| [1] | Kronfeld, Marcel and Planatscher, Hannes and Zell, Andreas. The {EvA2} Optimization Framework. In Learning and Intelligent Optimization Conference, Special Session
on Software for Optimization (LION-SWOP), pages 247-250,, Venice, Italy,jan, 2010. [url]Bibtex@INPROCEEDINGS{Kron10EvA2,author = {Kronfeld, Marcel and Planatscher, Hannes and Zell, Andreas}, title = {The {EvA2} Optimization Framework}, booktitle = {Learning and Intelligent Optimization Conference, Special Session on Software for Optimization (LION-SWOP)}, year = {2010}, editor = {Blum, Christian and Battiti, Roberto}, number = {6073}, series = {Lecture Notes in Computer Science, LNCS}, pages = {247-250}, address = {Venice, Italy}, month = {jan}, publisher = {Springer Verlag}, abstract = {We present EvA2, a comprehensive metaheuristic optimization framework with emphasis on Evolutionary Algorithms implemented in Java. It presents a modular structure of interfaces and abstract classes for the implementation of optimization problems. End users may choose among several layers of abstraction for an entrance point meeting their requirements on both ease of use and access to extensive functionality. The EvA2 framework has been applied successfully in several academic as well as industrial cooperations and is extended continuously. It is freely available under an open source license (LGPL).}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Kron10EvA2}, owner = {mkron}, project = {abt_zell, optimization, eva}, timestamp = {2010.03.01}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Kron10EvA2Short.pdf}, } |
| [2] | Kronfeld, Marcel and Zell, Andreas. Gaussian Process assisted Particle Swarm Optimization. In Learning and Intelligent Optimization Conference (LION IV), pages 139-153,, Venice, Italy,jan, 2010. Bibtex@INPROCEEDINGS{Kron10GPPSO,author = {Kronfeld, Marcel and Zell, Andreas}, title = {Gaussian Process assisted Particle Swarm Optimization}, booktitle = {Learning and Intelligent Optimization Conference (LION IV)}, year = {2010}, editor = {Blum, Christian and Battiti, Roberto}, number = {6073}, series = {Lecture Notes in Computer Science, LNCS}, pages = {139-153}, address = {Venice, Italy}, month = {jan}, publisher = {Springer Verlag}, abstract = {Real-world optimization problems often are non-convex, non-differentiable and highly multimodal, which is why stochastic, population-based metaheuristics are frequently applied. If the optimization problem is also computationally very expensive, only relatively few function evaluations can be afforded. We develop a model-assisted optimization approach as a coupling of Gaussian Process modeling, a regression technique from machine learning, with the Particle Swarm Optimization metaheuristic. It uses earlier function evaluations to predict areas of improvement and exploits the model information in the heuristic search. Under the assumption of a costly target function, it is shown that model-assistance improves the performance across a set of standard benchmark functions. In return, it is possible to reduce the number of target function evaluations to reach a certain fitness level to speed up the search.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Kron10GPPSO}, owner = {mkron}, project = {abt_zell, optimization, eva2}, timestamp = {2010.03.01}, } |
| [3] | Wrzodek, Clemens and Schröder, Adrian and Dräger, Andreas and
Wanke, Dierk and Berendzen, Kenneth W. and Kronfeld, Marcel and Harter,
Klaus and Zell, Andreas. {ModuleMaster}: A new tool to decipher transcriptional regulatory
networks. , pages 79--81,jan, 2010. [pdf , url]Bibtex@ARTICLE{Wrzodek2010,author = {Wrzodek, Clemens and Schröder, Adrian and Dräger, Andreas and Wanke, Dierk and Berendzen, Kenneth W. and Kronfeld, Marcel and Harter, Klaus and Zell, Andreas}, title = {{ModuleMaster}: A new tool to decipher transcriptional regulatory networks}, journal = {Biosystems}, year = {2010}, volume = {99}, pages = {79--81}, number = {1}, month = {jan}, abstract = {In this article we present ModuleMaster, a novel application for finding \emph{cis}-regulatory modules (CRMs) in sets of co-expressed genes. The application comes with a newly developed method which not only considers transcription factor binding information but also multivariate functional relationships between regulators and target genes to improve the detection of CRMs. Given only the results of a microarray and a subsequent clustering experiment, the program includes all necessary data and algorithms to perform every step to find CRMs. This workbench possesses an easy-to-use graphical user interface, together with job-processing and command-line options, making ModuleMaster a sophisticated program for large-scale batch processing. The detected CRMs can be visualized and evaluated in various ways, i.e., generating GraphML- and R-based whole regulatory network visualizations or generating SBML files for subsequent analytical processing and dynamic modeling. Availability: ModuleMaster is freely available to academics as a webstart application and for download at \url{http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/}, including comprehensive documentation.}, comment = {http://www.cogsys.cs.uni-tuebingen.de/software/ModuleMaster/}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Wrzodek2010.html}, doi = {10.1016/j.biosystems.2009.09.005}, issn = {0303-2647}, keywords = {Gene regulation, Cis-regulatory modules, Regulatory sequence analysis, Matrix scan, Transcription factors}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/wrzodek2010_ModuleMaster.pdf}, project = {abt_zell, bioinformatics, NGFNplus, HepatoSys}, publisher = {Elsevier}, url = {http://dx.doi.org/10.1016/j.biosystems.2009.09.005}, } |
| [4] | Kronfeld, Marcel and Weiss, Christian and Zell, Andreas. Swarm-supported Outdoor Localization with Sparse Visual Data. , pages 166-173,feb, 2010. [pdf , url]Bibtex@ARTICLE{Kron10LocRAS,author = {Kronfeld, Marcel and Weiss, Christian and Zell, Andreas}, title = {Swarm-supported Outdoor Localization with Sparse Visual Data}, journal = {Robotics and Autonomous Systems. Selected papers from the 2007 European Conference on Mobile Robots (ECMR 2007)}, year = {2010}, volume = {58}, pages = {166-173}, number = {2}, month = {feb}, abstract = {The localization of mobile systems with video data is a challenging field in robotic vision research. Apart from support technologies like GPS, a self-sufficient visual system is desirable. We introduce a new heuristic approach to outdoor localization in a scenario with sparse visual data and without odometry readings. Localization is interpreted as an optimization problem, and a swarm-based optimization method is adapted and applied, remaining independent of the specific visual feature type. The new method obtains similar or better localization results in our experiments while requiring only two-thirds of the number of image comparisons, indicating an all-over speed-up by 25%.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Kron10LocRAS}, doi = {10.1016/j.robot.2009.09.012}, keywords = {Outdoor robotics; Robot vision; Visual localization; Swarm intelligence; Particle swarm optimization}, owner = {mkron}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2009/Kron09SwarmSupp.pdf}, project = {abt_zell, optimization, swarm-intelligence, robotics}, timestamp = {2010.03.17}, url = {http://www.sciencedirect.com/science/article/B6V16-4X908T5-3/2/559434e23a220afad0b33d51ed559198}, } |
| [5] | Hoene, Miriam and Franken, Holger and Fritsche, Louise and Lehmann,
Rainer and Pohl, Ann Kathrin and Häring, Hans-Ulrich and Zell,
Andreas and Schleicher, Erwin D. and Weigert, Cora. Activation of the mitogen-activated protein kinase ({MAPK}) signalling
pathway in the liver of mice is related to plasma glucose levels
