Andreas Zell - Academia.edu (original) (raw)
Papers by Andreas Zell
Lecture Notes in Computer Science, 2002
... Two new mutation and recombination operators are studied within the memetic framework for clu... more ... Two new mutation and recombination operators are studied within the memetic framework for clustering gene expression data. ... The general memetic algorithm framework is described in section 2. In section 3, the new recombination and mutation oper-ator are introduced. ...
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We propose an approach that can reduce the feature extraction time of the Scale Invariant Feature... more We propose an approach that can reduce the feature extraction time of the Scale Invariant Feature Transform (SIFT). The main idea is to search for the keypoints around a set of randomly generated particles rather than to per-form exhaustive search in the whole difference of Gaussian pyramid. The proposed approach makes it possible to de-fine the required number of keypoints in advance. A relation between the number of required features and the feature ex-traction time can be drawn. The matching time of two sets of keypoints is consequently minimized. To demonstrate its performance, the approach is applied to the robot global lo-calization problem. The results are successful, with much less keypoints and less computation time than the original SIFT.
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Diabetologie und Stoffwechsel, 2009
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Asia-Pacific Bioinformatics Conference, 2007
The ability to measure the transcriptional response after a stimulus has drawn much attention to ... more The ability to measure the transcriptional response after a stimulus has drawn much attention to the underlying gene regulatory networks. Several machine learning related methods, such as Bayesian net- works and decision trees, have been proposed to deal with this difficult problem, but rarely a systematic comparison between different algorithms has been performed. In this work, we critically evaluate the
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Proceedings of the 5th Asia-Pacific Bioinformatics Conference, 2007
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2007 IEEE Congress on Evolutionary Computation, 2007
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2007 IEEE Congress on Evolutionary Computation, 2007
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2007 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007
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The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways.... more The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. Availability: KEGGtranslator is freely available as a Java™ Web Start application and for download at http://www.cogsys.cs.uni-tuebingen...
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The calibration of complex models of biological systems requires numer- ical simulation and optim... more The calibration of complex models of biological systems requires numer- ical simulation and optimization procedures to infer undetermined parameters and fit measured data. The optimization step typically employs heuristic global optimization algorithms, but due to measurement noise and the many degrees of freedom, it is not guaranteed that the identified single optimum is also the most meaningful parame- ter set. Multimodal optimization allows for identifying multiple optima in parallel. We consider high-dimensional benchmark functions and a realistic metabolic network model from systems biology to compare evolutionary and swarm-based multimodal methods. We show that an extended swarm based niching algorithm is able to find a considerable set of solutions in parallel, which have significantly more explanatory power. As an outline of the information gain, the variations in the set of high-quality solutions are contrasted to a state-of-the-art global sensitivity analysis.
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The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, commu... more The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization. Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX. Contact: an...
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International Conference on Intelligent Robots and Systems, 2004
The aim of this article is to present the potential of Kernel Principal Component Analysis (Kerne... more The aim of this article is to present the potential of Kernel Principal Component Analysis (Kernel PCA) in the field of vision based robot localization. Using Kernel PCA we can extract features from the visual scene of a mobile robot. The analysis is applied only to local features so as to guarantee better computational performance as well as translation invariance.
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Advanced Robotics, 2003
Gas source localisation with robots is usually per- formed in environments with a strong, unidire... more Gas source localisation with robots is usually per- formed in environments with a strong, unidirectional airflow created by artificial ventilation. This tends to create a strong, well defined analyte plume and enables upwind searching. By contrast, this paper presents experiments conducted in unventilated rooms. Here, the measured concentrations also indicate an analyte plume with, however, different properties concerning its shape,
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Informatik aktuell, 1999
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Proceedings of the 22nd international conference on Machine learning - ICML '05, 2005
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2006 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2006
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Informatik-Fachberichte, 1991
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Lecture Notes in Computer Science, 1999
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Lecture Notes in Computer Science, 2002
... Two new mutation and recombination operators are studied within the memetic framework for clu... more ... Two new mutation and recombination operators are studied within the memetic framework for clustering gene expression data. ... The general memetic algorithm framework is described in section 2. In section 3, the new recombination and mutation oper-ator are introduced. ...
