27 Search Results for "Liu, Chang"

Document
DOI: 10.4230/LIPIcs.COSIT.2024.6
Is Familiarity Reflected in the Spatial Knowledge Revealed by Sketch Maps?

Authors: Markus Kattenbeck, Daniel R. Montello, Martin Raubal, and Ioannis Giannopoulos

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
Despite the frequent use of sketch maps in assessing environmental knowledge, it remains unclear how and to what degree familiarity impacts sketch map content. In the present study, we assess whether different levels of familiarity relate to differences in the content and spatial accuracy of environmental knowledge depicted in sketch maps drawn for the purpose of route instructions. To this end, we conduct a real-world wayfinding study with 91 participants, all of whom have to walk along a pre-defined route of approximately 2.3km length. Prior to the walk, we collect self-report familiarity ratings from participants for both a set of 15 landmarks and a set of areas we define as hexagons along the route. Once participants finished walking the route, they were asked to sketch a map of the route, specifically a sketch that would enable a person who had never walked the route to follow it. We found that participants unfamiliar with the areas along the route sketched fewer features than familiar people did. Contrary to our expectations, however, we found that landmarks were sketched or not regardless of participants' level of familiarity with the landmarks. We were also surprised that the level of familiarity was not correlated to the accuracy of the sketched order of features along the route, of the position of sketched features in relation to the route, nor to the metric locational accuracy of feature placement on the sketches. These results lead us to conclude that different aspects of feature salience influence whether the features are included on sketch maps, independent of familiarity. They also point to the influence of task context on the content of sketch maps, again independent of familiarity. We propose further studies to more fully explore these ideas.
Cite as

Markus Kattenbeck, Daniel R. Montello, Martin Raubal, and Ioannis Giannopoulos. Is Familiarity Reflected in the Spatial Knowledge Revealed by Sketch Maps?. In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 6:1-6:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kattenbeck_et_al:LIPIcs.COSIT.2024.6,
  author =	{Kattenbeck, Markus and Montello, Daniel R. and Raubal, Martin and Giannopoulos, Ioannis},
  title =	{{Is Familiarity Reflected in the Spatial Knowledge Revealed by Sketch Maps?}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{6:1--6:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.6},
  URN =		{urn:nbn:de:0030-drops-208215},
  doi =		{10.4230/LIPIcs.COSIT.2024.6},
  annote =	{Keywords: Familiarity, Spatial Knowledge, Sketch Maps}
}
Document
Short Paper
DOI: 10.4230/LIPIcs.COSIT.2024.31
Large Language Models: Testing Their Capabilities to Understand and Explain Spatial Concepts (Short Paper)

Authors: Majid Hojati and Rob Feick

Published in: LIPIcs, Volume 315, 16th International Conference on Spatial Information Theory (COSIT 2024)

Abstract
Interest in applying Large Language Models (LLMs), which use natural language processing (NLP) to provide human-like responses to text-based questions, to geospatial tasks has grown rapidly. Research shows that LLMs can help generate software code and answer some types of geographic questions to varying degrees even without fine-tuning. However, further research is required to explore the types of spatial questions they answer correctly, their abilities to apply spatial reasoning, and the variability between models. In this paper we examine the ability of four LLM models (GPT3.5 and 4, LLAma2.0, Falcon40B) to answer spatial questions that range from basic calculations to more advanced geographic concepts. The intent of this comparison is twofold. First, we demonstrate an extensible method for evaluating LLM’s limitations to supporting spatial data science through correct calculations and code generation. Relatedly, we also consider how these models can aid geospatial learning by providing text-based explanations of spatial concepts and operations. Our research shows common strengths in more basic types of questions, and mixed results for questions relating to more advanced spatial concepts. These results provide insights that may be used to inform strategies for testing and fine-tuning these models to increase their understanding of key spatial concepts.
Cite as

