5 Search Results for "Holland, William L."

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.FSCD.2024.14

Two-Dimensional Kripke Semantics I: Presheaves

Authors: G. A. Kavvos

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

Abstract

The study of modal logic has witnessed tremendous development following the introduction of Kripke semantics. However, recent developments in programming languages and type theory have led to a second way of studying modalities, namely through their categorical semantics. We show how the two correspond.

Cite as

G. A. Kavvos. Two-Dimensional Kripke Semantics I: Presheaves. In 9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 299, pp. 14:1-14:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{kavvos:LIPIcs.FSCD.2024.14,
  author =	{Kavvos, G. A.},
  title =	{{Two-Dimensional Kripke Semantics I: Presheaves}},
  booktitle =	{9th International Conference on Formal Structures for Computation and Deduction (FSCD 2024)},
  pages =	{14:1--14:23},
  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.2024.14},
  URN =		{urn:nbn:de:0030-drops-203438},
  doi =		{10.4230/LIPIcs.FSCD.2024.14},
  annote =	{Keywords: modal logic, categorical semantics, Kripke semantics, duality, open maps}
}

Document

Track A: Algorithms, Complexity and Games

DOI: 10.4230/LIPIcs.ICALP.2024.84

The k-Opt Algorithm for the Traveling Salesman Problem Has Exponential Running Time for k ≥ 5

Authors: Sophia Heimann, Hung P. Hoang, and Stefan Hougardy

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

Abstract

The k-Opt algorithm is a local search algorithm for the Traveling Salesman Problem. Starting with an initial tour, it iteratively replaces at most k edges in the tour with the same number of edges to obtain a better tour. Krentel (FOCS 1989) showed that the Traveling Salesman Problem with the k-Opt neighborhood is complete for the class PLS (polynomial time local search) and that the k-Opt algorithm can have exponential running time for any pivot rule. However, his proof requires k ≫ 1000 and has a substantial gap. We show the two properties above for a much smaller value of k, addressing an open question by Monien, Dumrauf, and Tscheuschner (ICALP 2010). In particular, we prove the PLS-completeness for k ≥ 17 and the exponential running time for k ≥ 5.

Cite as

Sophia Heimann, Hung P. Hoang, and Stefan Hougardy. The k-Opt Algorithm for the Traveling Salesman Problem Has Exponential Running Time for k ≥ 5. In 51st International Colloquium on Automata, Languages, and Programming (ICALP 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 297, pp. 84:1-84:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{heimann_et_al:LIPIcs.ICALP.2024.84,
  author =	{Heimann, Sophia and Hoang, Hung P. and Hougardy, Stefan},
  title =	{{The k-Opt Algorithm for the Traveling Salesman Problem Has Exponential Running Time for k ≥ 5}},
  booktitle =	{51st International Colloquium on Automata, Languages, and Programming (ICALP 2024)},
  pages =	{84:1--84:18},
  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.2024.84},
  URN =		{urn:nbn:de:0030-drops-202270},
  doi =		{10.4230/LIPIcs.ICALP.2024.84},
  annote =	{Keywords: Traveling Salesman Problem, k-Opt algorithm, PLS-completeness}
}

Document

DOI: 10.4230/LIPIcs.ISAAC.2022.65

Succinct List Indexing in Optimal Time

Authors: William L. Holland

Published in: LIPIcs, Volume 248, 33rd International Symposium on Algorithms and Computation (ISAAC 2022)

Abstract

An indexed list supports (efficient) access to both the offsets and the items of an arbitrarily ordered set under the effect of insertions and deletions. Existing solutions are engaged in a space-time trade-off. On the one hand, time efficient solutions are composed as a package of data structures: a linked-list, a hash table and a tree-type structure to support indexing. This arrangement observes a memory commitment that is outside the information theoretic lower bound (for ordered sets) by a factor of 12. On the other hand, the memory lower bound can be satisfied, up to an additive lower order term, trivially with an array. However, operations incur time costs proportional to the length of the array. We revisit the list indexing problem by attempting to balance the competing demands of space and time efficiency. We prepare the first succinct indexed list that supports efficient query and update operations. To implement an ordered set of size n, drawn from the universe {1, …, m}, the solution occupies n(log m + o(log n)) bits (with high probability) and admits all operations optimally in 𝒪(log n/log log n) time.

Cite as

William L. Holland. Succinct List Indexing in Optimal Time. In 33rd International Symposium on Algorithms and Computation (ISAAC 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 248, pp. 65:1-65:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{holland:LIPIcs.ISAAC.2022.65,
  author =	{Holland, William L.},
  title =	{{Succinct List Indexing in Optimal Time}},
  booktitle =	{33rd International Symposium on Algorithms and Computation (ISAAC 2022)},
  pages =	{65:1--65:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-258-7},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{248},
  editor =	{Bae, Sang Won and Park, Heejin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2022.65},
  URN =		{urn:nbn:de:0030-drops-173506},
  doi =		{10.4230/LIPIcs.ISAAC.2022.65},
  annote =	{Keywords: Succinct Data Structures, Lists, Dynamic Data Structures}
}

Document

DOI: 10.4230/LIPIcs.ISAAC.2020.49

Recency Queries with Succinct Representation

Authors: William L. Holland, Anthony Wirth, and Justin Zobel

Published in: LIPIcs, Volume 181, 31st International Symposium on Algorithms and Computation (ISAAC 2020)

Abstract

In the context of the sliding-window set membership problem, and caching policies that require knowledge of item recency, we formalize the problem of Recency on a stream. Informally, the query asks, "when was the last time I saw item x?" Existing structures, such as hash tables, can support a recency query by augmenting item occurrences with timestamps. To support recency queries on a window of W items, this might require Θ(W log W) bits. We propose a succinct data structure for Recency. By combining sliding-window dictionaries in a hierarchical structure, and careful design of the underlying hash tables, we achieve a data structure that returns a 1+ε approximation to the recency of every item in O(log(ε W)) time, in only (1+o(1))(1+ε)(ℬ+Wlog(ε^(-1))) bits. Here, ℬ is the information-theoretic lower bound on the number of bits for a set of size W, in a universe of cardinality N.

Cite as

William L. Holland, Anthony Wirth, and Justin Zobel. Recency Queries with Succinct Representation. In 31st International Symposium on Algorithms and Computation (ISAAC 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 181, pp. 49:1-49:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{holland_et_al:LIPIcs.ISAAC.2020.49,
  author =	{Holland, William L. and Wirth, Anthony and Zobel, Justin},
  title =	{{Recency Queries with Succinct Representation}},
  booktitle =	{31st International Symposium on Algorithms and Computation (ISAAC 2020)},
  pages =	{49:1--49:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-173-3},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{181},
  editor =	{Cao, Yixin and Cheng, Siu-Wing and Li, Minming},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2020.49},
  URN =		{urn:nbn:de:0030-drops-133931},
  doi =		{10.4230/LIPIcs.ISAAC.2020.49},
  annote =	{Keywords: Succinct Data Structures, Data Streams, Sliding Dictionary}
}

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2 Holland, William L.
1 Heimann, Sophia
1 Hoang, Hung P.
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2 Theory of computation → Data structures design and analysis
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2 Succinct Data Structures
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