, namely NL4Opt (optimisation) and Logic Grid Puzzles (satisfaction), and a heterogeneous set of exercises from a CP course. The results show that pre-trained LLMs have promising potential for initialising the modelling process, with retrieval-augmented in-context learning significantly enhancing their modelling capabilities.
Cite as

Kostis Michailidis, Dimos Tsouros, and Tias Guns. Constraint Modelling with LLMs Using In-Context Learning. In 30th International Conference on Principles and Practice of Constraint Programming (CP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 307, pp. 20:1-20:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{michailidis_et_al:LIPIcs.CP.2024.20,
  author =	{Michailidis, Kostis and Tsouros, Dimos and Guns, Tias},
  title =	{{Constraint Modelling with LLMs Using In-Context Learning}},
  booktitle =	{30th International Conference on Principles and Practice of Constraint Programming (CP 2024)},
  pages =	{20:1--20:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-336-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{307},
  editor =	{Shaw, Paul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CP.2024.20},
  URN =		{urn:nbn:de:0030-drops-207053},
  doi =		{10.4230/LIPIcs.CP.2024.20},
  annote =	{Keywords: Constraint Modelling, Constraint Acquisition, Constraint Programming, Large Language Models, In-Context Learning, Natural Language Processing, Named Entity Recognition, Retrieval-Augmented Generation, Optimisation}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.9
Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation

Authors: Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The 𝒞-Orientation problem asks whether it is possible to orient an undirected graph to a directed phylogenetic network of a desired class 𝒞, and to find such an orientation if one exists. The problem can arise when visualising evolutionary data, for example, because popular phylogenetic network reconstruction methods such as Neighbor-Net are distance-based and thus inevitably produce undirected graphs. The complexity of 𝒞-Orientation remains open for many classes 𝒞, including binary tree-child networks, and practical methods are still lacking. In this paper, we propose an exponential but practically efficient FPT algorithm for 𝒞-Orientation, which is parameterised by the reticulation number and the maximum size of minimal basic cycles used in the computation. We also present a very fast heuristic for Tree-Child Orientation. To evaluate the empirical performance of the proposed methods, we compared their accuracy and execution time for Tree-Child Orientation with those of an exponential time 𝒞-orientation algorithm from the literature. Our experiments show that the proposed exact algorithm is significantly faster than the state-of-the-art exponential time algorithm. The proposed heuristic runs even faster but the accuracy decreases as the reticulation number increases.
Cite as

Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu. Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{urata_et_al:LIPIcs.WABI.2024.9,
  author =	{Urata, Tsuyoshi and Yokoyama, Manato and Hayamizu, Momoko},
  title =	{{Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{9:1--9:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.9},
  URN =		{urn:nbn:de:0030-drops-206531},
  doi =		{10.4230/LIPIcs.WABI.2024.9},
  annote =	{Keywords: Phylogenetic Networks, Tree-Child Networks, Graph Orientation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.23
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.
Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.12
Reconstructing Rearrangement Phylogenies of Natural Genomes

Authors: Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
We study the classical problem of inferring ancestral genomes from a set of extant genomes under a given phylogeny, known as the Small Parsimony Problem (SPP). Genomes are represented as sequences of oriented markers, organized in one or more linear or circular chromosomes. Any marker may appear in several copies, without restriction on orientation or genomic location, known as the natural genomes model. Evolutionary events along the branches of the phylogeny encompass large scale rearrangements, including segmental inversions, translocations, gain and loss (DCJ-indel model). Even under simpler rearrangement models, such as the classical breakpoint model without duplicates, the SPP is computationally intractable. Nevertheless, the SPP for natural genomes under the DCJ-indel model has been studied recently, with limited success. Here, we improve on that earlier work, giving a highly optimized ILP that is able to solve the SPP for sufficiently small phylogenies and gene families. A notable improvement w.r.t. the previous result is an optimized way of handling both circular and linear chromosomes. This is especially relevant to the SPP, since the chromosomal structure of ancestral genomes is unknown and the solution space for this chromosomal structure is typically large. We benchmark our method on simulated and real data. On simulated phylogenies we observe a considerable performance improvement on problems that include linear chromosomes. And even when the ground truth contains only one circular chromosome per genome, our method outperforms its predecessor due to its optimized handling of the solution space. The practical advantage becomes also visible in an analysis of seven Anopheles taxa.
Cite as

Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr. Reconstructing Rearrangement Phylogenies of Natural Genomes. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bohnenkamper_et_al:LIPIcs.WABI.2024.12,
  author =	{Bohnenk\"{a}mper, Leonard and Stoye, Jens and D\"{o}rr, Daniel},
  title =	{{Reconstructing Rearrangement Phylogenies of Natural Genomes}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.12},
  URN =		{urn:nbn:de:0030-drops-206564},
  doi =		{10.4230/LIPIcs.WABI.2024.12},
  annote =	{Keywords: genome rearrangement, ancestral reconstruction, small parsimony, integer linear programming, double-cut-and-join}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2023.30
How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks

Authors: Mark Jones and Jannik Schestag

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)

Abstract
Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. We consider an extension of PD to phylogenetic networks. Given a phylogenetic network with weighted edges and a subset S of leaves, the all-paths phylogenetic diversity of S is the summed weight of all edges on a path from the root to some leaf in S. The problem of finding a bounded-size set S that maximizes this measure is polynomial-time solvable on trees, but NP-hard on networks. We study the latter from a parameterized perspective. While this problem is W[2]-hard with respect to the size of S (and W[1]-hard with respect to the size of the complement of S), we show that it is FPT with respect to several other parameters, including the phylogenetic diversity of S, the acceptable loss of phylogenetic diversity, the number of reticulations in the network, and the treewidth of the underlying graph.
Cite as

Mark Jones and Jannik Schestag. How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 30:1-30:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{jones_et_al:LIPIcs.IPEC.2023.30,
  author =	{Jones, Mark and Schestag, Jannik},
  title =	{{How Can We Maximize Phylogenetic Diversity? Parameterized Approaches for Networks}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{30:1--30:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.30},
  URN =		{urn:nbn:de:0030-drops-194496},
  doi =		{10.4230/LIPIcs.IPEC.2023.30},
  annote =	{Keywords: Phylogenetic Networks, Phylogenetic Diversity, Parameterized Complexity, W-hierarchy, FPT algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2023.7
Making a Network Orchard by Adding Leaves

Authors: Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here, we study the minimum number of additional leaves needed to make a network orchard. We demonstrate that computing this proximity measure for a given network is NP-hard and describe a tight upper bound. We also give an equivalent measure based on vertex labellings to construct a mixed integer linear programming formulation. Our experimental results, which include both real-world and synthetic data, illustrate the efficiency of our implementation.
Cite as

Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami. Making a Network Orchard by Adding Leaves. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 7:1-7:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{vaniersel_et_al:LIPIcs.WABI.2023.7,
  author =	{van Iersel, Leo and Jones, Mark and Julien, Esther and Murakami, Yukihiro},
  title =	{{Making a Network Orchard by Adding Leaves}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{7:1--7:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.7},
  URN =		{urn:nbn:de:0030-drops-186333},
  doi =		{10.4230/LIPIcs.WABI.2023.7},
  annote =	{Keywords: Phylogenetics, Network, Orchard Networks, Proximity Measures, NP-hardness}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.69
Embedding Phylogenetic Trees in Networks of Low Treewidth

Authors: Leo van Iersel, Mark Jones, and Mathias Weller

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Abstract
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called Tree Containment, arises when validating networks constructed by phylogenetic inference methods. We present the first algorithm for (rooted) Tree Containment using the treewidth t of the input network N as parameter, showing that the problem can be solved in 2^O(t²)⋅|N| time and space.
Cite as

Leo van Iersel, Mark Jones, and Mathias Weller. Embedding Phylogenetic Trees in Networks of Low Treewidth. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 69:1-69:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{vaniersel_et_al:LIPIcs.ESA.2022.69,
  author =	{van Iersel, Leo and Jones, Mark and Weller, Mathias},
  title =	{{Embedding Phylogenetic Trees in Networks of Low Treewidth}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{69:1--69:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2022.69},
  URN =		{urn:nbn:de:0030-drops-170070},
  doi =		{10.4230/LIPIcs.ESA.2022.69},
  annote =	{Keywords: fixed-parameter tractability, treewidth, phylogenetic tree, phylogenetic network, display graph, tree containment, embedding}
}
Document
DOI: 10.4230/LIPIcs.CPM.2022.6
An FPT-Algorithm for Longest Common Subsequence Parameterized by the Maximum Number of Deletions

Authors: Laurent Bulteau, Mark Jones, Rolf Niedermeier, and Till Tantau

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

Abstract
In the NP-hard Longest Common Subsequence problem (LCS), given a set of strings, the task is to find a string that can be obtained from every input string using as few deletions as possible. LCS is one of the most fundamental string problems with numerous applications in various areas, having gained a lot of attention in the algorithms and complexity research community. Significantly improving on an algorithm by Irving and Fraser [CPM'92], featured as a research challenge in a 2014 survey paper, we show that LCS is fixed-parameter tractable (FPT) when parameterized by the maximum number of deletions per input string. Given the relatively moderate running time of our algorithm (linear time when the parameter is a constant) and small parameter values to be expected in several applications, we believe that our purely theoretical analysis could finally pave the way to a new, exact and practically useful algorithm for this notoriously hard string problem.
Cite as