after acute exercise. , pages 1131--1141,mar, 2010. [pdf , url]Bibtex@ARTICLE{Hoene2010,author = {Hoene, Miriam and Franken, Holger and Fritsche, Louise and Lehmann, Rainer and Pohl, Ann Kathrin and Häring, Hans-Ulrich and Zell, Andreas and Schleicher, Erwin D. and Weigert, Cora}, title = {Activation of the mitogen-activated protein kinase ({MAPK}) signalling pathway in the liver of mice is related to plasma glucose levels after acute exercise}, journal = {Diabetologia}, year = {2010}, volume = {53}, pages = {1131--1141}, number = {6}, month = {mar}, abstract = {AIMS/HYPOTHESIS: We aimed to identify, in the liver of mice, signal transduction pathways that show a pronounced regulation by acute exercise. We also aimed to elucidate the role of metabolic stress in this response. METHODS: C57Bl6 mice performed a 60 min run on a treadmill under non-exhaustive conditions. Hepatic RNA and protein lysates were prepared immediately after running and used for whole-genome-expression analysis, quantitative real-time PCR and immunoblotting. A subset of mice recovered for 3 h after the treadmill run. A further group of mice performed the treadmill run after having received a vitamin C- and vitamin E-enriched diet over 4 weeks. RESULTS: The highest number of genes differentially regulated by exercise in the liver was found in the mitogen-activated protein kinase (MAPK) signalling pathway, with a pronounced and transient upregulation of the transcription factors encoded by c-Fos (also known as Fos), c-Jun (also known as Jun), FosB (also known as Fosb) and JunB (also known as Junb) and phosphorylation of hepatic MAPK. Acute exercise also activated the p53 signalling pathway. A major role for oxidative stress is unlikely since the antioxidant-enriched diet did not prevent the activation of the MAPK pathway. In contrast, lower plasma glucose levels after running were related to enhanced levels of MAPK signalling proteins, similar to the upregulation of Igfbp1 and Pgc-1alpha (also known as Ppargc1a). In the working muscle the activation of the MAPK pathway was weak and not related to plasma glucose concentrations. CONCLUSIONS/INTERPRETATION: Metabolic stress evidenced as low plasma glucose levels appears to be an important determinant for the activation of the MAPK signalling pathway and the transcriptional response of the liver to acute exercise.}, doi = {10.1007/s00125-010-1666-3}, institution = {Division of Endocrinology, Diabetology, Angiology, Nephrology, Pathobiochemistry and Clinical Chemistry, Department of Internal Medicine, University Hospital of Tuebingen, Otfried-Mueller-Strasse 10, D-72076, Tuebingen, Germany.}, issn = {0012-186X}, language = {eng}, pst = {aheadofprint}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Hoene2010.pdf}, pmid = {20195842}, project = {diabetes, abt_zell, bioinformatics}, publisher = {Springer}, url = {http://dx.doi.org/10.1007/s00125-010-1666-3}, } |
| [6] | Peter Bayer and Michael de Paly and Claudius N. Bürger. Optimization of high-reliability-based hydrological design problems
by robust automatic sampling of critical model realizations. , pages W05504,may, 2010. [url]Bibtex@ARTICLE{DePalyWRR10,author = {Peter Bayer and Michael de Paly and Claudius N. Bürger}, title = {Optimization of high-reliability-based hydrological design problems by robust automatic sampling of critical model realizations}, journal = {Water Resources Research}, year = {2010}, volume = {46}, pages = {W05504}, number = {5}, month = {may}, abstract = {This study demonstrates the high efficiency of the so-called stack-ordering technique for optimizing a groundwater management problem under uncertain conditions. The uncertainty is expressed by multiple equally probable model representations, such as realizations of hydraulic conductivity. During optimization of a well-layout problem for contaminant control, a ranking mechanism is applied that extracts those realizations that appear most critical for the optimization problem. It is shown that this procedure works well for evolutionary optimization algorithms, which are to some extent robust against noisy objective functions. More precisely, differential evolution (DE) and the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) are applied. Stack ordering is comprehensively investigated for a plume management problem at a hypothetical template site based on parameter values measured at and on a geostatistical model developed for the Lauswiesen study site near Tübingen, Germany. The straightforward procedure yields computational savings above 90% in comparison to always evaluating the full set of realizations. This is confirmed by cross testing with four additional validation cases. The results show that both evolutionary algorithms obtain highly reliable near-optimal solutions. DE appears to be the better choice for cases with significant noise caused by small stack sizes. On the other hand, there seems to be a problem-specific threshold for the evaluation stack size above which the CMA-ES achieves solutions with both better fitness and higher reliability.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?DePalyWRR10}, doi = {10.1029/2009WR008081}, issn = {00431397}, keywords = {optimization groundwater management 1829 Hydrology: Groundwater hydrology 6309 Policy Sciences: Decision making under uncertainty 1805 Hydrology: Computational hydrology 6344 Policy Sciences: System operation and management}, owner = {paly}, project = {optimization, hydrogeo, extern, abt_zell}, publisher = {AGU}, timestamp = {2010.04.26}, url = {http://dx.doi.org/10.1029/2009WR008081}, } |
| [7] | Jahn, Andreas and Hinselmann, Georg and Fechner, Nikolas and Henneges,
Carsten and Zell, Andreas. Probabilistic Modeling of Conformational Space for 3D Machine Learning
Approaches. , pages 441--455,may, 2010. Bibtex@ARTICLE{Jahn2010,author = {Jahn, Andreas and Hinselmann, Georg and Fechner, Nikolas and Henneges, Carsten and Zell, Andreas}, title = {Probabilistic Modeling of Conformational Space for 3D Machine Learning Approaches}, journal = {Molecular Informatics}, year = {2010}, volume = {29}, pages = {441--455}, number = {5}, month = {may}, abstract = {We present a new probabilistic encoding of the conformational space of a molecule that allows for the integration into common similarity calculations. The method uses distance profiles of flexible atom-pairs and computes generative models that describe the distance distribution in the conformational space. The generative models permit the use of probabilistic kernel functions and, therefore, our approach can be used to extend existing 3D molecular kernel functions, as applied in support vector machines, to build QSAR models. The resulting kernels are valid 4D kernel functions and reduce the dependency of the model quality on suitable conformations of the molecules. We showed in several experiments the robust performance of the 4D kernel function, which was extended by our approach, in comparison to the original 3D-based kernel function. The new method compares the conformational space of two molecules within one kernel evaluation. Hence, the number of kernel evaluations is significantly reduced in comparison to common kernel-based conformational space averaging techniques. Additionally, the performance gain of the extended model correlates with the flexibility of the data set and enables an a priori estimation of the model improvement.}, doi = {10.1002/minf.201000036}, owner = {jahn}, project = {abt_zell, cheminformatics}, timestamp = {2010.04.27}, } |
| [8] | Huimin Lu and Hui Zhang and Shaowu Yang and Zhiqiang Zheng. Camera parameters auto-adjusting technique for robust robot vision. In 2010 IEEE International Conference on Robotics and Automation (ICRA
2010), pages 1518-1523,, Anchorage, Alaska, USA,may, 2010. [url]Bibtex@INPROCEEDINGS{Yangs2010,author = {Huimin Lu and Hui Zhang and Shaowu Yang and Zhiqiang Zheng}, title = {Camera parameters auto-adjusting technique for robust robot vision}, booktitle = {2010 IEEE International Conference on Robotics and Automation (ICRA 2010)}, year = {2010}, pages = {1518-1523}, address = {Anchorage, Alaska, USA}, month = {may}, days = {3-7}, owner = {yangs}, project = {extern}, timestamp = {2012.05.14}, url = {http://ieeexplore.ieee.org/xpl/freeabs_all.jsp?arnumber=5509978}, } |
