17 Search Results for "Lee, David J."


Document
What Is a Spatio-Temporal Model Good For?: Validity as a Function of Purpose and the Questions Answered by a Model

Authors: Simon Scheider and Judith A. Verstegen

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


Abstract
The concept of validity is a cornerstone of science. Given this central role, it is somewhat surprising to find that validity remains a rather obscure concept. Unfortunately, the term is often reduced to a matter of ground truth data, seemingly because we fail to come to grips with it. In this paper, instead, we take a purpose-based approach to the validity of spatio-temporal models. We argue that a model application is valid only if the model delivers an answer to a particular spatio-temporal question specifying some experiment including spatio-temporal controls and measures. Such questions constitute the information purposes of models, forming an intermediate layer in a pragmatic knowledge pyramid with corresponding levels of validity. We introduce a corresponding question-based grammar that allows us to formally distinguish among contemporary inference, prediction, retrodiction, projection, and retrojection models. We apply the grammar to corresponding examples and discuss the possibilities for validating such models as a means to a given end.

Cite as

Simon Scheider and Judith A. Verstegen. What Is a Spatio-Temporal Model Good For?: Validity as a Function of Purpose and the Questions Answered by a Model. In 16th International Conference on Spatial Information Theory (COSIT 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 315, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{scheider_et_al:LIPIcs.COSIT.2024.7,
  author =	{Scheider, Simon and Verstegen, Judith A.},
  title =	{{What Is a Spatio-Temporal Model Good For?: Validity as a Function of Purpose and the Questions Answered by a Model}},
  booktitle =	{16th International Conference on Spatial Information Theory (COSIT 2024)},
  pages =	{7:1--7:23},
  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.2024.7},
  URN =		{urn:nbn:de:0030-drops-208225},
  doi =		{10.4230/LIPIcs.COSIT.2024.7},
  annote =	{Keywords: validity, fitness-for-purpose, spatio-temporal modeling, pragmatics, question grammar}
}
Document
A Coq Formalization of Taylor Models and Power Series for Solving Ordinary Differential Equations

Authors: Sewon Park and Holger Thies

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


Abstract
In exact real computation real numbers are manipulated exactly without round-off errors, making it well-suited for high precision verified computation. In recent work we propose an axiomatic formalization of exact real computation in the Coq theorem prover. The formalization admits an extended extraction mechanism that lets us extract computational content from constructive parts of proofs to efficient programs built on top of AERN, a Haskell library for exact real computation. Many processes in science and engineering are modeled by ordinary differential equations (ODEs), and often safety-critical applications depend on computing their solutions correctly. The primary goal of the current work is to extend our framework to spaces of functions and to support computation of solutions to ODEs and other essential operators. In numerical mathematics, the most common way to represent continuous functions is to use polynomial approximations. This can be modeled by so-called Taylor models, that encode a function as a polynomial and a rigorous error-bound over some domain. We define types of classical functions that do not hold any computational content and formalize Taylor models to computationally approximate those classical functions. Classical functions are defined in a way to admit classical principles in their constructions and verification. We define various basic operations on Taylor models and verify their correctness based on the classical functions that they approximate. We then shift our interest to analytic functions as a generalization of Taylor models where polynomials are replaced by infinite power series. We use the formalization to develop a theory of non-linear polynomial ODEs. From the proofs we can extract certified exact real computation programs that compute solutions of ODEs on some time interval up to any precision.

Cite as

Sewon Park and Holger Thies. A Coq Formalization of Taylor Models and Power Series for Solving Ordinary Differential Equations. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 30:1-30:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{park_et_al:LIPIcs.ITP.2024.30,
  author =	{Park, Sewon and Thies, Holger},
  title =	{{A Coq Formalization of Taylor Models and Power Series for Solving Ordinary Differential Equations}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{30:1--30:19},
  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.2024.30},
  URN =		{urn:nbn:de:0030-drops-207581},
  doi =		{10.4230/LIPIcs.ITP.2024.30},
  annote =	{Keywords: Exact real computation, Taylor models, Analytic functions, Computable analysis, Program extraction}
}
Document
Completeness of Asynchronous Session Tree Subtyping in Coq

