22 Search Results for "Mark, David M."

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.ESA.2024.97
Engineering Edge Orientation Algorithms

Authors: Henrik Reinstädtler, Christian Schulz, and Bora Uçar

Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)

Abstract
Given an undirected graph G, the edge orientation problem asks for assigning a direction to each edge to convert G into a directed graph. The aim is to minimize the maximum out-degree of a vertex in the resulting directed graph. This problem, which is solvable in polynomial time, arises in many applications. An ongoing challenge in edge orientation algorithms is their scalability, particularly in handling large-scale networks with millions or billions of edges efficiently. We propose a novel algorithmic framework based on finding and manipulating simple paths to face this challenge. Our framework is based on an existing algorithm and allows many algorithmic choices. By carefully exploring these choices and engineering the underlying algorithms, we obtain an implementation which is more efficient and scalable than the current state-of-the-art. Our experiments demonstrate significant performance improvements compared to state-of-the-art solvers. On average our algorithm is 6.59 times faster when compared to the state-of-the-art.
Cite as

Henrik Reinstädtler, Christian Schulz, and Bora Uçar. Engineering Edge Orientation Algorithms. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 97:1-97:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{reinstadtler_et_al:LIPIcs.ESA.2024.97,
  author =	{Reinst\"{a}dtler, Henrik and Schulz, Christian and U\c{c}ar, Bora},
  title =	{{Engineering Edge Orientation Algorithms}},
  booktitle =	{32nd Annual European Symposium on Algorithms (ESA 2024)},
  pages =	{97:1--97:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-338-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{308},
  editor =	{Chan, Timothy and Fischer, Johannes and Iacono, John 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.2024.97},
  URN =		{urn:nbn:de:0030-drops-211682},
  doi =		{10.4230/LIPIcs.ESA.2024.97},
  annote =	{Keywords: edge orientation, pseudoarboricity, graph algorithms}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2024.6
Cross Module Quickening - The Curious Case of C Extensions

Authors: Felix Berlakovich and Stefan Brunthaler

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

Abstract
Dynamic programming languages such as Python offer expressive power and programmer productivity at the expense of performance. Although the topic of optimizing Python has received considerable attention over the years, a key obstacle remains elusive: C extensions. Time and again, optimized run-time environments, such as JIT compilers and optimizing interpreters, fall short of optimizing across C extensions, as they cannot reason about the native code hiding underneath. To bridge this gap, we present an analysis of C extensions for Python. The analysis data indicates that C extensions come in different varieties. One such variety is to merely speed up a single thing, such as reading a file and processing it directly in C. Another variety offers broad access through an API, resulting in a domain-specific language realized by function calls. While the former variety of C extensions offer little optimization potential for optimizing run-times, we find that the latter variety does offer considerable optimization potential. This optimization potential rests on dynamic locality that C extensions cannot readily tap. We introduce a new, interpreter-based optimization leveraging this untapped optimization potential called Cross-Module Quickening. The key idea is that C extensions can use an optimization interface to register highly-optimized operations on C extension-specific datatypes. A quickening interpreter uses these information to continuously specialize programs with C extensions. To quantify the attainable performance potential of going beyond C extensions, we demonstrate a concrete instantiation of Cross-Module Quickening for the CPython interpreter and the popular NumPy C extension. We evaluate our implementation with the NPBench benchmark suite and report performance improvements by a factor of up to 2.84.
Cite as

Felix Berlakovich and Stefan Brunthaler. Cross Module Quickening - The Curious Case of C Extensions. In 38th European Conference on Object-Oriented Programming (ECOOP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 313, pp. 6:1-6:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{berlakovich_et_al:LIPIcs.ECOOP.2024.6,
  author =	{Berlakovich, Felix and Brunthaler, Stefan},
  title =	{{Cross Module Quickening - The Curious Case of C Extensions}},
  booktitle =	{38th European Conference on Object-Oriented Programming (ECOOP 2024)},
  pages =	{6:1--6:29},
  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.2024.6},
  URN =		{urn:nbn:de:0030-drops-208557},
  doi =		{10.4230/LIPIcs.ECOOP.2024.6},
  annote =	{Keywords: interpreter, optimizations, C extensions, Python}
}
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.DNA.30.4
Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops

Authors: Antti Elonen and Pekka Orponen

Published in: LIPIcs, Volume 314, 30th International Conference on DNA Computing and Molecular Programming (DNA 30) (2024)