Majid Hojati and Rob Feick. Large Language Models: Testing Their Capabilities to Understand and Explain Spatial Concepts (Short Paper). In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 31:1-31:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hojati_et_al:LIPIcs.COSIT.2024.31,
  author =	{Hojati, Majid and Feick, Rob},
  title =	{{Large Language Models: Testing Their Capabilities to Understand and Explain Spatial Concepts}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{31:1--31:9},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-330-0},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{315},
  editor =	{Adams, Benjamin and Griffin, Amy L. and Scheider, Simon and McKenzie, Grant},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.COSIT.2024.31},
  URN =		{urn:nbn:de:0030-drops-208460},
  doi =		{10.4230/LIPIcs.COSIT.2024.31},
  annote =	{Keywords: Geospatial concepts, Large Language Models, LLM, GPT, Llama, Falcon}
}
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.2024.14
A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs

Authors: Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti

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

Abstract
Elastic Degenerate (ED) strings and Elastic Founder (EF) graphs are two versions of acyclic components of pangenomes. Both ED strings and EF graphs (which we collectively name variable strings) extend the well-known notion of indeterminate string. Recent work has extensively investigated algorithmic tasks over these structures, and over several other variable strings notions that they generalise. Among such tasks, the basic operation of matching a pattern into a text, which can serve as a toolkit for many pangenomic data analyses using these data structures, deserves special attention. In this paper we: (1) highlight a clear taxonomy within both ED strings and EF graphs ranging through variable strings of all types, from the linear string up to the most general one; (2) investigate the problem PvarT(X,Y) of matching a solid or variable pattern of type X into a variable text of type Y; (3) using as a reference the quadratic conditional lower bounds that are known for PvarT(solid,ED) and PvarT(solid,EF), for all possible types of variable strings X and Y we either prove the quadratic conditional lower bound for PvarT(X,Y), or provide non-trivial, often sub-quadratic, upper bounds, also exploiting the above-mentioned taxonomy.
Cite as

Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti. A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ascone_et_al:LIPIcs.WABI.2024.14,
  author =	{Ascone, Rocco and Bernardini, Giulia and Conte, Alessio and Equi, Massimo and Gabory, Esteban and Grossi, Roberto and Pisanti, Nadia},
  title =	{{A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{14:1--14:21},
  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.2024.14},
  URN =		{urn:nbn:de:0030-drops-206586},
  doi =		{10.4230/LIPIcs.WABI.2024.14},
  annote =	{Keywords: Pangenomics, pattern matching, degenerate string, founder graph, fine-grained complexity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.18
RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions

Authors: Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty

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

Abstract
RNAs composed of Triplet Repeats (TR) have recently attracted much attention in the field of synthetic biology. We study the mimimum free energy (MFE) secondary structures of such RNAs and give improved algorithms to compute the MFE and the partition function. Furthermore, we study the interaction of multiple RNAs and design a new algorithm for computing MFE and partition function for RNA-RNA interactions, improving the previously known factorial running time to exponential. In the case of TR, we show computational hardness but still obtain a parameterized algorithm. Finally, we propose a polynomial-time algorithm for computing interactions from a base set of RNA strands and conduct experiments on the interaction of TR based on this algorithm. For instance, we study the probability that a base pair is formed between two strands with the same triplet pattern, allowing an assessment of a notion of orthogonality between TR.
Cite as

Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty. RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 18:1-18:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{boehmer_et_al:LIPIcs.WABI.2024.18,
  author =	{Boehmer, Kimon and Berkemer, Sarah J. and Will, Sebastian and Ponty, Yann},
  title =	{{RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{18:1--18:23},
  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.2024.18},
  URN =		{urn:nbn:de:0030-drops-206625},
  doi =		{10.4230/LIPIcs.WABI.2024.18},
  annote =	{Keywords: RNA folding, RNA interactions, triplet repeats, dynamic programming, NP-hardness}
}
Document
DOI: 10.4230/LIPIcs.TQC.2024.3
Efficient Optimal Control of Open Quantum Systems

Authors: Wenhao He, Tongyang Li, Xiantao Li, Zecheng Li, Chunhao Wang, and Ke Wang

Published in: LIPIcs, Volume 310, 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)