Laurent Bulteau, Mark Jones, Rolf Niedermeier, and Till Tantau. An FPT-Algorithm for Longest Common Subsequence Parameterized by the Maximum Number of Deletions. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 6:1-6:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{bulteau_et_al:LIPIcs.CPM.2022.6,
  author =	{Bulteau, Laurent and Jones, Mark and Niedermeier, Rolf and Tantau, Till},
  title =	{{An FPT-Algorithm for Longest Common Subsequence Parameterized by the Maximum Number of Deletions}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{6:1--6:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.6},
  URN =		{urn:nbn:de:0030-drops-161338},
  doi =		{10.4230/LIPIcs.CPM.2022.6},
  annote =	{Keywords: NP-hard string problems, multiple sequence alignment, center string, parameterized complexity, search tree algorithms, enumerative algorithms}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2022.51
A Complete Linear Programming Hierarchy for Linear Codes

Authors: Leonardo Nagami Coregliano, Fernando Granha Jeronimo, and Chris Jones

Published in: LIPIcs, Volume 215, 13th Innovations in Theoretical Computer Science Conference (ITCS 2022)

Abstract
A longstanding open problem in coding theory is to determine the best (asymptotic) rate R₂(δ) of binary codes with minimum constant (relative) distance δ. An existential lower bound was given by Gilbert and Varshamov in the 1950s. On the impossibility side, in the 1970s McEliece, Rodemich, Rumsey and Welch (MRRW) proved an upper bound by analyzing Delsarte’s linear programs. To date these results remain the best known lower and upper bounds on R₂(δ) with no improvement even for the important class of linear codes. Asymptotically, these bounds differ by an exponential factor in the blocklength. In this work, we introduce a new hierarchy of linear programs (LPs) that converges to the true size A^{Lin}₂(n,d) of an optimum linear binary code (in fact, over any finite field) of a given blocklength n and distance d. This hierarchy has several notable features: 1) It is a natural generalization of the Delsarte LPs used in the first MRRW bound. 2) It is a hierarchy of linear programs rather than semi-definite programs potentially making it more amenable to theoretical analysis. 3) It is complete in the sense that the optimum code size can be retrieved from level O(n²). 4) It provides an answer in the form of a hierarchy (in larger dimensional spaces) to the question of how to cut Delsarte’s LP polytopes to approximate the true size of linear codes. We obtain our hierarchy by generalizing the Krawtchouk polynomials and MacWilliams inequalities to a suitable "higher-order" version taking into account interactions of 𝓁 words. Our method also generalizes to translation schemes under mild assumptions.
Cite as

Leonardo Nagami Coregliano, Fernando Granha Jeronimo, and Chris Jones. A Complete Linear Programming Hierarchy for Linear Codes. In 13th Innovations in Theoretical Computer Science Conference (ITCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 215, pp. 51:1-51:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{coregliano_et_al:LIPIcs.ITCS.2022.51,
  author =	{Coregliano, Leonardo Nagami and Jeronimo, Fernando Granha and Jones, Chris},
  title =	{{A Complete Linear Programming Hierarchy for Linear Codes}},
  booktitle =	{13th Innovations in Theoretical Computer Science Conference (ITCS 2022)},
  pages =	{51:1--51:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-217-4},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{215},
  editor =	{Braverman, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2022.51},
  URN =		{urn:nbn:de:0030-drops-156474},
  doi =		{10.4230/LIPIcs.ITCS.2022.51},
  annote =	{Keywords: Coding theory, code bounds, convex programming, linear programming hierarchy}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2022.89
Almost-Orthogonal Bases for Inner Product Polynomials

Authors: Chris Jones and Aaron Potechin

Published in: LIPIcs, Volume 215, 13th Innovations in Theoretical Computer Science Conference (ITCS 2022)

Abstract
In this paper, we consider low-degree polynomials of inner products between a collection of random vectors. We give an almost orthogonal basis for this vector space of polynomials when the random vectors are Gaussian, spherical, or Boolean. In all three cases, our basis admits an interesting combinatorial description based on the topology of the underlying graph of inner products. We also analyze the expected value of the product of two polynomials in our basis. In all three cases, we show that this expected value can be expressed in terms of collections of matchings on the underlying graph of inner products. In the Gaussian and Boolean cases, we show that this expected value is always non-negative. In the spherical case, we show that this expected value can be negative but we conjecture that if the underlying graph of inner products is planar then this expected value will always be non-negative.
Cite as

