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190 results on '"Zarges, Christine"'

1. A visualization tool to explore alphabet orderings for the Burrows-Wheeler Transform

Author

Major, Lily, Davies, Dave, Clare, Amanda, Daykin, Jacqueline W., Mora, Benjamin, and Zarges, Christine

Subjects
Computer Science - Human-Computer Interaction, H.5.2
Abstract

The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive uses particularly in lossless compression algorithms, indexing, and within bioinformatics for sequence alignment tasks. There has been recent interest in minimizing the number of identical character runs ($r$) for a transform and in finding useful alphabet orderings for the sorting step of the matrix associated with the BWT construction. This motivates the inspection of many transforms while developing algorithms. However, the full Burrows-Wheeler matrix is $O(n^2)$ space and therefore very difficult to display and inspect for large input sizes. In this paper we present a graphical user interface (GUI) for working with BWTs, which includes features for searching for matrix row prefixes, skipping over sections in the right-most column (the transform), and displaying BWTs while exploring alphabet orderings with the goal of minimizing the number of runs., Comment: 8 pages, 2 figures

Published
2024

2. Heuristics for the Run-length Encoded Burrows-Wheeler Transform Alphabet Ordering Problem

Author

Major, Lily, Clare, Amanda, Daykin, Jacqueline W., Mora, Benjamin, and Zarges, Christine

Subjects
Computer Science - Discrete Mathematics, I.2.8
Abstract

The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the ability to query the compressed data efficiently. However, these methods may not take full advantage of the compressibility of the BWT as they do not modify the alphabet ordering for the sorting step embedded in computing the BWT. Indeed, any such alteration of the alphabet ordering can have a considerable impact on the output of the BWT, in particular on the number of runs. For an alphabet $\Sigma$ containing $\sigma$ characters, the space of all alphabet orderings is of size $\sigma!$. While for small alphabets an exhaustive investigation is possible, finding the optimal ordering for larger alphabets is not feasible. Therefore, there is a need for a more informed search strategy than brute-force sampling the entire space, which motivates a new heuristic approach. In this paper, we explore the non-trivial cases for the problem of minimizing the size of a run-length encoded BWT (RLBWT) via selecting a new ordering for the alphabet. We show that random sampling of the space of alphabet orderings usually gives sub-optimal orderings for compression and that a local search strategy can provide a large improvement in relatively few steps. We also inspect a selection of initial alphabet orderings, including ASCII, letter appearance, and letter frequency. While this alphabet ordering problem is computationally hard we demonstrate gain in compressibility., Comment: 32 pages, 8 figures

Published
2024

5. Unlimited Budget Analysis of Randomised Search Heuristics

Author

He, Jun, Jansen, Thomas, and Zarges, Christine

Subjects
Computer Science - Neural and Evolutionary Computing, Mathematics - Optimization and Control
Abstract

Performance analysis of all kinds of randomised search heuristics is a rapidly growing and developing field. Run time and solution quality are two popular measures of the performance of these algorithms. The focus of this paper is on the solution quality an optimisation heuristic achieves, not on the time it takes to reach this goal, setting it far apart from runtime analysis. We contribute to its further development by introducing a novel analytical framework, called unlimited budget analysis, to derive the expected fitness value after arbitrary computational steps. It has its roots in the very recently introduced approximation error analysis and bears some similarity to fixed budget analysis. We present the framework, apply it to simple mutation-based algorithms, covering both, local and global search. We provide analytical results for a number of pseudo-Boolean functions for unlimited budget analysis and compare them to results derived within the fixed budget framework for the same algorithms and functions. There are also results of experiments to compare bounds obtained in the two different frameworks with the actual observed performance. The study show that unlimited budget analysis may lead to the same or more general estimation beyond fixed budget.

Published
2019

7. Oxidative protein folding in the intermembrane space of human mitochondria.

Author

Zarges, Christine and Riemer, Jan

Subjects
MITOCHONDRIAL proteins, BIOCHEMICAL substrates, PROTEIN stability, MITOCHONDRIA, PROTEINS, PROTEIN folding
Abstract

The mitochondrial intermembrane space hosts a machinery for oxidative protein folding, the mitochondrial disulfide relay. This machinery imports a large number of soluble proteins into the compartment, where they are retained through oxidative folding. Additionally, the disulfide relay enhances the stability of many proteins by forming disulfide bonds. In this review, we describe the mitochondrial disulfide relay in human cells, its components, and their coordinated collaboration in mechanistic detail. We also discuss the human pathologies associated with defects in this machinery and its protein substrates, providing a comprehensive overview of its biological importance and implications for health. [ABSTRACT FROM AUTHOR]