Abstract
The optimal control problem for open quantum systems can be formulated as a time-dependent Lindbladian that is parameterized by a number of time-dependent control variables. Given an observable and an initial state, the goal is to tune the control variables so that the expected value of some observable with respect to the final state is maximized. In this paper, we present algorithms for solving this optimal control problem efficiently, i.e., having a poly-logarithmic dependency on the system dimension, which is exponentially faster than best-known classical algorithms. Our algorithms are hybrid, consisting of both quantum and classical components. The quantum procedure simulates time-dependent Lindblad evolution that drives the initial state to the final state, and it also provides access to the gradients of the objective function via quantum gradient estimation. The classical procedure uses the gradient information to update the control variables. At the technical level, we provide the first (to the best of our knowledge) simulation algorithm for time-dependent Lindbladians with an 𝓁₁-norm dependence. As an alternative, we also present a simulation algorithm in the interaction picture to improve the algorithm for the cases where the time-independent component of a Lindbladian dominates the time-dependent part. On the classical side, we heavily adapt the state-of-the-art classical optimization analysis to interface with the quantum part of our algorithms. Both the quantum simulation techniques and the classical optimization analyses might be of independent interest.
Cite as

Wenhao He, Tongyang Li, Xiantao Li, Zecheng Li, Chunhao Wang, and Ke Wang. Efficient Optimal Control of Open Quantum Systems. In 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 310, pp. 3:1-3:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{he_et_al:LIPIcs.TQC.2024.3,
  author =	{He, Wenhao and Li, Tongyang and Li, Xiantao and Li, Zecheng and Wang, Chunhao and Wang, Ke},
  title =	{{Efficient Optimal Control of Open Quantum Systems}},
  booktitle =	{19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)},
  pages =	{3:1--3:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-328-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{310},
  editor =	{Magniez, Fr\'{e}d\'{e}ric and Grilo, Alex Bredariol},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2024.3},
  URN =		{urn:nbn:de:0030-drops-206733},
  doi =		{10.4230/LIPIcs.TQC.2024.3},
  annote =	{Keywords: Quantum algorithm, quantum optimal control, Lindbladian simulation, accelerated gradient descent}
}
Document
DOI: 10.4230/LIPIcs.TQC.2024.8
(Quantum) Complexity of Testing Signed Graph Clusterability

Authors: Kuo-Chin Chen, Simon Apers, and Min-Hsiu Hsieh

Published in: LIPIcs, Volume 310, 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)

Abstract
This study examines clusterability testing for a signed graph in the bounded-degree model. Our contributions are two-fold. First, we provide a quantum algorithm with query complexity Õ(N^{1/3}) for testing clusterability, which yields a polynomial speedup over the best classical clusterability tester known [Adriaens and Apers, 2023]. Second, we prove an Ω̃(√N) classical query lower bound for testing clusterability, which nearly matches the upper bound from [Adriaens and Apers, 2023]. This settles the classical query complexity of clusterability testing, and it shows that our quantum algorithm has an advantage over any classical algorithm.
Cite as

Kuo-Chin Chen, Simon Apers, and Min-Hsiu Hsieh. (Quantum) Complexity of Testing Signed Graph Clusterability. In 19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 310, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chen_et_al:LIPIcs.TQC.2024.8,
  author =	{Chen, Kuo-Chin and Apers, Simon and Hsieh, Min-Hsiu},
  title =	{{(Quantum) Complexity of Testing Signed Graph Clusterability}},
  booktitle =	{19th Conference on the Theory of Quantum Computation, Communication and Cryptography (TQC 2024)},
  pages =	{8:1--8:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-328-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{310},
  editor =	{Magniez, Fr\'{e}d\'{e}ric and Grilo, Alex Bredariol},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TQC.2024.8},
  URN =		{urn:nbn:de:0030-drops-206786},
  doi =		{10.4230/LIPIcs.TQC.2024.8},
  annote =	{Keywords: Quantum Algorithm, classical Query lower Bound, Graph Property testing}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2024.33
First-Fit Coloring of Forests in Random Arrival Model

Authors: Bartłomiej Bosek, Grzegorz Gutowski, Michał Lasoń, and Jakub Przybyło

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
We consider a graph coloring algorithm that processes vertices in order taken uniformly at random and assigns colors to them using First-Fit strategy. We show that this algorithm uses, in expectation, at most (1+o(1))⋅ln n / ln ln n different colors to color any forest with n vertices. We also construct a family of forests that shows that this bound is best possible.
Cite as