Authors: Burak Ekici and Nobuko Yoshida

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


Abstract
Multiparty session types (MPST) serve as a foundational framework for formally specifying and verifying message passing protocols. Asynchronous subtyping in MPST allows for typing optimised programs preserving type safety and deadlock freedom under asynchronous interactions where the message order is preserved and sending is non-blocking. The optimisation is obtained by message reordering, which allows for sending messages earlier or receiving them later. Sound subtyping algorithms have been extensively studied and implemented as part of various programming languages and tools including C, Rust and C-MPI. However, formalising all such permutations under sequencing, selection, branching and recursion in session types is an intricate task. Additionally, checking asynchronous subtyping has been proven to be undecidable. This paper introduces the first formalisation of asynchronous subtyping in MPST within the Coq proof assistant. We first decompose session types into session trees that do not involve branching and selection, and then establish a coinductive refinement relation over them to govern subtyping. To showcase our formalisation, we prove example subtyping schemas that appear in the literature, all of which cannot be verified, at the same time, by any of the existing decidable sound algorithms. Additionally, we take the (inductive) negation of the refinement relation from a prior work by Ghilezan et al. [Ghilezan et al., 2023] and re-implement it, significantly reducing the number of rules (from eighteen to eight). We establish the completeness of subtyping with respect to its negation in Coq, addressing the issues concerning the negation rules outlined in the previous work [Ghilezan et al., 2023]. In the formalisation, we use the greatest fixed point of the least fixed point technique, facilitated by the paco library, to define coinductive predicates. We employ parametrised coinduction to prove their properties. The formalisation consists of roughly 10K lines of Coq code, accessible at: https://github.com/ekiciburak/sessionTreeST/tree/itp2024.

Cite as

Burak Ekici and Nobuko Yoshida. Completeness of Asynchronous Session Tree Subtyping in Coq. In 15th International Conference on Interactive Theorem Proving (ITP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 309, pp. 13:1-13:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{ekici_et_al:LIPIcs.ITP.2024.13,
  author =	{Ekici, Burak and Yoshida, Nobuko},
  title =	{{Completeness of Asynchronous Session Tree Subtyping in Coq}},
  booktitle =	{15th International Conference on Interactive Theorem Proving (ITP 2024)},
  pages =	{13:1--13:20},
  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.2024.13},
  URN =		{urn:nbn:de:0030-drops-207418},
  doi =		{10.4230/LIPIcs.ITP.2024.13},
  annote =	{Keywords: asynchronous multiparty session types, session trees, subtyping, Coq}
}
Document
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
RobTL: Robustness Temporal Logic for CPS

Authors: Valentina Castiglioni, Michele Loreti, and Simone Tini

Published in: LIPIcs, Volume 311, 35th International Conference on Concurrency Theory (CONCUR 2024)


Abstract
We propose Robustness Temporal Logic (RobTL), a novel temporal logic for the specification and analysis of distances between the behaviours of Cyber-Physical Systems (CPS) over a finite time horizon. RobTL specifications allow us to measure the differences in the behaviours of systems with respect to various objectives and temporal constraints, and to study how those differences evolve in time. Specifically, the unique features of RobTL allow us to specify robustness properties of CPS against uncertainty and perturbations. As an example, we use RobTL to analyse the robustness of an engine system that is subject to attacks aimed at inflicting overstress of equipment.

Cite as

Valentina Castiglioni, Michele Loreti, and Simone Tini. RobTL: Robustness Temporal Logic for CPS. In 35th International Conference on Concurrency Theory (CONCUR 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 311, pp. 15:1-15:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{castiglioni_et_al:LIPIcs.CONCUR.2024.15,
  author =	{Castiglioni, Valentina and Loreti, Michele and Tini, Simone},
  title =	{{RobTL: Robustness Temporal Logic for CPS}},
  booktitle =	{35th International Conference on Concurrency Theory (CONCUR 2024)},
  pages =	{15:1--15:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-339-3},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{311},
  editor =	{Majumdar, Rupak and Silva, Alexandra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2024.15},
  URN =		{urn:nbn:de:0030-drops-207870},
  doi =		{10.4230/LIPIcs.CONCUR.2024.15},
  annote =	{Keywords: Cyber-physical systems, robustness, temporal logic, uncertainty}
}
Document
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
A*PA2: Up to 19× Faster Exact Global Alignment