| [9] | Philipp Vorst and Andreas Zell. Fully Autonomous Trajectory Estimation with Long-Range Passive {RFID}. In 2010 IEEE International Conference on Robotics and Automation (ICRA), pages 1867--1872,, Anchorage, Alaska, USA,may, 2010. [url]Bibtex@INPROCEEDINGS{vorst2010icra,author = {Philipp Vorst and Andreas Zell}, title = {Fully Autonomous Trajectory Estimation with Long-Range Passive {RFID}}, booktitle = {2010 IEEE International Conference on Robotics and Automation (ICRA)}, year = {2010}, pages = {1867--1872}, address = {Anchorage, Alaska, USA}, month = {may}, publisher = {IEEE}, abstract = {We present a novel approach which enables a mobile robot to estimate its trajectory in an unknown environment with long-range passive radio-frequency identification (RFID). The estimation is based only on odometry and RFID measurements. The technique requires no prior observation model and makes no assumptions on the RFID setup. In particular, it is adaptive to the power level, the way the RFID antennas are mounted on the robot, and environmental characteristics, which have major impact on long-range RFID measurements. Tag positions need not be known in advance, and only the arbitrary, given infrastructure of RFID tags in the environment is utilized. By a series of experiments with a mobile robot, we show that trajectory estimation is achieved accurately and robustly.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/vorst/publications/vorst2010icra.html}, doi = {10.1109/ROBOT.2010.5509810}, isbn = {978-1-4244-5040-4}, issn = {1050-4729}, project = {abt_zell, robotics, ambisense, rfid}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/vorst2010icra.pdf}, } |
| [10] | Marius Hofmeister and Philipp Vorst and Andreas Zell. A Comparison of Efficient Global Image Features for Localizing Small
Mobile Robots. In ISR/ROBOTIK 2010 (Proceedings of the joint conference of ISR 2010
(41st International Symposium on Robotics) and ROBOTIK 2010 (6th
German Conference on Robotics)), pages 143--150,jun, 2010. [url]Bibtex@INPROCEEDINGS{Hofmeister2010CompEff,author = {Marius Hofmeister and Philipp Vorst and Andreas Zell}, title = {A Comparison of Efficient Global Image Features for Localizing Small Mobile Robots}, booktitle = {ISR/ROBOTIK 2010 (Proceedings of the joint conference of ISR 2010 (41st International Symposium on Robotics) and ROBOTIK 2010 (6th German Conference on Robotics))}, year = {2010}, pages = {143--150}, month = {jun}, publisher = {VDE Verlag}, abstract = {Global image features are well-suited for the visual self-localization of mobile robots. They are fast to compute, to compare and do not require much storage space. Especially when using small mobile robots with limited processing capabilities and low-resolution cameras, global features can be preferred to local features. In this paper, we compare the accuracy and computation times of different global image features when localizing small mobile robots. We test the methods under realistic conditions, taking illumination changes and translations into account. By employing a particle filter and reducing the image resolution, we speed up the localization process considerably.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Hofmeister2010CompEff}, isbn = {978-3-8007-3273-9}, project = {abt_zell, robotics, ctbots}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/hofmeister2010isr.pdf}, } |
| [11] | Jin Hou and Dengsheng Zhang and Zeng Chen and Lixing Jiang and Huazhong
Zhang and Xue Qin. Web Image Search by Automatic Image Annotation and Translation. In 17th International Conference on Systems, Signals and Image Processing
(IWSSIP'10), Rio de Janeiro, Brazil,June, 2010. [url]Bibtex@INPROCEEDINGS{jiang_hou2010,author = {Jin Hou and Dengsheng Zhang and Zeng Chen and Lixing Jiang and Huazhong Zhang and Xue Qin}, title = {Web Image Search by Automatic Image Annotation and Translation}, booktitle = {17th International Conference on Systems, Signals and Image Processing (IWSSIP'10)}, year = {2010}, address = {Rio de Janeiro, Brazil}, month = {June}, project = {extern}, url = {http://www.creacteve.com.br/iwssip/nav/papers/paper_26.pdf}, } |
| [12] | Planatscher, Hannes and Supper, Jochen and Poetz, Oliver and Stoll,
Dieter and Joos, Thomas and Templin, Markus and Zell, Andreas. Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry. , pages 28,jun, 2010. [url]Bibtex@ARTICLE{Planatscher2010,author = {Planatscher, Hannes and Supper, Jochen and Poetz, Oliver and Stoll, Dieter and Joos, Thomas and Templin, Markus and Zell, Andreas}, title = {Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry}, journal = {Algorithms for Molecular Biology}, year = {2010}, volume = {5}, pages = {28}, number = {1}, month = {jun}, abstract = {BACKGROUND: Mass spectrometry (MS) based protein profiling has become one of the key technologies in biomedical research and biomarker discovery. One bottleneck in MS-based protein analysis is sample preparation and an efficient fractionation step to reduce the complexity of the biological samples, which are too complex to be analyzed directly with MS. Sample preparation strategies that reduce the complexity of tryptic digests by using immunoaffinity based methods have shown to lead to a substantial increase in throughput and sensitivity in the proteomic mass spectrometry approach. The limitation of using such immunoaffinity-based approaches is the availability of the appropriate peptide specific capture antibodies. Recent developments in these approaches, where subsets of peptides with short identical terminal sequences can be enriched using antibodies directed against short terminal epitopes, promise a significant gain in efficiency.RESULTS:We show that the minimal set of terminal epitopes for the coverage of a target protein list can be found by the formulation as a set cover problem, preceded by a filtering pipeline for the exclusion of peptides and target epitopes with undesirable properties.CONCLUSIONS:For small datasets (a few hundred proteins) it is possible to solve the problem to optimality with moderate computational effort using commercial or free solvers. Larger datasets, like full proteomes require the use of heuristics.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Planatscher2010}, doi = {10.1186/1748-7188-5-28}, isbn = {1748-7188}, project = {abt_zell, txp, bioinformatics}, url = {http://www.almob.org/content/5/1/28}, } |
| [13] | Philipp Vorst and Andreas Zell. A Comparison of Similarity Measures for Localization with Passive
{RFID} Fingerprints. In ISR/ROBOTIK 2010 (Proceedings of the joint conference of ISR 2010
(41st International Symposium on Robotics) and ROBOTIK 2010 (6th
German Conference on Robotics)), pages 354--361,jun, 2010. [url]Bibtex@INPROCEEDINGS{vorst2010isr,author = {Philipp Vorst and Andreas Zell}, title = {A Comparison of Similarity Measures for Localization with Passive {RFID} Fingerprints}, booktitle = {ISR/ROBOTIK 2010 (Proceedings of the joint conference of ISR 2010 (41st International Symposium on Robotics) and ROBOTIK 2010 (6th German Conference on Robotics))}, year = {2010}, pages = {354--361}, month = {jun}, publisher = {VDE Verlag}, abstract = {We present a novel approach to self-localization with passive RFID fingerprints using vector space similarity measures and weighted k-nearest neighbors (WKNN). Embedded in a particle filter, our technique provides robust and accurate position estimates. This is shown through various experiments with a mobile robot. The formulation of the observation model guarantees applicability to any type of off-the-shelf RFID reader which counts RFID tag detections. Different similarity measures are investigated, and a new measure is proposed.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/vorst/publications/vorst2010isr.html}, isbn = {978-3-8007-3273-9}, project = {abt_zell, robotics, ambisense, rfid}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/vorst2010isr.pdf}, } |