Published
2024
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9. Evaluation of a Permutation-Based Evolutionary Framework for Lyndon Factorizations

Author

Major, Lily, Clare, Amanda, Daykin, Jacqueline W., Mora, Benjamin, Peña Gamboa, Leonel Jose, Zarges, Christine, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Bäck, Thomas, editor, Preuss, Mike, editor, Deutz, André, editor, Wang, Hao, editor, Doerr, Carola, editor, Emmerich, Michael, editor, and Trautmann, Heike, editor

Published
2020
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10. Rough Set Theory as a Data Mining Technique: A Case Study in Epidemiology and Cancer Incidence Prediction

Author

Chelly Dagdia, Zaineb, Zarges, Christine, Schannes, Benjamin, Micalef, Martin, Galiana, Lino, Rolland, Benoît, de Fresnoye, Olivier, Benchoufi, Mehdi, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Brefeld, Ulf, editor, Curry, Edward, editor, Daly, Elizabeth, editor, MacNamee, Brian, editor, Marascu, Alice, editor, Pinelli, Fabio, editor, Berlingerio, Michele, editor, and Hurley, Neil, editor

Published
2019
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12. Workshops at PPSN 2018

Author

Purshouse, Robin, Zarges, Christine, Cussat-Blanc, Sylvain, Epitropakis, Michael G., Gallagher, Marcus, Jansen, Thomas, Kerschke, Pascal, Li, Xiaodong, Lobo, Fernando G., Miller, Julian, Oliveto, Pietro S., Preuss, Mike, Squillero, Giovanni, Tonda, Alberto, Wagner, Markus, Weise, Thomas, Wilson, Dennis, Wróbel, Borys, Zamuda, Aleš, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Auger, Anne, editor, Fonseca, Carlos M., editor, Lourenço, Nuno, editor, Machado, Penousal, editor, Paquete, Luís, editor, and Whitley, Darrell, editor

Published
2018
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13. Theoretical Analysis of Lexicase Selection in Multi-objective Optimization

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Auger, Anne, editor, Fonseca, Carlos M., editor, Lourenço, Nuno, editor, Machado, Penousal, editor, Paquete, Luís, editor, and Whitley, Darrell, editor

Published
2018
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14. Optimizing Monotone Functions Can Be Difficult

Author

Doerr, Benjamin, Jansen, Thomas, Sudholt, Dirk, Winzen, Carola, and Zarges, Christine

Subjects
Computer Science - Neural and Evolutionary Computing
Abstract

Extending previous analyses on function classes like linear functions, we analyze how the simple (1+1) evolutionary algorithm optimizes pseudo-Boolean functions that are strictly monotone. Contrary to what one would expect, not all of these functions are easy to optimize. The choice of the constant $c$ in the mutation probability $p(n) = c/n$ can make a decisive difference. We show that if $c < 1$, then the (1+1) evolutionary algorithm finds the optimum of every such function in $\Theta(n \log n)$ iterations. For $c=1$, we can still prove an upper bound of $O(n^{3/2})$. However, for $c > 33$, we present a strictly monotone function such that the (1+1) evolutionary algorithm with overwhelming probability does not find the optimum within $2^{\Omega(n)}$ iterations. This is the first time that we observe that a constant factor change of the mutation probability changes the run-time by more than constant factors., Comment: Preliminary version appeared at PPSN XI. Compared to version 1, a small bug in the constants was fixed ($\gamma$ is slightly larger now, thus ensuring that $\gamma$ is now strictly larger than $\rho$ in Lemma 5)

Published
2010

16. Example Landscapes to Support Analysis of Multimodal Optimisation

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Handl, Julia, editor, Hart, Emma, editor, Lewis, Peter R., editor, López-Ibáñez, Manuel, editor, Ochoa, Gabriela, editor, and Paechter, Ben, editor

Published
2016
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17. The Workshops at PPSN 2016

Author

Blum, Christian, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Handl, Julia, editor, Hart, Emma, editor, Lewis, Peter R., editor, López-Ibáñez, Manuel, editor, Ochoa, Gabriela, editor, and Paechter, Ben, editor

Published
2016
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20. Improving the Performance of the Germinal Center Artificial Immune System Using -Dominance: A Multi-objective Knapsack Problem Case Study

Author

Joshi, Ayush, Rowe, Jonathan E., Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Ochoa, Gabriela, editor, and Chicano, Francisco, editor

Published
2015
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22. An Immune-Inspired Algorithm for the Set Cover Problem