Authors: Ragnar Groot Koerkamp

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


Abstract
Motivation. Pairwise alignment is at the core of computational biology. Most commonly used exact methods are either based on O(ns) band doubling or O(n+s²) diagonal transition, where n is the sequence length and s the number of errors. However, as the length of sequences has grown, these exact methods are often replaced by approximate methods based on e.g. seed-and-extend and heuristics to bound the computed region. We would like to develop an exact method that matches the performance of these approximate methods. Recently, Astarix introduced the A* shortest path algorithm with the seed heuristic for exact sequence-to-graph alignment. A*PA adapted and improved this for pairwise sequence alignment and achieves near-linear runtime when divergence (error rate) is low, at the cost of being very slow when divergence is high. Methods. We introduce A*PA2, an exact global pairwise aligner with respect to edit distance. The goal of A*PA2 is to unify the near-linear runtime of A*PA on similar sequences with the efficiency of dynamic programming (DP) based methods. Like Edlib, A*PA2 uses Ukkonen’s band doubling in combination with Myers' bitpacking. A*PA2 1) uses large block sizes inspired by Block Aligner, 2) extends this with SIMD (single instruction, multiple data), 3) introduces a new profile for efficient computations, 4) introduces a new optimistic technique for traceback based on diagonal transition, 5) avoids recomputation of states where possible, and 6) applies the heuristics developed in A*PA and improves them using pre-pruning. Results. With the first 4 engineering optimizations, A*PA2-simple has complexity O(ns) and is 6× to 8× faster than Edlib for sequences ≥ 10 kbp. A*PA2-full also includes the heuristic and is often near-linear in practice for sequences with small divergence. The average runtime of A*PA2 is 19× faster than the exact aligners BiWFA and Edlib on >500 kbp long ONT (Oxford Nanopore Technologies) reads of a human genome having 6% divergence on average. On shorter ONT reads of 11% average divergence the speedup is 5.6× (avg. length 11 kbp) and 0.81× (avg. length 800 bp). On all tested datasets, A*PA2 is competitive with or faster than approximate methods.

Cite as

Ragnar Groot Koerkamp. A*PA2: Up to 19× Faster Exact Global Alignment. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{grootkoerkamp:LIPIcs.WABI.2024.17,
  author =	{Groot Koerkamp, Ragnar},
  title =	{{A*PA2: Up to 19× Faster Exact Global Alignment}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{17:1--17:25},
  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.2024.17},
  URN =		{urn:nbn:de:0030-drops-206610},
  doi =		{10.4230/LIPIcs.WABI.2024.17},
  annote =	{Keywords: Edit distance, Pairwise alignment, A*, Shortest path, Dynamic programming}
}
Document
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
Local Search k-means++ with Foresight

Authors: Theo Conrads, Lukas Drexler, Joshua Könen, Daniel R. Schmidt, and Melanie Schmidt

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


Abstract
Since its introduction in 1957, Lloyd’s algorithm for k-means clustering has been extensively studied and has undergone several improvements. While in its original form it does not guarantee any approximation factor at all, Arthur and Vassilvitskii (SODA 2007) proposed k-means++ which enhances Lloyd’s algorithm by a seeding method which guarantees a 𝒪(log k)-approximation in expectation. More recently, Lattanzi and Sohler (ICML 2019) proposed LS++ which further improves the solution quality of k-means++ by local search techniques to obtain a 𝒪(1)-approximation. On the practical side, the greedy variant of k-means++ is often used although its worst-case behaviour is provably worse than for the standard k-means++ variant. We investigate how to improve LS++ further in practice. We study two options for improving the practical performance: (a) Combining LS++ with greedy k-means++ instead of k-means++, and (b) Improving LS++ by better entangling it with Lloyd’s algorithm. Option (a) worsens the theoretical guarantees of k-means++ but improves the practical quality also in combination with LS++ as we confirm in our experiments. Option (b) is our new algorithm, Foresight LS++. We experimentally show that FLS++ improves upon the solution quality of LS++. It retains its asymptotic runtime and its worst-case approximation bounds.

Cite as

Theo Conrads, Lukas Drexler, Joshua Könen, Daniel R. Schmidt, and Melanie Schmidt. Local Search k-means++ with Foresight. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 7:1-7:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{conrads_et_al:LIPIcs.SEA.2024.7,
  author =	{Conrads, Theo and Drexler, Lukas and K\"{o}nen, Joshua and Schmidt, Daniel R. and Schmidt, Melanie},
  title =	{{Local Search k-means++ with Foresight}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{7:1--7:20},
  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.2024.7},
  URN =		{urn:nbn:de:0030-drops-203727},
  doi =		{10.4230/LIPIcs.SEA.2024.7},
  annote =	{Keywords: k-means clustering, kmeans++, greedy, local search}
}
Document
IMELL Cut Elimination with Linear Overhead

Authors: Beniamino Accattoli and Claudio Sacerdoti Coen

Published in: LIPIcs, Volume 299, 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)


Abstract
Recently, Accattoli introduced the Exponential Substitution Calculus (ESC) given by untyped proof terms for Intuitionistic Multiplicative Exponential Linear Logic (IMELL), endowed with rewriting rules at-a-distance for cut elimination. He also introduced a new cut elimination strategy, dubbed the good strategy, and showed that its number of steps is a time cost model with polynomial overhead for ESC/IMELL, and the first such one. Here, we refine Accattoli’s result by introducing an abstract machine for ESC and proving that it implements the good strategy and computes cut-free terms/proofs within a linear overhead.