Chris Jones and Aaron Potechin. Almost-Orthogonal Bases for Inner Product Polynomials. In 13th Innovations in Theoretical Computer Science Conference (ITCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 215, pp. 89:1-89:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{jones_et_al:LIPIcs.ITCS.2022.89,
  author =	{Jones, Chris and Potechin, Aaron},
  title =	{{Almost-Orthogonal Bases for Inner Product Polynomials}},
  booktitle =	{13th Innovations in Theoretical Computer Science Conference (ITCS 2022)},
  pages =	{89:1--89:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-217-4},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{215},
  editor =	{Braverman, Mark},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2022.89},
  URN =		{urn:nbn:de:0030-drops-156853},
  doi =		{10.4230/LIPIcs.ITCS.2022.89},
  annote =	{Keywords: Orthogonal polynomials, Fourier analysis, combinatorics}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2015.43
Parameterized and Approximation Algorithms for the Load Coloring Problem

Authors: Florian Barbero, Gregory Gutin, Mark Jones, and Bin Sheng

Published in: LIPIcs, Volume 43, 10th International Symposium on Parameterized and Exact Computation (IPEC 2015)

Abstract
Let c, k be two positive integers. Given a graph G=(V,E), the c-Load Coloring problem asks whether there is a c-coloring varphi: V => [c] such that for every i in [c], there are at least k edges with both endvertices colored i. Gutin and Jones (IPL 2014) studied this problem with c=2. They showed 2-Load Coloring to be fixed-parameter tractable (FPT) with parameter k by obtaining a kernel with at most 7k vertices. In this paper, we extend the study to any fixed c by giving both a linear-vertex and a linear-edge kernel. In the particular case of c=2, we obtain a kernel with less than 4k vertices and less than 8k edges. These results imply that for any fixed c >= 2, c-Load Coloring is FPT and the optimization version of c-Load Coloring (where k is to be maximized) has an approximation algorithm with a constant ratio.
Cite as

Florian Barbero, Gregory Gutin, Mark Jones, and Bin Sheng. Parameterized and Approximation Algorithms for the Load Coloring Problem. In 10th International Symposium on Parameterized and Exact Computation (IPEC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 43, pp. 43-54, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{barbero_et_al:LIPIcs.IPEC.2015.43,
  author =	{Barbero, Florian and Gutin, Gregory and Jones, Mark and Sheng, Bin},
  title =	{{Parameterized and Approximation Algorithms for the Load Coloring Problem}},
  booktitle =	{10th International Symposium on Parameterized and Exact Computation (IPEC 2015)},
  pages =	{43--54},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-92-7},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{43},
  editor =	{Husfeldt, Thore and Kanj, Iyad},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2015.43},
  URN =		{urn:nbn:de:0030-drops-55703},
  doi =		{10.4230/LIPIcs.IPEC.2015.43},
  annote =	{Keywords: Load Coloring, fixed-parameter tractability, kernelization}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2015.66
On the Workflow Satisfiability Problem with Class-independent Constraints

Authors: Jason Crampton, Andrei Gagarin, Gregory Gutin, and Mark Jones

Published in: LIPIcs, Volume 43, 10th International Symposium on Parameterized and Exact Computation (IPEC 2015)

Abstract
A workflow specification defines sets of steps and users. An authorization policy determines for each user a subset of steps the user is allowed to perform. Other security requirements, such as separation-of-duty, impose constraints on which subsets of users may perform certain subsets of steps. The workflow satisfiability problem (WSP) is the problem of determining whether there exists an assignment of users to workflow steps that satisfies all such authorizations and constraints. An algorithm for solving WSP is important, both as a static analysis tool for workflow specifications, and for the construction of run-time reference monitors for workflow management systems. Given the computational difficulty of WSP, it is important, particularly for the second application, that such algorithms are as efficient as possible. We introduce class-independent constraints, enabling us to model scenarios where the set of users is partitioned into groups, and the identities of the user groups are irrelevant to the satisfaction of the constraint. We prove that solving WSP is fixed-parameter tractable (FPT) for this class of constraints and develop an FPT algorithm that is useful in practice. We compare the performance of the FPT algorithm with that of SAT4J (a pseudo-Boolean SAT solver) in computational experiments, which show that our algorithm significantly outperforms SAT4J for many instances of WSP. User-independent constraints, a large class of constraints including many practical ones, are a special case of class-independent constraints for which WSP was proved to be FPT (Cohen et al., J. Artif. Intel. Res. 2014). Thus our results considerably extend our knowledge of the fixed-parameter tractability of WSP.
Cite as