| [14] | Markus Beck and Jozsef Hecht-Mendez and Michael de Paly and Peter
Bayer and Philipp Blum and Andreas Zell. Optimization of the Energy Extraction of a Shallow Geothermal System. In Proceedings of the IEEE Congress on Evolutionary Computation (CEC), pages 3622-3628,, Barcelona, Spain,jul, 2010. Bibtex@INPROCEEDINGS{Beck10,author = {Markus Beck and Jozsef Hecht-Mendez and Michael de Paly and Peter Bayer and Philipp Blum and Andreas Zell}, title = {Optimization of the Energy Extraction of a Shallow Geothermal System}, booktitle = {Proceedings of the IEEE Congress on Evolutionary Computation (CEC)}, year = {2010}, pages = {3622-3628}, address = {Barcelona, Spain}, month = {jul}, abstract = {Geothermal energy use from shallow groundwater systems is attractive for the supply of heat and hot water to buildings. It offers economic and environmental advantages over traditional fossil-fuel based technologies, in particular when large scale systems are well adapted to the always unique hydrogeological conditions. Computer based numerical simulations are used to examine the performance of multiple borehole heat exchangers installed in the ground. This paper demonstrates how evolutionary algorithms can be utilized to configure the elements of a geothermal system in an ideal way, and thus substantially enhance the energy extraction rate in comparison to standardized approaches. Differential evolution (DE), evolution strategies (ES) and particle swarm optimizers (PSO) are combined with a local search approach and compared with respect to their efficiency in the optimization of synthetic, real case oriented and static systems. First results are promising, especially for the PSO and the DE with the local search approach.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Beck10}, doi = {10.1109/CEC.2010.5585921}, owner = {paly}, project = {abt_zell, hydrogeo, eva2, optimization}, timestamp = {2010.04.26}, } |
| [15] | Dräger, Andreas and Schröder, Adrian and Zell, Andreas. Systems Biology for Signaling Networks. , pages 159--205,jul, 2010. [url]Bibtex@INBOOK{Draeger2010a,chapter = {Automating mathematical modeling of biochemical reaction networks}, pages = {159--205}, title = {Systems Biology for Signaling Networks}, publisher = {Springer-Verlag}, year = {2010}, editor = {Choi, Sangdun}, author = {Dräger, Andreas and Schröder, Adrian and Zell, Andreas}, volume = {1}, series = {Systems Biology}, month = {jul}, abstract = {In this chapter we introduce a five-step modeling pipeline that ultimately leads to a mathematical description of a biochemical reaction system. We discuss how to automate each single step and how to put these steps together: First, we have to create a topology of interconversion processes and mutual influences between reactive species. An automated modeling procedure requires an appropriate data format that encodes the model in a computer-readable form. A standard like the Systems Biology Markup Language (SBML) serves this purpose and allows us to add semantic information to each component of the model. Second, from such an annotated network the procedure SBMLsqueezer generates kinetic equations in a context sensitive manner. The resulting model can then be combined with already existing models. Third, we estimate the values of all newly introduced parameters in each created rate law. This procedure requires a time series of quantitative measurements of the reactive species within this system to be available, because we calibrate the parameters with the aim that the model will fit these experimental data. Fourth, an experimental validation of the resulting model is advisable. Finally, a model report should be generated to document the model with all of its components. For a better understanding, we start our consideration with an introduction into necessary standardization attempts in today's systems biology and generalized approaches for common rate equations before we discuss the computer-aided modeling, parameter estimation, and automatic report generation. We complete this chapter with a discussion on possible further improvements of our modeling pipeline.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Draeger2010a.html}, doi = {10.1007/978-1-4419-5797-9_7}, project = {abt_zell, bioinformatics, NGFN-II, NGFNplus, HepatoSys, metabolic_network_identification, SBML2LaTeX, SBMLsqueezer}, url = {http://www.springerlink.com/content/n77k80h76vj17806}, } |
| [16] | Kanjanawanishkul, Kiattisin and Hofmeister, Marius and Zell, Marius. Experiments on Formation Switching for Mobile Robots. In IEEE/ASME International Conference on Advanced Intelligent Mechatronics
(AIM 2010), pages 323--328,, Montr{\'e}al, Canada,July, 2010. [url]Bibtex@INPROCEEDINGS{kanjanaw_AIM2010,author = {Kanjanawanishkul, Kiattisin and Hofmeister, Marius and Zell, Marius}, title = {Experiments on Formation Switching for Mobile Robots}, booktitle = {IEEE/ASME International Conference on Advanced Intelligent Mechatronics (AIM 2010)}, year = {2010}, pages = {323--328}, address = {Montr{\'e}al, Canada}, month = {July}, project = {abt_zell, robotics, ctbots}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/kanjanaw2010aim.pdf}, } |
| [17] | Koch, Artur. Fast and Scalable {CPU}/{GPU} Collision Detection for Rigid and Deformable
Surfaces. jul, 2010. [url]Bibtex@Diplomarbeit{koch2010thesis,author = {Koch, Artur}, title = {Fast and Scalable {CPU}/{GPU} Collision Detection for Rigid and Deformable Surfaces}, school = {University of Tuebingen}, year = {2010}, month = {jul}, abstract = {...}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?koch2010thesis}, project = {extern}, url = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/koch/publications/koch2010diplomathesis.pdf}, } |
| [18] | Kronfeld, Marcel and Zell, Andreas. Towards Scalability in Niching Methods. In Proceedings of the IEEE Congress on Evolutionary Computation (CEC), pages 4409--4416,, Barcelona, Spain,jul, 2010. [url]Bibtex@INPROCEEDINGS{Kron10Niching,author = {Kronfeld, Marcel and Zell, Andreas}, title = {Towards Scalability in Niching Methods}, booktitle = {Proceedings of the IEEE Congress on Evolutionary Computation (CEC)}, year = {2010}, pages = {4409--4416}, address = {Barcelona, Spain}, month = {jul}, abstract = {The scaling properties of multimodal optimization methods have seldom been studied, and existing studies often concentrated on the idea that all local optima of a multimodal function can be found and their number can be estimated a priori. We argue that this approach is impractical for complex, high-dimensional target functions, and we formulate alternative criteria for scalable multimodal optimization methods. We suggest that a scalable niching method should return the more local optima the longer it is run, without relying on a fixed number of expected optima. This can be fulfilled by sequential and semi-sequential niching methods, several of which are presented and analyzed in that respect. Results show that, while sequential local search is very successful on simpler functions, a clustering-based particle swarm approach is most successful on multi-funnel functions, offering scalability even under deceptive multimodality, and denoting it a starting point towards effective scalable niching.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Kron10Niching}, isbn = {978-1-4244-6910-9}, owner = {mkron}, project = {abt_zell, swarm-intelligence, eva2, optimization}, timestamp = {2010.04.22}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Kron10Scaling.pdf}, } |
| [19] | Lambeck, Sandro and Dräger, Andreas and Guthke, Reinhard. Network Inference by Considering Multiple Objectives: Insights from
In Vivo Transcriptomic Data Generated by a Synthetic Network. In International Conference on Bioinformatics and Computational Biology,