Cite as

Beniamino Accattoli and Claudio Sacerdoti Coen. IMELL Cut Elimination with Linear Overhead. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 24:1-24:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{accattoli_et_al:LIPIcs.FSCD.2024.24,
  author =	{Accattoli, Beniamino and Sacerdoti Coen, Claudio},
  title =	{{IMELL Cut Elimination with Linear Overhead}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{24:1--24:24},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-323-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{299},
  editor =	{Rehof, Jakob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2024.24},
  URN =		{urn:nbn:de:0030-drops-203539},
  doi =		{10.4230/LIPIcs.FSCD.2024.24},
  annote =	{Keywords: Lambda calculus, linear logic, abstract machines}
}
Document
Shared Resource Contention in MCUs: A Reality Check and the Quest for Timeliness

Authors: Daniel Oliveira, Weifan Chen, Sandro Pinto, and Renato Mancuso

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)


Abstract
Microcontrollers (MCUs) are steadily embracing multi-core technology to meet growing performance demands. This trend marks a shift from their traditionally simple, deterministic designs to more complex and inherently less predictable architectures. While shared resource contention is well-studied in mid to high-end embedded systems, the emergence of multi-core architectures in MCUs introduces unique challenges and characteristics that existing research has not fully explored. In this paper, we conduct an in-depth investigation of both mainstream and next-generation MCU-based platforms, aiming to identify the sources of contention on systems typically lacking these problems. We empirically demonstrate substantial contention effects across different MCU architectures (i.e., from single- to multi-core configurations), highlighting significant application slowdowns. Notably, we observe that slowdowns can reach several orders of magnitude, with the most extreme cases showing up to a 3800x (times, not percent) increase in execution time. To address these issues, we propose and evaluate muTPArtc, a novel mechanism designed for Timely Progress Assessment (TPA) and TPA-based runtime control specifically tailored to MCUs. muTPArtc is an MCU-specialized TPA-based mechanism that leverages hardware facilities widely available in commercial off-the-shelf MCUs (i.e., hardware breakpoints and cycle counters) to successfully monitor applications' progress, detect, and mitigate timing violations. Our results demonstrate that muTPArtc effectively manages performance degradation due to interference, requiring only minimal modifications to the build pipeline and no changes to the source code of the target application, while incurring minor overheads.

Cite as

Daniel Oliveira, Weifan Chen, Sandro Pinto, and Renato Mancuso. Shared Resource Contention in MCUs: A Reality Check and the Quest for Timeliness. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 5:1-5:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{oliveira_et_al:LIPIcs.ECRTS.2024.5,
  author =	{Oliveira, Daniel and Chen, Weifan and Pinto, Sandro and Mancuso, Renato},
  title =	{{Shared Resource Contention in MCUs: A Reality Check and the Quest for Timeliness}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{5:1--5:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.5},
  URN =		{urn:nbn:de:0030-drops-203088},
  doi =		{10.4230/LIPIcs.ECRTS.2024.5},
  annote =	{Keywords: multi-core microcontrollers, shared resources contention, progress-aware regulation}
}
Document
Track B: Automata, Logic, Semantics, and Theory of Programming
T-Rex: Termination of Recursive Functions Using Lexicographic Linear Combinations

Authors: Raphael Douglas Giles, Vincent Jackson, and Christine Rizkallah

Published in: LIPIcs, Volume 297, 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)


Abstract
We introduce a powerful termination algorithm for structurally recursive functions that improves on the core ideas behind lexicographic termination algorithms for functional programs. The algorithm generates linear-lexicographic combinations of primitive measure functions measuring the recursive structure of terms. We introduce a measure language that enables the simplification and comparison of measures and we prove meta-theoretic properties of our measure language. Moreover, we demonstrate our algorithm, on an untyped first-order functional language and prove its soundness and that it runs in polynomial time. We also provide a Haskell implementation. As part of this work, we also show how to solve the maximisation of negative vector-components as a linear program.