Jason Crampton, Andrei Gagarin, Gregory Gutin, and Mark Jones. On the Workflow Satisfiability Problem with Class-independent Constraints. In 10th International Symposium on Parameterized and Exact Computation (IPEC 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 43, pp. 66-77, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)

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@InProceedings{crampton_et_al:LIPIcs.IPEC.2015.66,
  author =	{Crampton, Jason and Gagarin, Andrei and Gutin, Gregory and Jones, Mark},
  title =	{{On the Workflow Satisfiability Problem with Class-independent Constraints}},
  booktitle =	{10th International Symposium on Parameterized and Exact Computation (IPEC 2015)},
  pages =	{66--77},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-92-7},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{43},
  editor =	{Husfeldt, Thore and Kanj, Iyad},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2015.66},
  URN =		{urn:nbn:de:0030-drops-55727},
  doi =		{10.4230/LIPIcs.IPEC.2015.66},
  annote =	{Keywords: Workflow Satisfiability Problem; Constraint Satisfaction Problem; fixed-parameter tractability; user-independent constraints}
}
Document
DOI: 10.4230/LIPIcs.FSTTCS.2013.43
Polynomial Kernels for lambda-extendible Properties Parameterized Above the Poljak-Turzik Bound

Authors: Robert Crowston, Mark Jones, Gabriele Muciaccia, Geevarghese Philip, Ashutosh Rai, and Saket Saurabh

Published in: LIPIcs, Volume 24, IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2013)

Abstract
Poljak and Turzik (Discrete Mathematics 1986) introduced the notion of lambda-extendible properties of graphs as a generalization of the property of being bipartite. They showed that for any 0<lambda<1 and lambda-extendible property Pi, any connected graph G on n vertices and m edges contains a spanning subgraph H in Pi with at least lambda*m+(1-lambda)(n-1)/2 edges. The property of being bipartite is lambda-extendible for lambda =1/2, and so the Poljak-Turzik bound generalizes the well-known Edwards-Erdos bound for Max Cut. Other examples of lambda-extendible properties include: being an acyclic oriented graph, a balanced signed graph, or a q-colorable graph for some q in N. Mnich et al. (FSTTCS 2012) defined the closely related notion of strong lambda-extendibility. They showed that the problem of finding a subgraph satisfying a given strongly lambda-extendible property Pi is fixed-parameter tractable (FPT) when parameterized above the Poljak-Turzik bound---does there exist a spanning subgraph H of a connected graph G such that H in Pi and H has at least lambda*m+(1-lambda)(n-1)/2+k edges?---subject to the condition that the problem is FPT on a certain simple class of graphs called almost-forests of cliques. This generalized an earlier result of Crowston et al. (ICALP 2012) for Max Cut, to all strongly lambda-extendible properties which satisfy the additional criterion. In this paper we settle the kernelization complexity of nearly all problems parameterized above Poljak-Turzik bounds, in the affirmative. We show that these problems admit quadratic kernels (cubic when lambda=1/2), without using the assumption that the problem is FPT on almost-forests of cliques. Thus our results not only remove the technical condition of being FPT on almost-forests of cliques from previous results, but also unify and extend previously known kernelization results in this direction. Our results add to the select list of generic kernelization results known in the literature.
Cite as

Robert Crowston, Mark Jones, Gabriele Muciaccia, Geevarghese Philip, Ashutosh Rai, and Saket Saurabh. Polynomial Kernels for lambda-extendible Properties Parameterized Above the Poljak-Turzik Bound. In IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2013). Leibniz International Proceedings in Informatics (LIPIcs), Volume 24, pp. 43-54, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)

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@InProceedings{crowston_et_al:LIPIcs.FSTTCS.2013.43,
  author =	{Crowston, Robert and Jones, Mark and Muciaccia, Gabriele and Philip, Geevarghese and Rai, Ashutosh and Saurabh, Saket},
  title =	{{Polynomial Kernels for lambda-extendible Properties Parameterized Above the Poljak-Turzik Bound}},
  booktitle =	{IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2013)},
  pages =	{43--54},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-64-4},
  ISSN =	{1868-8969},
  year =	{2013},
  volume =	{24},
  editor =	{Seth, Anil and Vishnoi, Nisheeth K.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2013.43},
  URN =		{urn:nbn:de:0030-drops-43599},
  doi =		{10.4230/LIPIcs.FSTTCS.2013.43},
  annote =	{Keywords: Kernelization, Lambda Extension, Above-Guarantee Parameterization, MaxCut}
}
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