Abstract
We present a general design technique for rendering any 3D wireframe model, that is any connected graph linearly embedded in 3D space, as an RNA origami nanostructure with a minimum number of kissing loops. The design algorithm, which applies some ideas and methods from topological graph theory, produces renderings that contain at most one kissing-loop pair for many interesting model families, including for instance all fully triangulated wireframes and the wireframes of all Platonic solids. The design method is already implemented and available for use in the design tool DNAforge (https://dnaforge.org).
Cite as

Antti Elonen and Pekka Orponen. Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops. In 30th International Conference on DNA Computing and Molecular Programming (DNA 30). Leibniz International Proceedings in Informatics (LIPIcs), Volume 314, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{elonen_et_al:LIPIcs.DNA.30.4,
  author =	{Elonen, Antti and Orponen, Pekka},
  title =	{{Designing 3D RNA Origami Nanostructures with a Minimum Number of Kissing Loops}},
  booktitle =	{30th International Conference on DNA Computing and Molecular Programming (DNA 30)},
  pages =	{4:1--4:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-344-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{314},
  editor =	{Seki, Shinnosuke and Stewart, Jaimie Marie},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.DNA.30.4},
  URN =		{urn:nbn:de:0030-drops-209325},
  doi =		{10.4230/LIPIcs.DNA.30.4},
  annote =	{Keywords: RNA origami, wireframe nanostructures, polyhedra, kissing loops, topological graph embeddings, self-assembly}
}
Document
DOI: 10.4230/LIPIcs.ITP.2024.35
Formal Verification of the Empty Hexagon Number

Authors: Bernardo Subercaseaux, Wojciech Nawrocki, James Gallicchio, Cayden Codel, Mario Carneiro, and Marijn J. H. Heule

Published in: LIPIcs, Volume 309, 15th International Conference on Interactive Theorem Proving (ITP 2024)

Abstract
A recent breakthrough in computer-assisted mathematics showed that every set of 30 points in the plane in general position (i.e., no three points on a common line) contains an empty convex hexagon. Heule and Scheucher solved this problem with a combination of geometric insights and automated reasoning techniques by constructing CNF formulas ϕ_n, with O(n⁴) clauses, such that if ϕ_n is unsatisfiable then every set of n points in general position must contain an empty convex hexagon. An unsatisfiability proof for n = 30 was then found with a SAT solver using 17 300 CPU hours of parallel computation. In this paper, we formalize and verify this result in the Lean theorem prover. Our formalization covers ideas in discrete computational geometry and SAT encoding techniques by introducing a framework that connects geometric objects to propositional assignments. We see this as a key step towards the formal verification of other SAT-based results in geometry, since the abstractions we use have been successfully applied to similar problems. Overall, we hope that our work sets a new standard for the verification of geometry problems relying on extensive computation, and that it increases the trust the mathematical community places in computer-assisted proofs.
Cite as

Bernardo Subercaseaux, Wojciech Nawrocki, James Gallicchio, Cayden Codel, Mario Carneiro, and Marijn J. H. Heule. Formal Verification of the Empty Hexagon Number. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 35:1-35:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{subercaseaux_et_al:LIPIcs.ITP.2024.35,
  author =	{Subercaseaux, Bernardo and Nawrocki, Wojciech and Gallicchio, James and Codel, Cayden and Carneiro, Mario and Heule, Marijn J. H.},
  title =	{{Formal Verification of the Empty Hexagon Number}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{35:1--35:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-337-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{309},
  editor =	{Bertot, Yves and Kutsia, Temur and Norrish, Michael},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITP.2024.35},
  URN =		{urn:nbn:de:0030-drops-207633},
  doi =		{10.4230/LIPIcs.ITP.2024.35},
  annote =	{Keywords: Empty Hexagon Number, Discrete Computational Geometry, Erd\H{o}s-Szekeres}
}
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.CP.2024.10
Anytime Weighted Model Counting with Approximation Guarantees for Probabilistic Inference