Cite as

Raphael Douglas Giles, Vincent Jackson, and Christine Rizkallah. T-Rex: Termination of Recursive Functions Using Lexicographic Linear Combinations. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 139:1-139:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{giles_et_al:LIPIcs.ICALP.2024.139,
  author =	{Giles, Raphael Douglas and Jackson, Vincent and Rizkallah, Christine},
  title =	{{T-Rex: Termination of Recursive Functions Using Lexicographic Linear Combinations}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{139:1--139:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-322-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{297},
  editor =	{Bringmann, Karl and Grohe, Martin and Puppis, Gabriele and Svensson, Ola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2024.139},
  URN =		{urn:nbn:de:0030-drops-202827},
  doi =		{10.4230/LIPIcs.ICALP.2024.139},
  annote =	{Keywords: Termination, Recursive functions}
}
Document
Telescoping Filter: A Practical Adaptive Filter

Authors: David J. Lee, Samuel McCauley, Shikha Singh, and Max Stein

Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)


Abstract
Filters are small, fast, and approximate set membership data structures. They are often used to filter out expensive accesses to a remote set S for negative queries (that is, filtering out queries x ∉ S). Filters have one-sided errors: on a negative query, a filter may say "present" with a tunable false-positive probability of ε. Correctness is traded for space: filters only use log (1/ε) + O(1) bits per element. The false-positive guarantees of most filters, however, hold only for a single query. In particular, if x is a false positive, a subsequent query to x is a false positive with probability 1, not ε. With this in mind, recent work has introduced the notion of an adaptive filter. A filter is adaptive if each query is a false positive with probability ε, regardless of answers to previous queries. This requires "fixing" false positives as they occur. Adaptive filters not only provide strong false positive guarantees in adversarial environments but also improve query performance on practical workloads by eliminating repeated false positives. Existing work on adaptive filters falls into two categories. On the one hand, there are practical filters, based on the cuckoo filter, that attempt to fix false positives heuristically without meeting the adaptivity guarantee. On the other hand, the broom filter is a very complex adaptive filter that meets the optimal theoretical bounds. In this paper, we bridge this gap by designing the telescoping adaptive filter (TAF), a practical, provably adaptive filter. We provide theoretical false-positive and space guarantees for our filter, along with empirical results where we compare its performance against state-of-the-art filters. We also implement the broom filter and compare it to the TAF. Our experiments show that theoretical adaptivity can lead to improved false-positive performance on practical inputs, and can be achieved while maintaining throughput that is similar to non-adaptive filters.

Cite as

David J. Lee, Samuel McCauley, Shikha Singh, and Max Stein. Telescoping Filter: A Practical Adaptive Filter. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 60:1-60:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{lee_et_al:LIPIcs.ESA.2021.60,
  author =	{Lee, David J. and McCauley, Samuel and Singh, Shikha and Stein, Max},
  title =	{{Telescoping Filter: A Practical Adaptive Filter}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{60:1--60:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-204-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{204},
  editor =	{Mutzel, Petra and Pagh, Rasmus 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.2021.60},
  URN =		{urn:nbn:de:0030-drops-146410},
  doi =		{10.4230/LIPIcs.ESA.2021.60},
  annote =	{Keywords: Filters, approximate-membership query data structures (AMQs), Bloom filters, quotient filters, cuckoo filters, adaptivity, succinct data structures}
}
Document
Simple Heuristics Yield Provable Algorithms for Masked Low-Rank Approximation

Authors: Cameron Musco, Christopher Musco, and David P. Woodruff

Published in: LIPIcs, Volume 185, 12th Innovations in Theoretical Computer Science Conference (ITCS 2021)


