8 Search Results for "Noe, Alexander"

Document
DOI: 10.4230/LIPIcs.SEA.2026.15
Computational Generation of Substrate-Specific Molecular Cages

Authors: Noé Demange, Yann Strozecki, and Sandrine Vial

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
In this paper, we propose a method to build molecular cages designed to capture a specific substrate. We model a cage as a graph of atoms with coordinates in space, and several constraints on their edges (degree, length and angle). We use a simple method to place binding patterns which are able to interact with certain parts of the substrate. We then propose an algorithm which considers all possible ways of connecting these binding patterns and try to construct the smallest possible molecular paths realizing these connections. We investigate many variants of our method in order to obtain the most efficient algorithm, able to build cages of more than a hundred atoms.
Cite as

Noé Demange, Yann Strozecki, and Sandrine Vial. Computational Generation of Substrate-Specific Molecular Cages. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 15:1-15:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{demange_et_al:LIPIcs.SEA.2026.15,
  author =	{Demange, No\'{e} and Strozecki, Yann and Vial, Sandrine},
  title =	{{Computational Generation of Substrate-Specific Molecular Cages}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{15:1--15:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.15},
  URN =		{urn:nbn:de:0030-drops-260191},
  doi =		{10.4230/LIPIcs.SEA.2026.15},
  annote =	{Keywords: Enumeration, Molecular Cage, Cheminformatics, Geometric Algorithms, Experimental Algorithms}
}
Document
DOI: 10.4230/LIPIcs.SEA.2026.26
Engineering Algorithms for Dynamic Greedy Set Cover

Authors: Amitai Uzrad

Published in: LIPIcs, Volume 371, 24th International Symposium on Experimental Algorithms (SEA 2026)

Abstract
In the dynamic set cover problem, the input is a dynamic universe of elements and a fixed collection of sets. As elements are inserted or deleted, the goal is to efficiently maintain an approximate minimum set cover. While the past decade has seen significant theoretical breakthroughs for this problem, a notable gap remains between theoretical design and practical performance, as no comprehensive experimental study currently exists to validate these results. In this paper, we bridge this gap by implementing and evaluating four greedy-based dynamic algorithms across a diverse range of real-world instances. We derive our implementations from state-of-the-art frameworks - such as [GKKP(STOC'17); SU(STOC'23); SUZ(FOCS'24)] - which we simplify by identifying and modifying intricate subroutines that optimize asymptotic bounds but hinder practical performance. We evaluate these algorithms based on solution quality (set cover size) and efficiency, which comprises update time - the time required to update the solution following each insertion/deletion - and recourse - the number of changes made to the solution per update. Each algorithm uses a parameter β to balance quality against efficiency; we investigate the influence of this tradeoff parameter on each algorithm and then perform a comparative analysis to evaluate the algorithms against each other. Our results provide the first practical insights into which algorithmic strategies provide the most value in realistic scenarios.
Cite as

Amitai Uzrad. Engineering Algorithms for Dynamic Greedy Set Cover. In 24th International Symposium on Experimental Algorithms (SEA 2026). Leibniz International Proceedings in Informatics (LIPIcs), Volume 371, pp. 26:1-26:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2026)

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@InProceedings{uzrad:LIPIcs.SEA.2026.26,
  author =	{Uzrad, Amitai},
  title =	{{Engineering Algorithms for Dynamic Greedy Set Cover}},
  booktitle =	{24th International Symposium on Experimental Algorithms (SEA 2026)},
  pages =	{26:1--26:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-422-2},
  ISSN =	{1868-8969},
  year =	{2026},
  volume =	{371},
  editor =	{Aum\"{u}ller, Martin and Finocchi, Irene},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2026.26},
  URN =		{urn:nbn:de:0030-drops-260308},
  doi =		{10.4230/LIPIcs.SEA.2026.26},
  annote =	{Keywords: Dynamic graphs, set cover, recourse}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.47
Fast and Lightweight Distributed Suffix Array Construction

Authors: Manuel Haag, Florian Kurpicz, Peter Sanders, and Matthias Schimek

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
The suffix array contains the lexicographical order of all suffixes of a text. It is one of the most well-studied text indices with applications in bioinformatics, compression, and pattern matching. The main bottleneck of distributed-memory suffix array construction algorithms is their memory requirements. Even careful implementations require 30×-60× the input size as working memory. We present a scalable and lightweight distributed-memory adaptation of the difference cover (DCX) suffix array construction algorithm. Our approach relies on novel bucketing and random chunk redistribution techniques which reduce our memory requirement to 20×-26× the input size for medium-sized inputs and to 14×-15× for large-sized inputs. Regarding running time, we achieve speedups of up to 5× over current state-of-the-art distributed suffix array construction algorithms.
Cite as