Bartłomiej Bosek, Grzegorz Gutowski, Michał Lasoń, and Jakub Przybyło. First-Fit Coloring of Forests in Random Arrival Model. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 33:1-33:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bosek_et_al:LIPIcs.MFCS.2024.33,
  author =	{Bosek, Bart{\l}omiej and Gutowski, Grzegorz and Laso\'{n}, Micha{\l} and Przyby{\l}o, Jakub},
  title =	{{First-Fit Coloring of Forests in Random Arrival Model}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{33:1--33:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.33},
  URN =		{urn:nbn:de:0030-drops-205892},
  doi =		{10.4230/LIPIcs.MFCS.2024.33},
  annote =	{Keywords: First-Fit, Online Algorithms, Graph Coloring, Random Arrival Model}
}
Document
Invited Paper
DOI: 10.4230/OASIcs.WCET.2024.6
Invited Paper: Statistical, Stochastic or Probabilistic (Worst-Case Execution) Execution Time? - What Impact on the Multicore Composability

Authors: Liliana Cucu-Grosjean

Published in: OASIcs, Volume 121, 22nd International Workshop on Worst-Case Execution Time Analysis (WCET 2024)

Abstract
The problem of estimating worst-case execution times of programs on processors has appeared within the context of critical industries like avionics or space. Rapidly adopted by the real-time scheduling community, worst-case execution time estimates of programs or tasks are mandatory to understand the time behaviour of a real-time system. Analyzing such time behaviour is done, often, with an important pessimism due to the consideration of worst-case scenarios. A decreased pessimism has been obtained by understanding that large execution times of a program have low probability of appearance. Probabilistic (worst-case) execution time notion has been proposed. Nevertheless, independence hypotheses makes difficult today to calculate the probabilistic worst-case execution time of a program and current approaches are built, often, on statistical estimators based on the use of Extreme Value Theory or concentration inequalities. Thus, future probabilistic time analyses are expected to consider worst-case execution times estimates obtained by using statistical estimators on measured execution times instead of probabilistic (worst-case) execution times estimations. Within this paper, we discuss the opportunity of differentiating probabilistic (worst-case) execution times from statistical (worst-case) execution times and how dependence between execution times are better or easier captured by each of the definition, while stochastic execution times could be, also, an appropriate alternative.
Cite as

Liliana Cucu-Grosjean. Invited Paper: Statistical, Stochastic or Probabilistic (Worst-Case Execution) Execution Time? - What Impact on the Multicore Composability. In 22nd International Workshop on Worst-Case Execution Time Analysis (WCET 2024). Open Access Series in Informatics (OASIcs), Volume 121, pp. 6:1-6:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cucugrosjean:OASIcs.WCET.2024.6,
  author =	{Cucu-Grosjean, Liliana},
  title =	{{Invited Paper: Statistical, Stochastic or Probabilistic (Worst-Case Execution) Execution Time? - What Impact on the Multicore Composability}},
  booktitle =	{22nd International Workshop on Worst-Case Execution Time Analysis (WCET 2024)},
  pages =	{6:1--6:10},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-346-1},
  ISSN =	{2190-6807},
  year =	{2024},
  volume =	{121},
  editor =	{Carle, Thomas},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/OASIcs.WCET.2024.6},
  URN =		{urn:nbn:de:0030-drops-204746},
  doi =		{10.4230/OASIcs.WCET.2024.6},
  annote =	{Keywords: Worst-case execution time, probabilistic analyses, statistical estimator}
}
Document
DOI: 10.4230/LIPIcs.AofA.2024.8
Galled Tree-Child Networks

Authors: Yu-Sheng Chang, Michael Fuchs, and Guan-Ru Yu

Published in: LIPIcs, Volume 302, 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)