Author

Joshi, Ayush, Rowe, Jonathan E., Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bartz-Beielstein, Thomas, editor, Branke, Jürgen, editor, Filipič, Bogdan, editor, and Smith, Jim, editor

Published
2014
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23. On the Runtime Analysis of Fitness Sharing Mechanisms

Author

Oliveto, Pietro S., Sudholt, Dirk, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bartz-Beielstein, Thomas, editor, Branke, Jürgen, editor, Filipič, Bogdan, editor, and Smith, Jim, editor

Published
2014
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25. Workshops at PPSN 2018

Author

Purshouse, Robin, primary, Zarges, Christine, additional, Cussat-Blanc, Sylvain, additional, Epitropakis, Michael G., additional, Gallagher, Marcus, additional, Jansen, Thomas, additional, Kerschke, Pascal, additional, Li, Xiaodong, additional, Lobo, Fernando G., additional, Miller, Julian, additional, Oliveto, Pietro S., additional, Preuss, Mike, additional, Squillero, Giovanni, additional, Tonda, Alberto, additional, Wagner, Markus, additional, Weise, Thomas, additional, Wilson, Dennis, additional, Wróbel, Borys, additional, and Zamuda, Aleš, additional

Published
2018
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29. Computing Longest Common Subsequences with the B-Cell Algorithm

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Coello Coello, Carlos A., editor, Greensmith, Julie, editor, Krasnogor, Natalio, editor, Liò, Pietro, editor, Nicosia, Giuseppe, editor, and Pavone, Mario, editor

Published
2012
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30. On the Analysis of the Immune-Inspired B-Cell Algorithm for the Vertex Cover Problem

Author

Jansen, Thomas, Oliveto, Pietro S., Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Liò, Pietro, editor, Nicosia, Giuseppe, editor, and Stibor, Thomas, editor

Published
2011
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31. Variation in Artificial Immune Systems: Hypermutations with Mutation Potential

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Liò, Pietro, editor, Nicosia, Giuseppe, editor, and Stibor, Thomas, editor

Published
2011
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32. Analysis of an Iterated Local Search Algorithm for Vertex Coloring

Author

Sudholt, Dirk, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cheong, Otfried, editor, Chwa, Kyung-Yong, editor, and Park, Kunsoo, editor

Published
2010
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33. On the Benefits of Aging and the Importance of Details

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Hart, Emma, editor, McEwan, Chris, editor, Timmis, Jon, editor, and Hone, Andy, editor

Published
2010
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35. Comparing Different Aging Operators

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Andrews, Paul S., editor, Timmis, Jon, editor, Owens, Nick D. L., editor, Aickelin, Uwe, editor, Hart, Emma, editor, Hone, Andrew, editor, and Tyrrell, Andy M., editor

Published
2009
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36. A Theoretical Analysis of Immune Inspired Somatic Contiguous Hypermutations for Function Optimization

Author

Jansen, Thomas, Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Andrews, Paul S., editor, Timmis, Jon, editor, Owens, Nick D. L., editor, Aickelin, Uwe, editor, Hart, Emma, editor, Hone, Andrew, editor, and Tyrrell, Andy M., editor

Published
2009
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37. Rigorous Runtime Analysis of Inversely Fitness Proportional Mutation Rates

Author

Zarges, Christine, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Rudolph, Günter, editor, Jansen, Thomas, editor, Beume, Nicola, editor, Lucas, Simon, editor, and Poloni, Carlo, editor

Published
2008
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47. Stagnation Detection with Randomized Local Search

Author

Zarges, Christine, Verel, Sébastien, Rajabi, Amirhossein, Witt, Carsten, Zarges, Christine, Verel, Sébastien, Rajabi, Amirhossein, and Witt, Carsten

Abstract

Recently a mechanism called stagnation detection was proposed that automatically adjusts the mutation rate of evolutionary algorithms when they encounter local optima. The so-called SD-(1+1) EA introduced by Rajabi and Witt (GECCO 2020) adds stagnation detection to the classical (1+1) EA with standard bit mutation, which flips each bit independently with some mutation rate, and raises the mutation rate when the algorithm is likely to have encountered local optima. In this paper, we investigate stagnation detection in the context of the k-bit flip operator of randomized local search that flips k bits chosen uniformly at random and let stagnation detection adjust the parameter k. We obtain improved runtime results compared to the SD-(1+1) EA amounting to a speed-up of up to e= 2.71 ⋯ Moreover, we propose additional schemes that prevent infinite optimization times even if the algorithm misses a working choice of k due to unlucky events. Finally, we present an example where standard bit mutation still outperforms the local k-bit flip with stagnation detection.

Published
2021

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