BIOCOMP 2010, pages 734--742,jul, 2010. [url]Bibtex@INPROCEEDINGS{Lambeck2010,author = {Lambeck, Sandro and Dräger, Andreas and Guthke, Reinhard}, title = {Network Inference by Considering Multiple Objectives: Insights from In Vivo Transcriptomic Data Generated by a Synthetic Network}, booktitle = {International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010}, year = {2010}, editor = {Arabnia, Hamid R. and Tran, Quoc-Nam and Chang, Rui and He, Matthew and Marsh, Andy and Solo, Ashu M. G. and Yang, Jack Y.}, volume = {2}, pages = {734--742}, month = {jul}, publisher = {CSREA Press}, abstract = {This paper addresses the problem of finding gene regulatory networks for various data sets derived from the same underlying network, but challenged to different stimuli. To this end, we propose to adapt solutions of systems of non-linear difference equations by including multiple objectives. The model structure and parameter estimation, is facilitated by application of an hybrid Evolutionary Multi-Objective Algorithm. Furthermore, we compare the fit of the logistic and double logistic transfer function. The application is driven by data obtained from a recently published synthetic gene regulatory network, being especially designed for the assessment of network inference methods. Inferred networks were in high accordance with the designed structure and indicated the favor of a multi-objective approach including all available data. The double logistic transfer function outperformed the logistic transfer function to model saturation effects. Results also suggested that the protein-protein interaction should be integrated in the model of transcriptional regulation.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Lambeck2010.html}, isbn = {1-60132-134-1}, keywords = {Network Inference; Synthetic Biology; Multiple Objective Optimization}, project = {extern, bioinformatics, HepatoSys}, url = {http://www.cs.uga.edu/~hra/2010-proceedings-final/biocomp/papers.pdf}, } |
| [20] | Michael de Paly and Niels Schuetze and Andreas Zell. Determining Crop-Production Functions using Multi-Objective Evolutionary
Algorithms. In Proceedings of the IEEE Congress on Evolutionary Computation (CEC), pages 1870 - 1877,, Barcelona, Spain,jul, 2010. Bibtex@INPROCEEDINGS{DePaly10,author = {Michael de Paly and Niels Schuetze and Andreas Zell}, title = {Determining Crop-Production Functions using Multi-Objective Evolutionary Algorithms}, booktitle = {Proceedings of the IEEE Congress on Evolutionary Computation (CEC)}, year = {2010}, pages = {1870 - 1877}, address = {Barcelona, Spain}, month = {jul}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?DePaly10}, doi = {10.1109/CEC.2010.5586147}, project = {abt_zell, irrigation, hydrogeo, eva2, optimization}, timestamp = {2010.04.26}, } |
| [21] | Hofmeister, Marius and Kronfeld, Marcel. Multi-robot Coverage Considering Line-of-sight Conditions. In 7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV), Lecce, Italy,sep, 2010. [url]Bibtex@INPROCEEDINGS{hofmeistIAV,author = {Hofmeister, Marius and Kronfeld, Marcel}, title = {Multi-robot Coverage Considering Line-of-sight Conditions}, booktitle = {7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV)}, year = {2010}, address = {Lecce, Italy}, month = {sep}, project = {abt_zell, robotics, ctbots, hetTeam}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/hofmeister2010iav.pdf}, } |
| [22] | Kiattisin Kanjanawanishkul and Marius Hofmeister and Andreas Zell. Path Following with an Optimal Forward Velocity for a Mobile Robot. In 7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV), Lecce, Italy,sep, 2010. [url]Bibtex@INPROCEEDINGS{kanjanaw_IAV2010_1,author = {Kiattisin Kanjanawanishkul and Marius Hofmeister and Andreas Zell}, title = {Path Following with an Optimal Forward Velocity for a Mobile Robot}, booktitle = {7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV)}, year = {2010}, address = {Lecce, Italy}, month = {sep}, project = {abt_zell, robotics, ctbots}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/kanjanaw2010iav.pdf}, } |
| [23] | Kiattisin Kanjanawanishkul and Andreas Zell. Distributed Role Assignment in Multi-robot Formation. In 7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV), Lecce, Italy,sep, 2010. Bibtex@INPROCEEDINGS{kanjanaw_IAV2010_2,author = {Kiattisin Kanjanawanishkul and Andreas Zell}, title = {Distributed Role Assignment in Multi-robot Formation}, booktitle = {7th IFAC Symposium on Intelligent Autonomous Vehicles (IAV)}, year = {2010}, address = {Lecce, Italy}, month = {sep}, abtract = {In this paper, we study the problem of distributed role assignment for multiple mobile robots. This problem arises when a mobile robot in the team must decide what role to take on in a desired formation configuration. In some applications, in which the center and orientation of a desired formation are not predetermined, the rotation and translation of the formation can be computed by using average consensus protocols. A conflict arises when the same role is assigned to more than one robot. This problem is resolved by using a negotiation strategy, while each assigned robot is traveling to the target position. Furthermore, dynamic consensus is used to measure the degree of task completion in this work. Once the consensus reaches a preset threshold, implying that robots should abandon the current task and start the next one. We verify our proposed framework through simulations on a team of nonholonomic mobile robots performing distributed formation switching.}, project = {abt_zell, robotics, ctbots}, } |
| [24] | Komma, Philippe and Zell, Andreas. Clustering Vibration Data Using a Temporally Coherent {E}xpectation
{M}aximization Approach. In 7th Symposium on Intelligent Autonomous Vehicles (IAV 2010), pages 1-6,, Lecce, Italy,sep, 2010. Bibtex@INPROCEEDINGS{komma10a,author = {Komma, Philippe and Zell, Andreas}, title = {Clustering Vibration Data Using a Temporally Coherent {E}xpectation {M}aximization Approach}, booktitle = {7th Symposium on Intelligent Autonomous Vehicles (IAV 2010)}, year = {2010}, pages = {1-6}, address = {Lecce, Italy}, month = {sep}, project = {abt_zell, robotics}, } |
| [25] | Komma, Philippe and Zell, Andreas. Markov Random Field-based Clustering of Vibration Data. In IEEE/RSJ International Conference on Intelligent Robots and Systems
(IROS 2010), pages 1902-1908,, Taipei, Taiwan,oct, 2010. [url]Bibtex@INPROCEEDINGS{komma10b,author = {Komma, Philippe and Zell, Andreas}, title = {Markov Random Field-based Clustering of Vibration Data}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2010)}, year = {2010}, pages = {1902-1908}, address = {Taipei, Taiwan}, month = {oct}, note = {Best Paper Award Nominee}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/komma2010iros-mrfcluster.pdf}, } |
| [26] | Xingzhe Xie and Heng Wang and Ran Liu and Wen-qiang Xiang and Ming
Jiang. 3D Terrain Reconstruction for Patrol Robot Using Point Grey Research
Stereo Vision Cameras. In Proceedings of the 2010 International Conference on Artificial Intelligence
and Computational Intelligence (AICI '10), pages 47--51,, Sanya, China,October, 2010. Bibtex@INPROCEEDINGS{Liu2010:3D,author = {Xingzhe Xie and Heng Wang and Ran Liu and Wen-qiang Xiang and Ming Jiang}, title = {3D Terrain Reconstruction for Patrol Robot Using Point Grey Research Stereo Vision Cameras}, booktitle = {Proceedings of the 2010 International Conference on Artificial Intelligence and Computational Intelligence (AICI '10)}, year = {2010}, volume = {1}, pages = {47--51}, address = {Sanya, China}, month = {October}, abstract = {This paper uses Bumblebee stereo vision system to reconstruct the 3D terrain for patrol robot. Firstly, with the selected points in the disparity image, the ground plane equation of the current frame is calculated by the RANSAC (Random Sample Consensus) algorithm, and then estimated and predicted by the Kalman filter. Secondly, the elevation image is obtained through the distance between the obstacle and the ground plane, which is calculated on basis of the formula from the point to the plane. Finally, the noise points in the elevation image are removed through erosion and dilation operations, and the location and size of obstacles are determined via the connected component analysis method. The actual test in substation environment verified the reliability of the system.}, acmid = {1917716}, days = {23-24}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Liu2010:3D}, doi = {http://dx.doi.org/10.1109/AICI.2010.17}, isbn = {978-0-7695-4225-6}, keywords = {patrol robot, RANSAC algorithm, Kalman filter, connected component analysis}, numpages = {5}, project = {extern}, } |