Abstract
We propose the class of galled tree-child networks which is obtained as intersection of the classes of galled networks and tree-child networks. For the latter two classes, (asymptotic) counting results and stochastic results have been proved with very different methods. We show that a counting result for the class of galled tree-child networks follows with similar tools as used for galled networks, however, the result has a similar pattern as the one for tree-child networks. In addition, we also consider the (suitably scaled) numbers of reticulation nodes of random galled tree-child networks and show that they are asymptotically normal distributed. This is in contrast to the limit laws of the corresponding quantities for galled networks and tree-child networks which have been both shown to be discrete.
Cite as

Yu-Sheng Chang, Michael Fuchs, and Guan-Ru Yu. Galled Tree-Child Networks. In 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 302, pp. 8:1-8:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chang_et_al:LIPIcs.AofA.2024.8,
  author =	{Chang, Yu-Sheng and Fuchs, Michael and Yu, Guan-Ru},
  title =	{{Galled Tree-Child Networks}},
  booktitle =	{35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)},
  pages =	{8:1--8:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-329-4},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{302},
  editor =	{Mailler, C\'{e}cile and Wild, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AofA.2024.8},
  URN =		{urn:nbn:de:0030-drops-204439},
  doi =		{10.4230/LIPIcs.AofA.2024.8},
  annote =	{Keywords: Phylogenetic Network, galled Network, tree-child Network, asymptotic Enumeration, Limit Law, Lagrange Inversion}
}
Document
DOI: 10.4230/LIPIcs.AofA.2024.15
Asymptotics of Relaxed k-Ary Trees

Authors: Manosij Ghosh Dastidar and Michael Wallner

Published in: LIPIcs, Volume 302, 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)

Abstract
A relaxed k-ary tree is an ordered directed acyclic graph with a unique source and sink in which every node has out-degree k. These objects arise in the compression of trees in which some repeated subtrees are factored and repeated appearances are replaced by pointers. We prove an asymptotic theta-result for the number of relaxed k-ary tree with n nodes for n → ∞. This generalizes the previously proved binary case to arbitrary finite arity, and shows that the seldom observed phenomenon of a stretched exponential term e^{c n^{1/3}} appears in all these cases. We also derive the recurrences for compacted k-ary trees in which all subtrees are unique and minimal deterministic finite automata accepting a finite language over a finite alphabet.
Cite as

Manosij Ghosh Dastidar and Michael Wallner. Asymptotics of Relaxed k-Ary Trees. In 35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 302, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{ghoshdastidar_et_al:LIPIcs.AofA.2024.15,
  author =	{Ghosh Dastidar, Manosij and Wallner, Michael},
  title =	{{Asymptotics of Relaxed k-Ary Trees}},
  booktitle =	{35th International Conference on Probabilistic, Combinatorial and Asymptotic Methods for the Analysis of Algorithms (AofA 2024)},
  pages =	{15:1--15:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-329-4},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{302},
  editor =	{Mailler, C\'{e}cile and Wild, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.AofA.2024.15},
  URN =		{urn:nbn:de:0030-drops-204506},
  doi =		{10.4230/LIPIcs.AofA.2024.15},
  annote =	{Keywords: Asymptotic enumeration, stretched exponential, Airy function, directed acyclic graph, Dyck paths, compacted trees, minimal automata}
}
Document
DOI: 10.4230/LIPIcs.CCC.2024.7
Polynomial Pass Semi-Streaming Lower Bounds for K-Cores and Degeneracy

Authors: Sepehr Assadi, Prantar Ghosh, Bruno Loff, Parth Mittal, and Sagnik Mukhopadhyay

Published in: LIPIcs, Volume 300, 39th Computational Complexity Conference (CCC 2024)

