Andreas Zell - Academia.edu (original) (raw)

Papers by Andreas Zell

Research paper thumbnail of Clustering Gene Expression Profiles with Memetic Algorithms

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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Research paper thumbnail of Global robot localization using iterative scale invariant feature transform

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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Research paper thumbnail of Supplementary note for "Prediction of breast cancer by proflling of urinary RNA metabolites using Support Vector Machine-based feature selection

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Research paper thumbnail of Metabolomics – eine Strategie zur Identifizierung von prä-diabetischen Stoffwechselveränderungen und neuen Biomarkern?

Diabetologie und Stoffwechsel, 2009

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Research paper thumbnail of Inferring Gene Regulatory Networks by Machine Learning Methods

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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Research paper thumbnail of INFERRING GENE REGULATORY NETWORKS BY MACHINE LEARNING METHODS

Proceedings of the 5th Asia-Pacific Bioinformatics Conference, 2007

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Research paper thumbnail of Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum

2007 IEEE Congress on Evolutionary Computation, 2007

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Research paper thumbnail of Benchmarking evolutionary algorithms on convenience kinetics models of the valine and leucine biosynthesis in C. glutamicum

2007 IEEE Congress on Evolutionary Computation, 2007

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Research paper thumbnail of A hybrid approach for vision-based outdoor robot localization using global and local image features

2007 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007

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Research paper thumbnail of KEGGtranslator

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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Research paper thumbnail of On the Benefits of Multimodal Optimization for Metablic Network Modeling

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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Research paper thumbnail of SBML2L

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Research paper thumbnail of SBML2LaTEX

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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Research paper thumbnail of Vision based Localization of Mobile Robots using Kernel approaches

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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Research paper thumbnail of Gas Distribution in Unventilated Indoor Environments Inspected by a Mobile Robot

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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Research paper thumbnail of Online-Positionskorrektur für mobile Roboter durch Korrelation lokaler Gitterkarten

Informatik aktuell, 1999

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Research paper thumbnail of Optimal assignment kernels for attributed molecular graphs

Proceedings of the 22nd international conference on Machine learning - ICML '05, 2005

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Research paper thumbnail of Vibration-based Terrain Classification Using Support Vector Machines

2006 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2006

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Research paper thumbnail of The SNNS Neural Network Simulator

Informatik-Fachberichte, 1991

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Research paper thumbnail of Design and Evaluation of the T-Team of the University of Tuebingen for RoboCup’98

Lecture Notes in Computer Science, 1999

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Research paper thumbnail of Clustering Gene Expression Profiles with Memetic Algorithms

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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Research paper thumbnail of Global robot localization using iterative scale invariant feature transform

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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Research paper thumbnail of Supplementary note for "Prediction of breast cancer by proflling of urinary RNA metabolites using Support Vector Machine-based feature selection

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Metabolomics – eine Strategie zur Identifizierung von prä-diabetischen Stoffwechselveränderungen und neuen Biomarkern?

Diabetologie und Stoffwechsel, 2009

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Research paper thumbnail of Inferring Gene Regulatory Networks by Machine Learning Methods

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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Research paper thumbnail of INFERRING GENE REGULATORY NETWORKS BY MACHINE LEARNING METHODS

Proceedings of the 5th Asia-Pacific Bioinformatics Conference, 2007

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Research paper thumbnail of Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum

2007 IEEE Congress on Evolutionary Computation, 2007

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Benchmarking evolutionary algorithms on convenience kinetics models of the valine and leucine biosynthesis in C. glutamicum

2007 IEEE Congress on Evolutionary Computation, 2007

Bookmarks Related papers MentionsView impact

Research paper thumbnail of A hybrid approach for vision-based outdoor robot localization using global and local image features

2007 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2007

Bookmarks Related papers MentionsView impact

Research paper thumbnail of KEGGtranslator

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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Research paper thumbnail of On the Benefits of Multimodal Optimization for Metablic Network Modeling

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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Research paper thumbnail of SBML2L

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Research paper thumbnail of SBML2LaTEX

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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Research paper thumbnail of Vision based Localization of Mobile Robots using Kernel approaches

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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Research paper thumbnail of Gas Distribution in Unventilated Indoor Environments Inspected by a Mobile Robot

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

Research paper thumbnail of Online-Positionskorrektur für mobile Roboter durch Korrelation lokaler Gitterkarten

Informatik aktuell, 1999

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Research paper thumbnail of Optimal assignment kernels for attributed molecular graphs

Proceedings of the 22nd international conference on Machine learning - ICML '05, 2005

Bookmarks Related papers MentionsView impact

Research paper thumbnail of Vibration-based Terrain Classification Using Support Vector Machines

2006 IEEE/RSJ International Conference on Intelligent Robots and Systems, 2006

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Research paper thumbnail of The SNNS Neural Network Simulator

Informatik-Fachberichte, 1991

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Research paper thumbnail of Design and Evaluation of the T-Team of the University of Tuebingen for RoboCup’98

Lecture Notes in Computer Science, 1999

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