| [27] | Schauwecker, Konstantin and Klette, Reinhard. {A Comparative Study of Two Vertical Road Modelling Techniques}. In ACCV Workshop: Computer Vision in Vehicle Technology, pages 174--183,, Queenstown, New Zealand,November, 2010. [url]Bibtex@INPROCEEDINGS{Schauwecker2010,author = {Schauwecker, Konstantin and Klette, Reinhard}, title = {{A Comparative Study of Two Vertical Road Modelling Techniques}}, booktitle = {ACCV Workshop: Computer Vision in Vehicle Technology}, year = {2010}, pages = {174--183}, address = {Queenstown, New Zealand}, month = {November}, publisher = {Springer}, abstract = {Binocular vision combined with stereo matching algorithms can be used in vehicles to gatherdata of the spatial proximity. To utilize this data we propose a new method for modeling thevertical road profile from a disparity map. This method is based on a region-growing technique,which iteratively performs a least-squares fit of a B-spline curve to a region of selectedpoints. We compare this technique to two variants of the $v$-disparity method using either anenvelope function or a planarity assumption. Our findings are that the proposed road-modelingtechnique outperforms both variants of the $v$-disparity technique, for which the planarityassumption is slightly better than the envelope version.}, owner = {schauwecker}, project = {extern}, url = {http://www.springerlink.com/content/gh26u84p44037834/}, } |
| [28] | Schröder, Adrian and Eichner, Johannes and Supper, Jochen and Eichner,
Jonas and Wanke, Dierk and Henneges, Carsten and Zell, Andreas. {Predicting DNA-Binding Specificities of Eukaryotic Transcription
Factors}. , pages e13876,nov, 2010. [pdf , url]Bibtex@ARTICLE{Schroeder2010,author = {Schröder, Adrian and Eichner, Johannes and Supper, Jochen and Eichner, Jonas and Wanke, Dierk and Henneges, Carsten and Zell, Andreas}, title = {{Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2010}, volume = {5}, pages = {e13876}, number = {11}, month = {nov}, abstract = {Today, annotated amino acid sequences of more and more transcription factors (TFs) are readily available. Quantitative information about their DNA-binding specificities, however, are hard to obtain. Position frequency matrices (PFMs), the most widely used models to represent binding specificities, are experimentally characterized only for a small fraction of all TFs. Even for some of the most intensively studied eukaryotic organisms (i.e., human, rat and mouse), roughly one-sixth of all proteins with annotated DNA-binding domain have been characterized experimentally. Here, we present a new method based on support vector regression for predicting quantitative DNA-binding specificities of TFs in different eukaryotic species. This approach estimates a quantitative measure for the PFM similarity of two proteins, based on various features derived from their protein sequences. The method is trained and tested on a dataset containing 1 239 TFs with known DNA-binding specificity, and used to predict specific DNA target motifs for 645 TFs with high accuracy.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Schroeder2010}, doi = {10.1371/journal.pone.0013876}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/schroederTFBSPrediction.pdf}, project = {abt_zell, bioinformatics}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0013876}, } |
| [29] | Ulrich Weiss and Peter Biber and Stefan Laible and Karsten Bohlmann
and Andreas Zell. Plant Species Classification Using a 3D LIDAR Sensor and Machine
Learning. In Machine Learning and Applications (ICMLA), 2010 Ninth International
Conference on, pages 339--345,, Washington, D.C., USA,dec., 2010. [url]Bibtex@INPROCEEDINGS{weiss2010icmla,author = {Ulrich Weiss and Peter Biber and Stefan Laible and Karsten Bohlmann and Andreas Zell}, title = {Plant Species Classification Using a 3D LIDAR Sensor and Machine Learning}, booktitle = {Machine Learning and Applications (ICMLA), 2010 Ninth International Conference on}, year = {2010}, pages = {339--345}, address = {Washington, D.C., USA}, month = {dec.}, organization = {IEEE Computer Society}, publisher = {IEEE}, abstract = {In the domain of agricultural robotics, one major application is crop scouting, e.g., for the task of weed control. For this task a key enabler is a robust detection and classification of the plant and species. Automatically distinguishing between plant species is a challenging task, because some species look very similar. It is also difficult to translate the symbolic high level description of the appearances and the differences between the plants used by humans, into a formal, computer understandable form. Also it is not possible to reliably detect structures, like leaves and branches in 3D data provided by our sensor. One approach to solve this problem is to learn how to classify the species by using a set of example plants and machine learning methods. In this paper we are introducing a method for distinguishing plant species using a 3D LIDAR sensor and supervised learning. For that we have developed a set of size and rotation invariant features and evaluated experimentally which are the most descriptive ones. Besides these features we have also compared different learning methods using the toolbox Weka. It turned out that the best methods for our application are simple logistic regression functions, support vector machines and neural networks. In our experiments we used six different plant species, typically available at common nurseries, and about 20 examples of each species. In the laboratory we were able to identify over 98% of these plants correctly.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?weiss2010icmla}, doi = {10.1109/ICMLA.2010.57}, keywords = {3D LIDAR sensor;Weka;agricultural robotics;crop scouting;logistic regression;machine learning;neural networks;plant species classification;supervised learning;support vector machines;agriculture;biology computing;botany;learning (artificial intelligence);neural nets;optical radar;robots;support vector machines;}, owner = {laible}, project = {abt_zell, robotics, bonirob}, timestamp = {2010.10.06}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/weiss2010icmla.pdf}, } |
| [30] | Bertsch, Andreas and Jung, Stephan and Zerck, Alexandra and Pfeifer,
Nico and Nahnsen, Sven and Henneges, Carsten and Nordheim, Alfred
and Kohlbacher, Oliver. Optimal de novo Design of MRM Experiments for Rapid Assay Development
in Targeted Proteomics. , pages 2696-2704,2010. [url]Bibtex@ARTICLE{Bertsch2010,author = {Bertsch, Andreas and Jung, Stephan and Zerck, Alexandra and Pfeifer, Nico and Nahnsen, Sven and Henneges, Carsten and Nordheim, Alfred and Kohlbacher, Oliver}, title = {Optimal de novo Design of MRM Experiments for Rapid Assay Development in Targeted Proteomics}, journal = {Journal of Proteome Research}, year = {2010}, volume = {9}, pages = {2696-2704}, number = {5}, note = {PMID: 20201589}, doi = {10.1021/pr1001803}, eprint = {http://pubs.acs.org/doi/pdf/10.1021/pr1001803}, project = {abt_zell, bioinformatics}, url = {http://pubs.acs.org/doi/abs/10.1021/pr1001803}, } |
| [31] | Fechner, Nikolas and Hinselmann, Georg and Jahn, Andreas and Rosenbaum,
Lars and Zell,Andreas. A {F}ree-{W}ilson-like approach to analyze {QSAR} models based on