Abstract
The following question arises naturally in the study of graph streaming algorithms: Is there any graph problem which is "not too hard", in that it can be solved efficiently with total communication (nearly) linear in the number n of vertices, and for which, nonetheless, any streaming algorithm with Õ(n) space (i.e., a semi-streaming algorithm) needs a polynomial n^Ω(1) number of passes? Assadi, Chen, and Khanna [STOC 2019] were the first to prove that this is indeed the case. However, the lower bounds that they obtained are for rather non-standard graph problems. Our first main contribution is to present the first polynomial-pass lower bounds for natural "not too hard" graph problems studied previously in the streaming model: k-cores and degeneracy. We devise a novel communication protocol for both problems with near-linear communication, thus showing that k-cores and degeneracy are natural examples of "not too hard" problems. Indeed, previous work have developed single-pass semi-streaming algorithms for approximating these problems. In contrast, we prove that any semi-streaming algorithm for exactly solving these problems requires (almost) Ω(n^{1/3}) passes. The lower bound follows by a reduction from a generalization of the hidden pointer chasing (HPC) problem of Assadi, Chen, and Khanna, which is also the basis of their earlier semi-streaming lower bounds. Our second main contribution is improved round-communication lower bounds for the underlying communication problems at the basis of these reductions: - We improve the previous lower bound of Assadi, Chen, and Khanna for HPC to achieve optimal bounds for this problem. - We further observe that all current reductions from HPC can also work with a generalized version of this problem that we call MultiHPC, and prove an even stronger and optimal lower bound for this generalization. These two results collectively allow us to improve the resulting pass lower bounds for semi-streaming algorithms by a polynomial factor, namely, from n^{1/5} to n^{1/3} passes.
Cite as

Sepehr Assadi, Prantar Ghosh, Bruno Loff, Parth Mittal, and Sagnik Mukhopadhyay. Polynomial Pass Semi-Streaming Lower Bounds for K-Cores and Degeneracy. In 39th Computational Complexity Conference (CCC 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 300, pp. 7:1-7:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{assadi_et_al:LIPIcs.CCC.2024.7,
  author =	{Assadi, Sepehr and Ghosh, Prantar and Loff, Bruno and Mittal, Parth and Mukhopadhyay, Sagnik},
  title =	{{Polynomial Pass Semi-Streaming Lower Bounds for K-Cores and Degeneracy}},
  booktitle =	{39th Computational Complexity Conference (CCC 2024)},
  pages =	{7:1--7:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-331-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{300},
  editor =	{Santhanam, Rahul},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2024.7},
  URN =		{urn:nbn:de:0030-drops-204035},
  doi =		{10.4230/LIPIcs.CCC.2024.7},
  annote =	{Keywords: Graph streaming, Lower bounds, Communication complexity, k-Cores and degeneracy}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.3
Practical Minimum Path Cover

Authors: Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
Computing a minimum path cover (MPC) of a directed acyclic graph (DAG) is a fundamental problem with a myriad of applications, including reachability. Although it is known how to solve the problem by a simple reduction to minimum flow, recent theoretical advances exploit this idea to obtain algorithms parameterized by the number of paths of an MPC, known as the width. These results obtain fast [Mäkinen et al., TALG 2019] and even linear time [Cáceres et al., SODA 2022] algorithms in the small-width regime. In this paper, we present the first publicly available high-performance implementation of state-of-the-art MPC algorithms, including the parameterized approaches. Our experiments on random DAGs show that parameterized algorithms are orders-of-magnitude faster on dense graphs. Additionally, we present new fast pre-processing heuristics based on transitive edge sparsification. We show that our heuristics improve MPC-solvers by orders of magnitude.
Cite as

Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu. Practical Minimum Path Cover. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{caceres_et_al:LIPIcs.SEA.2024.3,
  author =	{C\'{a}ceres, Manuel and Mumey, Brendan and Toivonen, Santeri and Tomescu, Alexandru I.},
  title =	{{Practical Minimum Path Cover}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{3:1--3:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.3},
  URN =		{urn:nbn:de:0030-drops-203687},
  doi =		{10.4230/LIPIcs.SEA.2024.3},
  annote =	{Keywords: minimum path cover, directed acyclic graph, maximum flow, parameterized algorithms, edge sparsification, algorithm engineering}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.17
Barcode Selection and Layout Optimization in Spatial Transcriptomics