Manuel Haag, Florian Kurpicz, Peter Sanders, and Matthias Schimek. Fast and Lightweight Distributed Suffix Array Construction. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 47:1-47:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{haag_et_al:LIPIcs.ESA.2025.47,
  author =	{Haag, Manuel and Kurpicz, Florian and Sanders, Peter and Schimek, Matthias},
  title =	{{Fast and Lightweight Distributed Suffix Array Construction}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{47:1--47:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian 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.2025.47},
  URN =		{urn:nbn:de:0030-drops-245154},
  doi =		{10.4230/LIPIcs.ESA.2025.47},
  annote =	{Keywords: Distributed Computing, Suffix Array Construction}
}
Document
DOI: 10.4230/LIPIcs.SEA.2025.22
Concurrent Iterated Local Search for the Maximum Weight Independent Set Problem

Authors: Ernestine Großmann, Kenneth Langedal, and Christian Schulz

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
The Maximum Weight Independent Set problem is a fundamental NP-hard problem in combinatorial optimization with several real-world applications. Given an undirected vertex-weighted graph, the problem is to find a subset of the vertices with the highest possible weight under the constraint that no two vertices in the set can share an edge. This work presents a new iterated local search heuristic called CHILS (Concurrent Hybrid Iterated Local Search). The implementation of CHILS is specifically designed to handle large graphs of varying densities. CHILS outperforms the current state-of-the-art on commonly used benchmark instances, especially on the largest instances. As an added benefit, CHILS can run in parallel to leverage the power of multicore processors. The general technique used in CHILS is a new concurrent metaheuristic called Concurrent Difference-Core Heuristic that can also be applied to other combinatorial problems.
Cite as

Ernestine Großmann, Kenneth Langedal, and Christian Schulz. Concurrent Iterated Local Search for the Maximum Weight Independent Set Problem. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{gromann_et_al:LIPIcs.SEA.2025.22,
  author =	{Gro{\ss}mann, Ernestine and Langedal, Kenneth and Schulz, Christian},
  title =	{{Concurrent Iterated Local Search for the Maximum Weight Independent Set Problem}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{22:1--22:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.22},
  URN =		{urn:nbn:de:0030-drops-232600},
  doi =		{10.4230/LIPIcs.SEA.2025.22},
  annote =	{Keywords: Randomized Local Search, Heuristics, Maximum Weight Independent Set, Algorithm Engineering, Parallel Computing}
}
Document
DOI: 10.4230/LIPIcs.ITCS.2025.48
Robust Restaking Networks

Authors: Naveen Durvasula and Tim Roughgarden

Published in: LIPIcs, Volume 325, 16th Innovations in Theoretical Computer Science Conference (ITCS 2025)

Abstract
We study the risks of validator reuse across multiple services in a restaking protocol. We characterize the robust security of a restaking network as a function of the buffer between the costs and profits from attacks. For example, our results imply that if attack costs always exceed attack profits by 10%, then a sudden loss of .1% of the overall stake (e.g., due to a software error) cannot result in the ultimate loss of more than 1.1% of the overall stake. We also provide local analogs of these overcollateralization conditions and robust security guarantees that apply specifically for a target service or coalition of services. All of our bounds on worst-case stake loss are the best possible. Finally, we bound the maximum-possible length of a cascade of attacks. Our results suggest measures of robustness that could be exposed to the participants in a restaking protocol. We also suggest polynomial-time computable sufficient conditions that can proxy for these measures.
Cite as

Naveen Durvasula and Tim Roughgarden. Robust Restaking Networks. In 16th Innovations in Theoretical Computer Science Conference (ITCS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 325, pp. 48:1-48:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{durvasula_et_al:LIPIcs.ITCS.2025.48,
  author =	{Durvasula, Naveen and Roughgarden, Tim},
  title =	{{Robust Restaking Networks}},
  booktitle =	{16th Innovations in Theoretical Computer Science Conference (ITCS 2025)},
  pages =	{48:1--48:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-361-4},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{325},
  editor =	{Meka, Raghu},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ITCS.2025.48},
  URN =		{urn:nbn:de:0030-drops-226769},
  doi =		{10.4230/LIPIcs.ITCS.2025.48},
  annote =	{Keywords: Proof of stake, Restaking, Staking Risks}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.45
A Local Search Algorithm for Large Maximum Weight Independent Set Problems

Authors: Yuanyuan Dong, Andrew V. Goldberg, Alexander Noe, Nikos Parotsidis, Mauricio G.C. Resende, and Quico Spaen

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

Abstract
Motivated by a real-world vehicle routing application, we consider the maximum-weight independent set problem: Given a node-weighted graph, find a set of independent (mutually nonadjacent) nodes whose node-weight sum is maximum. Some of the graphs arising in the vehicle routing application are large, having hundreds of thousands of nodes and hundreds of millions of edges. To solve instances of this size, we develop a new local search algorithm, which is a metaheuristic based on the greedy randomized adaptive search (GRASP) framework. This algorithm, named METAMIS, uses a wider range of simple local search operations than previously described in the literature. We introduce data structures that make these operations efficient. A new variant of path-relinking is introduced to escape local optima and so is a new alternating augmenting-path local search move that improves algorithm performance. We compare an implementation of our algorithm with a state-of-the-art publicly available code on public benchmark sets, including some large instances. Our algorithm is, in general, competitive and outperforms this openly available code on large vehicle routing instances of the maximum weight independent set problem. We hope that our results will lead to even better maximum-weight independent set algorithms.
Cite as