graph decomposition kernels. , pages 491-497,2010. [url]Bibtex@ARTICLE{Fechner2010b,author = {Fechner, Nikolas and Hinselmann, Georg and Jahn, Andreas and Rosenbaum, Lars and Zell,Andreas}, title = {A {F}ree-{W}ilson-like approach to analyze {QSAR} models based on graph decomposition kernels}, journal = {Molecular Informatics}, year = {2010}, volume = {29}, pages = {491-497}, doi = {10.1002/minf.201000053}, project = {abt_zell, cheminformatics}, url = {http://www3.interscience.wiley.com/journal/123567123/abstract}, } |
| [32] | Nikolas Fechner and Georg Hinselmann and Jörg Kurt Wegner. Handbook of Chemoinformatics Algorithms. , pages 89-143,2010. Bibtex@INBOOK{Fechner2010a,chapter = {Molecular Descriptors}, pages = {89-143}, title = {Handbook of Chemoinformatics Algorithms}, publisher = {Chapman \& Hall/CRC Mathematical \& Computational Biology}, year = {2010}, editor = {Jean-Loup Faulon and Andreas Bender}, author = {Nikolas Fechner and Georg Hinselmann and Jörg Kurt Wegner}, project = {extern, cheminformatics}, } |
| [33] | Fechner, Nikolas and Jahn, Andreas and Hinselmann, Georg and Zell,
Andreas. Estimation of the applicability domain of kernel-based machine learning
models for virtual screening. , pages 2,2010. [url]Bibtex@ARTICLE{Fechner2010,author = {Fechner, Nikolas and Jahn, Andreas and Hinselmann, Georg and Zell, Andreas}, title = {Estimation of the applicability domain of kernel-based machine learning models for virtual screening}, journal = {Journal of Cheminformatics}, year = {2010}, volume = {2}, pages = {2}, number = {1}, abstract = {BACKGROUND:The virtual screening of large compound databases is an important application of structural-activity relationship models. Due to the high structural diversity of these data sets, it is impossible for machine learning based QSAR models, which rely on a specific training set, to give reliable results for all compounds. Thus, it is important to consider the subset of the chemical space in which the model is applicable. The approaches to this problem that have been published so far mostly use vectorial descriptor representations to define this domain of applicability of the model. Unfortunately, these cannot be extended easily to structured kernel-based machine learning models. For this reason, we propose three approaches to estimate the domain of applicability of a kernel-based QSAR model.RESULTS:We evaluated three kernel-based applicability domain estimations using three different structured kernels on three virtual screening tasks. Each experiment consisted of the training of a kernel-based QSAR model using support vector regression and the ranking of a disjoint screening data set according to the predicted activity. For each prediction, the applicability of the model for the respective compound is quantitatively described using a score obtained by an applicability domain formulation. The suitability of the applicability domain estimation is evaluated by comparing the model performance on the subsets of the screening data sets obtained by different thresholds for the applicability scores. This comparison indicates that it is possible to separate the part of the chemspace, in which the model gives reliable predictions, from the part consisting of structures too dissimilar to the training set to apply the model successfully. A closer inspection reveals that the virtual screening performance of the model is considerably improved if half of the molecules, those with the lowest applicability scores, are omitted from the screening.CONCLUSION:The proposed applicability domain formulations for kernel-based QSAR models can successfully identify compounds for which no reliable predictions can be expected from the model. The resulting reduction of the search space and the elimination of some of the active compounds should not be considered as a drawback, because the results indicate that, in most cases, these omitted ligands would not be found by the model anyway.}, doi = {10.1186/1758-2946-2-2}, issn = {1758-2946}, project = {abt_zell, cheminformatics}, url = {http://www.jcheminf.com/content/2/1/2}, } |
| [34] | Henneges, Carsten and Laskov, Pavel and Darmawan, Endang and Backhaus,
Juergen and Kammerer, Bernd and Zell, Andreas. A factorization method for the classification of infrared spectra. , pages 561,2010. [url]Bibtex@ARTICLE{21078178,author = {Henneges, Carsten and Laskov, Pavel and Darmawan, Endang and Backhaus, Juergen and Kammerer, Bernd and Zell, Andreas}, title = {A factorization method for the classification of infrared spectra}, journal = {BMC Bioinformatics}, year = {2010}, volume = {11}, pages = {561}, number = {1}, abstract = {BACKGROUND:Bioinformatics data analysis often deals with additive mixtures of signals for which only class labels are known. Then, the overall goal is to estimate class related signals for data mining purposes. A convenient application is metabolic monitoring of patients using infrared spectroscopy. Within an infrared spectrum each single compound contributes quantitatively to the measurement.RESULTS:In this work, we propose a novel factorization technique for additive signal factorization that allows learning from classified samples. We define a composed loss function for this task and analytically derive a closed form equation such that training a model reduces to searching for an optimal threshold vector. Our experiments, carried out on synthetic and clinical data, show a sensitivity of up to 0.958 and specificity of up to 0.841 for a 15-class problem of disease classification. Using class and regression information in parallel, our algorithm outperforms linear SVM for training cases having many classes and few data.CONCLUSIONS:The presented factorization method provides a simple and generative model and, therefore, represents a first step towards predictive factorization methods.}, doi = {10.1186/1471-2105-11-561}, issn = {1471-2105}, project = {abt_zell, bioinformatics}, pubmedid = {21078178}, url = {http://www.biomedcentral.com/1471-2105/11/561}, } |
| [35] | Georg Hinselmann and Nikolas Fechner and Andreas Jahn and Matthias
Eckert and Andreas Zell. Graph kernels for chemical compounds using topological and three-dimensional
local atom pair environments. , pages 219-229,2010. [url]Bibtex@ARTICLE{Hinselmann2010,author = {Georg Hinselmann and Nikolas Fechner and Andreas Jahn and Matthias Eckert and Andreas Zell}, title = {Graph kernels for chemical compounds using topological and three-dimensional local atom pair environments}, journal = {Neurocomputing}, year = {2010}, volume = {74}, pages = {219-229}, number = {1-3}, doi = {10.1016/j.neucom.2010.03.008}, issn = {0925-2312}, keywords = {Graph Kernel}, project = {abt_zell, cheminformatics}, url = {http://www.sciencedirect.com/science/article/B6V10-4YP8TKR-2/2/4b8b4c3246c074e37b2964d79794f335}, } |
| [36] | Komma, Philippe and Zell, Andreas. Posterior Probability Estimation Techniques Embedded in a Bayes Filter
for Vibration-Based Terrain Classification. , pages 79-89,2010. Bibtex@ARTICLE{komma10c,author = {Komma, Philippe and Zell, Andreas}, title = {Posterior Probability Estimation Techniques Embedded in a Bayes Filter for Vibration-Based Terrain Classification}, journal = {Springer Tracts in Advanced Robotics}, year = {2010}, volume = {62}, pages = {79-89}, project = {abt_zell, robotics}, } |
| [37] | Simon Pabst and Artur Koch and Wolfgang Straßer. Fast and Scalable {CPU}/{GPU} Collision Detection for Rigid and Deformable