Authors: Alexandre Dubray, Pierre Schaus, and Siegfried Nijssen

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

Abstract
Weighted model counting (WMC) plays a central role in probabilistic reasoning. Given that this problem is #P-hard, harder instances can generally only be addressed using approximate techniques based on sampling, which provide statistical convergence guarantees: the longer a sampling process runs, the more accurate the WMC is likely to be. In this work, we propose a deterministic search-based approach that can also be stopped at any time and provides hard lower- and upper-bound guarantees on the true WMC. This approach uses a value heuristic that guides exploration first towards models with a high weight and leverages Limited Discrepancy Search to make the bounds converge faster. The validity, scalability, and convergence of our approach are tested and compared with state-of-the-art baseline methods on the problem of computing marginal probabilities in Bayesian networks and reliability estimation in probabilistic graphs.
Cite as

Alexandre Dubray, Pierre Schaus, and Siegfried Nijssen. Anytime Weighted Model Counting with Approximation Guarantees for Probabilistic Inference. In 30th International Conference on Principles and Practice of Constraint Programming (CP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 307, pp. 10:1-10:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dubray_et_al:LIPIcs.CP.2024.10,
  author =	{Dubray, Alexandre and Schaus, Pierre and Nijssen, Siegfried},
  title =	{{Anytime Weighted Model Counting with Approximation Guarantees for Probabilistic Inference}},
  booktitle =	{30th International Conference on Principles and Practice of Constraint Programming (CP 2024)},
  pages =	{10:1--10:16},
  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.2024.10},
  URN =		{urn:nbn:de:0030-drops-206956},
  doi =		{10.4230/LIPIcs.CP.2024.10},
  annote =	{Keywords: Projected Weighted Model Counting, Limited Discrepancy Search, Approximate Method, Probabilistic Inference}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

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

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  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.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, 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.2024.8
Applying the Safe-And-Complete Framework to Practical Genome Assembly

Authors: Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu

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

Abstract
Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.
Cite as

Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8,
  author =	{Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.},
  title =	{{Applying the Safe-And-Complete Framework to Practical Genome Assembly}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{8:1--8:16},
  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.2024.8},
  URN =		{urn:nbn:de:0030-drops-206520},
  doi =		{10.4230/LIPIcs.WABI.2024.8},
  annote =	{Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation}
}
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.SAT.2024.15
Antichain with SAT and Tries

Authors: Lukáš Holík and Pavol Vargovčík

Published in: LIPIcs, Volume 305, 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)

Abstract
We introduce a SAT-enabled version of an antichain algorithm for checking language emptiness of alternating finite automata (AFA) with complex transition relations encoded as compact logical formulae. The SAT solver is used to compute predecessors of AFA configurations, and at the same time, to evaluate the subsumption of newly found configurations in the antichain of the previously found ones. The algorithm could be naively implemented by an incremental SAT solver where the growing antichain is represented by adding new clauses. To make it efficient, we 1) force the SAT solver to prioritize largest/subsumption-strongest predecessors (so that weaker configurations are not even generated), and 2) store the antichain clauses in a special variant of a trie that allows fast subsumption testing. The experimental results suggest that the resulting emptiness checker is very efficient compared to the state of the art and that our techniques improve the performance of the SAT solver.
Cite as

Lukáš Holík and Pavol Vargovčík. Antichain with SAT and Tries. In 27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 305, pp. 15:1-15:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{holik_et_al:LIPIcs.SAT.2024.15,
  author =	{Hol{\'\i}k, Luk\'{a}\v{s} and Vargov\v{c}{\'\i}k, Pavol},
  title =	{{Antichain with SAT and Tries}},
  booktitle =	{27th International Conference on Theory and Applications of Satisfiability Testing (SAT 2024)},
  pages =	{15:1--15:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-334-8},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{305},
  editor =	{Chakraborty, Supratik and Jiang, Jie-Hong Roland},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAT.2024.15},
  URN =		{urn:nbn:de:0030-drops-205372},
  doi =		{10.4230/LIPIcs.SAT.2024.15},
  annote =	{Keywords: SAT, Trie, Antichain, Alternating automata, Subset query}
}
Document
DOI: 10.4230/DagMan.10.1.1
Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282)

Authors: James P. Delgrande, Birte Glimm, Thomas Meyer, Miroslaw Truszczynski, and Frank Wolter

Published in: Dagstuhl Manifestos, Volume 10, Issue 1 (2024)