Yuanyuan Dong, Andrew V. Goldberg, Alexander Noe, Nikos Parotsidis, Mauricio G.C. Resende, and Quico Spaen. A Local Search Algorithm for Large Maximum Weight Independent Set Problems. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 45:1-45:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{dong_et_al:LIPIcs.ESA.2022.45,
  author =	{Dong, Yuanyuan and Goldberg, Andrew V. and Noe, Alexander and Parotsidis, Nikos and Resende, Mauricio G.C. and Spaen, Quico},
  title =	{{A Local Search Algorithm for Large Maximum Weight Independent Set Problems}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{45:1--45:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2022.45},
  URN =		{urn:nbn:de:0030-drops-169839},
  doi =		{10.4230/LIPIcs.ESA.2022.45},
  annote =	{Keywords: GRASP, local search, maximum-weight independent set, path-relinking, heuristic, metaheuristic}
}
Document
DOI: 10.4230/LIPIcs.ESA.2020.59
Finding All Global Minimum Cuts in Practice

Authors: Monika Henzinger, Alexander Noe, Christian Schulz, and Darren Strash

Published in: LIPIcs, Volume 173, 28th Annual European Symposium on Algorithms (ESA 2020)

Abstract
We present a practically efficient algorithm that finds all global minimum cuts in huge undirected graphs. Our algorithm uses a multitude of kernelization rules to reduce the graph to a small equivalent instance and then finds all minimum cuts using an optimized version of the algorithm of Nagamochi, Nakao and Ibaraki. In shared memory we are able to find all minimum cuts of graphs with up to billions of edges and millions of minimum cuts in a few minutes. We also give a new linear time algorithm to find the most balanced minimum cuts given as input the representation of all minimum cuts.
Cite as

Monika Henzinger, Alexander Noe, Christian Schulz, and Darren Strash. Finding All Global Minimum Cuts in Practice. In 28th Annual European Symposium on Algorithms (ESA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 173, pp. 59:1-59:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{henzinger_et_al:LIPIcs.ESA.2020.59,
  author =	{Henzinger, Monika and Noe, Alexander and Schulz, Christian and Strash, Darren},
  title =	{{Finding All Global Minimum Cuts in Practice}},
  booktitle =	{28th Annual European Symposium on Algorithms (ESA 2020)},
  pages =	{59:1--59:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-162-7},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{173},
  editor =	{Grandoni, Fabrizio and Herman, Grzegorz and Sanders, Peter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2020.59},
  URN =		{urn:nbn:de:0030-drops-129255},
  doi =		{10.4230/LIPIcs.ESA.2020.59},
  annote =	{Keywords: Minimum Cut, Graph Algorithm, Algorithm Engineering, Cut Enumeration, Balanced Cut, Global Minimum Cut, Large-scale Graph Analysis}
}
Document
DOI: 10.4230/LIPIcs.SEA.2018.4
ILP-based Local Search for Graph Partitioning

Authors: Alexandra Henzinger, Alexander Noe, and Christian Schulz

Published in: LIPIcs, Volume 103, 17th International Symposium on Experimental Algorithms (SEA 2018)

Abstract
Computing high-quality graph partitions is a challenging problem with numerous applications. In this paper, we present a novel meta-heuristic for the balanced graph partitioning problem. Our approach is based on integer linear programs that solve the partitioning problem to optimality. However, since those programs typically do not scale to large inputs, we adapt them to heuristically improve a given partition. We do so by defining a much smaller model that allows us to use symmetry breaking and other techniques that make the approach scalable. For example, in Walshaw's well-known benchmark tables we are able to improve roughly half of all entries when the number of blocks is high.
Cite as

Alexandra Henzinger, Alexander Noe, and Christian Schulz. ILP-based Local Search for Graph Partitioning. In 17th International Symposium on Experimental Algorithms (SEA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 103, pp. 4:1-4:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{henzinger_et_al:LIPIcs.SEA.2018.4,
  author =	{Henzinger, Alexandra and Noe, Alexander and Schulz, Christian},
  title =	{{ILP-based Local Search for Graph Partitioning}},
  booktitle =	{17th International Symposium on Experimental Algorithms (SEA 2018)},
  pages =	{4:1--4:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-070-5},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{103},
  editor =	{D'Angelo, Gianlorenzo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2018.4},
  URN =		{urn:nbn:de:0030-drops-89399},
  doi =		{10.4230/LIPIcs.SEA.2018.4},
  annote =	{Keywords: Graph Partitioning, Integer Linear Programming}
}
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