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We propose an approach that can reduce the feature extraction time of the Scale Invariant Feature... more We propose an approach that can reduce the feature extraction time of the Scale Invariant Feature Transform (SIFT). The main idea is to search for the keypoints around a set of randomly generated particles rather than to per-form exhaustive search in the whole difference of Gaussian pyramid. The proposed approach makes it possible to de-fine the required number of keypoints in advance. A relation between the number of required features and the feature ex-traction time can be drawn. The matching time of two sets of keypoints is consequently minimized. To demonstrate its performance, the approach is applied to the robot global lo-calization problem. The results are successful, with much less keypoints and less computation time than the original SIFT.
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Bookmarks Related papers MentionsView impact
Diabetologie und Stoffwechsel, 2009
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Asia-Pacific Bioinformatics Conference, 2007
The ability to measure the transcriptional response after a stimulus has drawn much attention to ... more The ability to measure the transcriptional response after a stimulus has drawn much attention to the underlying gene regulatory networks. Several machine learning related methods, such as Bayesian net- works and decision trees, have been proposed to deal with this difficult problem, but rarely a systematic comparison between different algorithms has been performed. In this work, we critically evaluate the
Bookmarks Related papers MentionsView impact
Proceedings of the 5th Asia-Pacific Bioinformatics Conference, 2007
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2007 IEEE Congress on Evolutionary Computation, 2007
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2007 IEEE Congress on Evolutionary Computation, 2007
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2007 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007
Bookmarks Related papers MentionsView impact
The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways.... more The KEGG PATHWAY database provides a widely used service for metabolic and nonmetabolic pathways. It contains manually drawn pathway maps with information about the genes, reactions and relations contained therein. To store these pathways, KEGG uses KGML, a proprietary XML-format. Parsers and translators are needed to process the pathway maps for usage in other applications and algorithms. We have developed KEGGtranslator, an easy-to-use stand-alone application that can visualize and convert KGML formatted XML-files into multiple output formats. Unlike other translators, KEGGtranslator supports a plethora of output formats, is able to augment the information in translated documents (e.g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those. Availability: KEGGtranslator is freely available as a Java™ Web Start application and for download at http://www.cogsys.cs.uni-tuebingen...
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The calibration of complex models of biological systems requires numer- ical simulation and optim... more The calibration of complex models of biological systems requires numer- ical simulation and optimization procedures to infer undetermined parameters and fit measured data. The optimization step typically employs heuristic global optimization algorithms, but due to measurement noise and the many degrees of freedom, it is not guaranteed that the identified single optimum is also the most meaningful parame- ter set. Multimodal optimization allows for identifying multiple optima in parallel. We consider high-dimensional benchmark functions and a realistic metabolic network model from systems biology to compare evolutionary and swarm-based multimodal methods. We show that an extended swarm based niching algorithm is able to find a considerable set of solutions in parallel, which have significantly more explanatory power. As an outline of the information gain, the variations in the set of high-quality solutions are contrasted to a state-of-the-art global sensitivity analysis.
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The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, commu... more The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization. Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX. Contact: an...
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International Conference on Intelligent Robots and Systems, 2004
The aim of this article is to present the potential of Kernel Principal Component Analysis (Kerne... more The aim of this article is to present the potential of Kernel Principal Component Analysis (Kernel PCA) in the field of vision based robot localization. Using Kernel PCA we can extract features from the visual scene of a mobile robot. The analysis is applied only to local features so as to guarantee better computational performance as well as translation invariance.
Bookmarks Related papers MentionsView impact
Advanced Robotics, 2003
Gas source localisation with robots is usually per- formed in environments with a strong, unidire... more Gas source localisation with robots is usually per- formed in environments with a strong, unidirectional airflow created by artificial ventilation. This tends to create a strong, well defined analyte plume and enables upwind searching. By contrast, this paper presents experiments conducted in unventilated rooms. Here, the measured concentrations also indicate an analyte plume with, however, different properties concerning its shape,
Bookmarks Related papers MentionsView impact
Informatik aktuell, 1999
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Proceedings of the 22nd international conference on Machine learning - ICML '05, 2005
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2006 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2006
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Informatik-Fachberichte, 1991
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Lecture Notes in Computer Science, 1999
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