Authors: Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
An important special case of the quadratic assignment problem arises in the synthesis of DNA microarrays for high-resolution spatial transcriptomics. The task is to select a suitable subset from a set of barcodes, i. e. short DNA strings that serve as unique identifiers, and to assign the selected barcodes to positions on a two-dimensional array in such a way that a position-dependent cost function is minimized. A typical microarray with dimensions of 768×1024 requires 786,432 many barcodes to be placed, leading to very challenging large-scale combinatorial optimization problems. The general quadratic assignment problem is well-known for its hardness, both in theory and in practice. It turns out that this also holds for the special case of the barcode layout problem. We show that the problem is even hard to approximate: It is MaxSNP-hard. An ILP formulation theoretically allows the computation of optimal results, but it is only applicable for tiny instances. Therefore, we have developed layout constructing and improving heuristics with the aim of computing near-optimal solutions for instances of realistic size. These include a sorting-based algorithm, a greedy algorithm, 2-OPT-based local search and a genetic algorithm. To assess the quality of the results, we compare the generated solutions with the expected cost of a random layout and with lower bounds. A combination of the greedy algorithm and 2-OPT local search produces the most promising results in terms of both quality and runtime. Solutions to large-scale instances with arrays of dimension 768×1024 show a 37% reduction in cost over a random solution and can be computed in about 3 minutes. Since the universe of suitable barcodes is much larger than the number of barcodes needed, this can be exploited. Experiments with different surpluses of barcodes show that a significant improvement in layout quality can be achieved at the cost of a reasonable increase in runtime. Another interesting finding is that the restriction of the barcode design space by biochemical constraints is actually beneficial for the overall layout cost.
Cite as

Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann. Barcode Selection and Layout Optimization in Spatial Transcriptomics. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 17:1-17:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{jatzkowski_et_al:LIPIcs.SEA.2024.17,
  author =	{Jatzkowski, Frederik L. and Schmidt, Antonia and Mank, Robert and Sch\"{u}ler, Steffen and M\"{u}ller-Hannemann, Matthias},
  title =	{{Barcode Selection and Layout Optimization in Spatial Transcriptomics}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{17:1--17:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.17},
  URN =		{urn:nbn:de:0030-drops-203821},
  doi =		{10.4230/LIPIcs.SEA.2024.17},
  annote =	{Keywords: Spatial Transcriptomics, Array Layout, Optimization, Computational Complexity, GPU Computing, Integer Linear Programming, Metaheuristics}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.27
Improved Cut Strategy for Tensor Network Contraction Orders

Authors: Christoph Staudt, Mark Blacher, Julien Klaus, Farin Lippmann, and Joachim Giesen

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
In the field of quantum computing, simulating quantum systems on classical computers is crucial. Tensor networks are fundamental in simulating quantum systems. A tensor network is a collection of tensors, that need to be contracted into a result tensor. Tensor contraction is a generalization of matrix multiplication to higher order tensors. The contractions can be performed in different orders, and the order has a significant impact on the number of floating point operations (flops) needed to get the result tensor. It is known that finding an optimal contraction order is NP-hard. The current state-of-the-art approach for finding efficient contraction orders is to combinine graph partitioning with a greedy strategy. Although heavily used in practice, the current approach ignores so-called free indices, chooses node weights without regarding previous computations, and requires numerous hyperparameters that need to be tuned at runtime. In this paper, we address these shortcomings by developing a novel graph cut strategy. The proposed modifications yield contraction orders that significantly reduce the number of flops in the tensor contractions compared to the current state of the art. Moreover, by removing the need for hyperparameter tuning at runtime, our approach converges to an efficient solution faster, which reduces the required optimization time by at least an order of magnitude.
Cite as

Christoph Staudt, Mark Blacher, Julien Klaus, Farin Lippmann, and Joachim Giesen. Improved Cut Strategy for Tensor Network Contraction Orders. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 27:1-27:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{staudt_et_al:LIPIcs.SEA.2024.27,
  author =	{Staudt, Christoph and Blacher, Mark and Klaus, Julien and Lippmann, Farin and Giesen, Joachim},
  title =	{{Improved Cut Strategy for Tensor Network Contraction Orders}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{27:1--27:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.27},
  URN =		{urn:nbn:de:0030-drops-203924},
  doi =		{10.4230/LIPIcs.SEA.2024.27},
  annote =	{Keywords: tensor network, contraction order, graph partitioniong, quantum simulation}
}
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