Abstract
Knowledge Representation and Reasoning is a central, longstanding, and active area of Artificial Intelligence. Over the years it has evolved significantly; more recently it has been challenged and complemented by research in areas such as machine learning and reasoning under uncertainty. In July 2022,sser a Dagstuhl Perspectives workshop was held on Knowledge Representation and Reasoning. The goal of the workshop was to describe the state of the art in the field, including its relation with other areas, its shortcomings and strengths, together with recommendations for future progress. We developed this manifesto based on the presentations, panels, working groups, and discussions that took place at the Dagstuhl Workshop. It is a declaration of our views on Knowledge Representation: its origins, goals, milestones, and current foci; its relation to other disciplines, especially to Artificial Intelligence; and on its challenges, along with key priorities for the next decade.
Cite as

James P. Delgrande, Birte Glimm, Thomas Meyer, Miroslaw Truszczynski, and Frank Wolter. Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282). In Dagstuhl Manifestos, Volume 10, Issue 1, pp. 1-61, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{delgrande_et_al:DagMan.10.1.1,
  author =	{Delgrande, James P. and Glimm, Birte and Meyer, Thomas and Truszczynski, Miroslaw and Wolter, Frank},
  title =	{{Current and Future Challenges in Knowledge Representation and Reasoning (Dagstuhl Perspectives Workshop 22282)}},
  pages =	{1--61},
  journal =	{Dagstuhl Manifestos},
  ISSN =	{2193-2433},
  year =	{2024},
  volume =	{10},
  number =	{1},
  editor =	{Delgrande, James P. and Glimm, Birte and Meyer, Thomas and Truszczynski, Miroslaw and Wolter, Frank},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagMan.10.1.1},
  URN =		{urn:nbn:de:0030-drops-201403},
  doi =		{10.4230/DagMan.10.1.1},
  annote =	{Keywords: Knowledge representation and reasoning, Applications of logics, Declarative representations, Formal logic}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2022.111
Beating the Folklore Algorithm for Dynamic Matching

Authors: Mohammad Roghani, Amin Saberi, and David Wajc

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

Abstract
The maximum matching problem in dynamic graphs subject to edge updates (insertions and deletions) has received much attention over the last few years; a multitude of approximation/time tradeoffs were obtained, improving upon the folklore algorithm, which maintains a maximal (and hence 2-approximate) matching in O(n) worst-case update time in n-node graphs. We present the first deterministic algorithm which outperforms the folklore algorithm in terms of both approximation ratio and worst-case update time. Specifically, we give a (2-Ω(1))-approximate algorithm with O(m^{3/8}) = O(n^{3/4}) worst-case update time in n-node, m-edge graphs. For sufficiently small constant ε > 0, no deterministic (2+ε)-approximate algorithm with worst-case update time O(n^{0.99}) was known. Our second result is the first deterministic (2+ε)-approximate weighted matching algorithm with O_ε(1)⋅ O(∜{m}) = O_ε(1)⋅ O(√n) worst-case update time. Neither of our results were previously known to be achievable by a randomized algorithm against an adaptive adversary. Our main technical contributions are threefold: first, we characterize the tight cases for kernels, which are the well-studied matching sparsifiers underlying much of the (2+ε)-approximate dynamic matching literature. This characterization, together with multiple ideas - old and new - underlies our result for breaking the approximation barrier of 2. Our second technical contribution is the first example of a dynamic matching algorithm whose running time is improved due to improving the recourse of other dynamic matching algorithms. Finally, we show how to use dynamic bipartite matching algorithms as black-box subroutines for dynamic matching in general graphs without incurring the natural 3/2 factor in the approximation ratio which such approaches naturally incur (reminiscent of the integrality gap of the fractional matching polytope in general graphs).
Cite as

Mohammad Roghani, Amin Saberi, and David Wajc. Beating the Folklore Algorithm for Dynamic Matching. In 13th Innovations in Theoretical Computer Science Conference (ITCS 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 215, pp. 111:1-111:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{roghani_et_al:LIPIcs.ITCS.2022.111,
  author =	{Roghani, Mohammad and Saberi, Amin and Wajc, David},
  title =	{{Beating the Folklore Algorithm for Dynamic Matching}},
  booktitle =	{13th Innovations in Theoretical Computer Science Conference (ITCS 2022)},
  pages =	{111:1--111:23},
  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.2022.111},
  URN =		{urn:nbn:de:0030-drops-157077},
  doi =		{10.4230/LIPIcs.ITCS.2022.111},
  annote =	{Keywords: dynamic matching, dynamic graph algorithms, sublinear algorithms}
}
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