Surfaces. , pages 1605-1612,2010. [pdf]Bibtex@ARTICLE{PabstKS10,author = {Simon Pabst and Artur Koch and Wolfgang Straßer}, title = {Fast and Scalable {CPU}/{GPU} Collision Detection for Rigid and Deformable Surfaces}, journal = {Computer Graphics Forum}, year = {2010}, volume = {29}, pages = {1605-1612}, number = {5}, abstract = {We present a new hybrid CPU/GPU collision detection technique for rigid and deformable objects based on spatial subdivision. Our approach efficiently exploits the massive computational capabilities of modern CPUs and GPUs commonly found in off-the-shelf computer systems. The algorithm is specifically tailored to be highly scalable on both the CPU and the GPU sides. We can compute discrete and continuous external and self-collisions of non-penetrating rigid and deformable objects consisting of many tens of thousands of triangles in few milliseconds on a modern PC. Our approach is orders of magnitude faster than earlier CPU-based approaches and up to twice as fast as the most recent GPU-based techniques.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?PabstKS10}, doi = {10.1111/j.1467-8659.2010.01769.x}, pdf = {http://www.gris.uni-tuebingen.de/people/staff/spabst/pdf/hashing-SGP10.pdf}, project = {extern}, } |
| [38] | Niels Schuetze and Michael de Paly and Uri Shamir. Novel simulation-based algorithms for optimal open-loop and closed-loop. 2010. [url]Bibtex@ARTICLE{DePaly10HydroInf,author = {Niels Schuetze and Michael de Paly and Uri Shamir}, title = {Novel simulation-based algorithms for optimal open-loop and closed-loop}, journal = {Journal of Hydroinformatics}, year = {2010}, abstract = {The scarcity of water compared with the abundance of land constitutes the main drawback within agricultural production. Besides the improvement of irrigation techniques a task of primary importance is solving the problem of intra-seasonal irrigation scheduling under limited seasonal water supply. An efficient scheduling algorithm has to take into account the crops' response to water stress at different stages throughout the growing season. Furthermore, for large scale planning tools compact presentations of the relationship between irrigation practices and grain yield, such as crop water production functions, are often used which also rely on an optimal scheduling of the considered irrigation systems. In this study, two new optimization algorithms for single-crop intra-seasonal scheduling of deficit irrigation systems are introduced which are able to operate with general crop growth simulation models. First, a tailored evolutionary optimization technique (EA) searches for optimal schedules over a whole growing season within an open-loop optimization framework. Second, a neuro-dynamic programming technique (NDP) is used for determining optimal irrigation policy. In this paper, different management schemes are considered and crop-yield functions generated with both the EA and the NDP optimization algorithms compared.}, doi = {10.2166/hydro.2011.073}, project = {hydrogeo, optimization, irrigation, extern, abt_zell}, url = {http://www.iwaponline.com/jh/up/jh2011073.htm}, } |
| [39] | Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell. {Automatic Take Off, Tracking and Landing of a Miniature UAV on a
Moving Carrier Vehicle}. , pages 221-238,2010. [url]Bibtex@ARTICLE{wenzel2010c,author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {{Automatic Take Off, Tracking and Landing of a Miniature UAV on a Moving Carrier Vehicle}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2010}, volume = {61}, pages = {221-238}, abstract = {We present a system consisting of a miniature unmanned aerial vehicle (UAV) and a small carrier vehicle, in which the UAV is capable of autonomously starting from the moving ground vehicle, tracking it at a constant distance and landing on a platform on the carrier in motion. Our visual tracking approach differs from other methods by using low-cost, lightweight commodity consumer hardware. As main sensor we use a Wii remote infrared (IR) camera, which allows robust tracking of a pattern of IR lights in conditions without direct sunlight. The system does not need to communicate with the ground vehicle and works with an onboard 8-bit microcontroller. Nevertheless the position and orientation relative to the IR pattern is estimated at a frequency of approximately 50 Hz. This enables the UAV to fly fully autonomously, performing flight control, self-stabilisation and visual tracking of the ground vehicle. We present experiments in which our UAV performs autonomous flights with a moving ground carrier describing a circular path and where the carrier is rotating. The system provides small errors and allows for safe, autonomous indoor flights.}, affiliation = {Department of Computer Science, University of Tuebingen, Sand 1, 72076 Tübingen, Germany}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?wenzel2010c}, doi = {10.1007/s10846-010-9473-0}, editor = {Kimon P. Valavanis}, issn = {0921-0296}, issue = {1}, keyword = {Engineering}, owner = {wenzel}, project = {abt_zell, robotics, uav, lowcost}, publisher = {Springer}, timestamp = {2010.12.21}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Wenzel2010uav.pdf}, } |
| [40] | Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell. {Automatic Take Off, Tracking and Landing of a Miniature UAV on a
Moving Carrier Vehicle}. In Proceedings of UAV'10 3rd International Symposium on Unmanned Aerial
Vehicles, pages 1-18,, Dubai, UAE,2010. [url]Bibtex@INPROCEEDINGS{wenzel2010a,author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {{Automatic Take Off, Tracking and Landing of a Miniature UAV on a Moving Carrier Vehicle}}, booktitle = {Proceedings of UAV'10 3rd International Symposium on Unmanned Aerial Vehicles}, year = {2010}, pages = {1-18}, address = {Dubai, UAE}, publisher = {Kimon P. Valavanis}, abstract = {We present a system consisting of a miniature unmanned aerial vehicle (UAV) and a small carrier vehicle, in which the UAV is capable of autonomously starting from the moving ground vehicle, tracking it at a constant distance and landing on a platform on the carrier in motion. Our visual tracking approach differs from other methods by using low-cost, light-weight commodity consumer hardware. As main sensor we use a Wii remote infrared (IR) camera, which allows robust tracking of a pattern of IR lights in conditions without direct sunlight. The system does not need to communicate with the ground vehicle and works with an onboard 8-bit microcontroller. Nevertheless the position and orientation relative to the IR pattern is estimated at a frequency of approximately 50 Hz. This enables the UAV to fly fully autonomously, performing flight control, self-stabilisation and visual tracking of the ground vehicle.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?wenzel2010a}, project = {abt_zell, robotics, uav, lowcost}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Wenzel2010uav.pdf}, } |
| [41] | Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell. {A Quadrocopter Hovering above a Person Wearing a Modified Cap}. In Proceedings of International Micro Air Vehicle Conference and Flight
Competition, pages 1-7,, Braunschweig, Germany,2010. [url]Bibtex@INPROCEEDINGS{Wenzel2010b,author = {Karl Engelbert Wenzel and Andreas Masselli and Andreas Zell}, title = {{A Quadrocopter Hovering above a Person Wearing a Modified Cap}}, booktitle = {Proceedings of International Micro Air Vehicle Conference and Flight Competition}, year = {2010}, pages = {1-7}, address = {Braunschweig, Germany}, publisher = {DGON}, abstract = {We here describe an application of a quadrocopter hovering stably above a person wearing a cap with 4 infrared LEDs. The application has originally been developed in the context of wearable computing. Our ``wearable helicopter'' hovers above the user. In further work, the system could send a birds-eye view of the area to the operator, while the robot follows autonomously. The entire aerial robot works autonomously, all processing is done onboard. We use a miniature quadrocopter with an inertial measurement unit and a low-cost Wii remote camera, i.e., commodity consumer hardware. This proof of concept gives an insight into flight control and some experiments.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?wenzel2010b}, project = {abt_zell, robotics, uav, lowcost}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2010/Wenzel2010imav.pdf}, } |