Abstract
In the masked low-rank approximation problem, one is given data matrix A ∈ ℝ^{n × n} and binary mask matrix W ∈ {0,1}^{n × n}. The goal is to find a rank-k matrix L for which: cost(L) := ∑_{i=1}^n ∑_{j=1}^n W_{i,j} ⋅ (A_{i,j} - L_{i,j})² ≤ OPT + ε ‖A‖_F², where OPT = min_{rank-k L̂} cost(L̂) and ε is a given error parameter. Depending on the choice of W, the above problem captures factor analysis, low-rank plus diagonal decomposition, robust PCA, low-rank matrix completion, low-rank plus block matrix approximation, low-rank recovery from monotone missing data, and a number of other important problems. Many of these problems are NP-hard, and while algorithms with provable guarantees are known in some cases, they either 1) run in time n^Ω(k²/ε) or 2) make strong assumptions, for example, that A is incoherent or that the entries in W are chosen independently and uniformly at random. In this work, we show that a common polynomial time heuristic, which simply sets A to 0 where W is 0, and then finds a standard low-rank approximation, yields bicriteria approximation guarantees for this problem. In particular, for rank k' > k depending on the public coin partition number of W, the heuristic outputs rank-k' L with cost(L) ≤ OPT + ε ‖A‖_F². This partition number is in turn bounded by the randomized communication complexity of W, when interpreted as a two-player communication matrix. For many important cases, including all those listed above, this yields bicriteria approximation guarantees with rank k' = k ⋅ poly(log n/ε). Beyond this result, we show that different notions of communication complexity yield bicriteria algorithms for natural variants of masked low-rank approximation. For example, multi-player number-in-hand communication complexity connects to masked tensor decomposition and non-deterministic communication complexity to masked Boolean low-rank factorization.

Cite as

Cameron Musco, Christopher Musco, and David P. Woodruff. Simple Heuristics Yield Provable Algorithms for Masked Low-Rank Approximation. In 12th Innovations in Theoretical Computer Science Conference (ITCS 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 185, pp. 6:1-6:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{musco_et_al:LIPIcs.ITCS.2021.6,
  author =	{Musco, Cameron and Musco, Christopher and Woodruff, David P.},
  title =	{{Simple Heuristics Yield Provable Algorithms for Masked Low-Rank Approximation}},
  booktitle =	{12th Innovations in Theoretical Computer Science Conference (ITCS 2021)},
  pages =	{6:1--6:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-177-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{185},
  editor =	{Lee, James R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2021.6},
  URN =		{urn:nbn:de:0030-drops-135452},
  doi =		{10.4230/LIPIcs.ITCS.2021.6},
  annote =	{Keywords: low-rank approximation, communication complexity, weighted low-rank approximation, bicriteria approximation algorithms}
}
Document
Erasure-Resilient Sublinear-Time Graph Algorithms

Authors: Amit Levi, Ramesh Krishnan S. Pallavoor, Sofya Raskhodnikova, and Nithin Varma

Published in: LIPIcs, Volume 185, 12th Innovations in Theoretical Computer Science Conference (ITCS 2021)


Abstract
We investigate sublinear-time algorithms that take partially erased graphs represented by adjacency lists as input. Our algorithms make degree and neighbor queries to the input graph and work with a specified fraction of adversarial erasures in adjacency entries. We focus on two computational tasks: testing if a graph is connected or ε-far from connected and estimating the average degree. For testing connectedness, we discover a threshold phenomenon: when the fraction of erasures is less than ε, this property can be tested efficiently (in time independent of the size of the graph); when the fraction of erasures is at least ε, then a number of queries linear in the size of the graph representation is required. Our erasure-resilient algorithm (for the special case with no erasures) is an improvement over the previously known algorithm for connectedness in the standard property testing model and has optimal dependence on the proximity parameter ε. For estimating the average degree, our results provide an "interpolation" between the query complexity for this computational task in the model with no erasures in two different settings: with only degree queries, investigated by Feige (SIAM J. Comput. `06), and with degree queries and neighbor queries, investigated by Goldreich and Ron (Random Struct. Algorithms `08) and Eden et al. (ICALP `17). We conclude with a discussion of our model and open questions raised by our work.

Cite as

Amit Levi, Ramesh Krishnan S. Pallavoor, Sofya Raskhodnikova, and Nithin Varma. Erasure-Resilient Sublinear-Time Graph Algorithms. In 12th Innovations in Theoretical Computer Science Conference (ITCS 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 185, pp. 80:1-80:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)


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@InProceedings{levi_et_al:LIPIcs.ITCS.2021.80,
  author =	{Levi, Amit and Pallavoor, Ramesh Krishnan S. and Raskhodnikova, Sofya and Varma, Nithin},
  title =	{{Erasure-Resilient Sublinear-Time Graph Algorithms}},
  booktitle =	{12th Innovations in Theoretical Computer Science Conference (ITCS 2021)},
  pages =	{80:1--80:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-177-1},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{185},
  editor =	{Lee, James R.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2021.80},
  URN =		{urn:nbn:de:0030-drops-136192},
  doi =		{10.4230/LIPIcs.ITCS.2021.80},
  annote =	{Keywords: Graph property testing, Computing with incomplete information, Approximating graph parameters}
}
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