| [1] | Konstantin Schauwecker and Andreas Zell. {On-Board Dual-Stereo-Vision for the Navigation of an Autonomous
MAV}. , pages 1--16,January, 2014. [pdf , url]Bibtex@ARTICLE{Schauwecker2014,author = {Konstantin Schauwecker and Andreas Zell}, title = {{On-Board Dual-Stereo-Vision for the Navigation of an Autonomous MAV}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2014}, volume = {74}, pages = {1--16}, number = {1-2}, month = {January}, note = {[The final publication is available at link.springer.com].}, abstract = {We present a quadrotor Micro Aerial Vehicle (MAV) equipped with four cameras, which are arranged in two stereo configurations. The MAV is able to perform stereo matching for each camera pair on-board and in real-time, using an efficient sparse stereo method. In case of the camera pair that is facing forward, the stereo matching results are used for a reduced stereo SLAM system. The other camera pair, which is facing downwards, is used for ground plane detection and tracking. Hence, we are able to obtain a full 6DoF pose estimate from each camera pair, which we fuse with inertial measurements in an extended Kalman filter. Special care is taken to compensate various drift errors. In an evaluation we show that using two instead of one camera pair significantly increases the pose estimation accuracy and robustness.}, owner = {schauwecker}, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2013/schauwecker_jint2013.pdf}, project = {abt_zell, robotics, stereo_mav, uav}, publisher = {Springer}, url = {http://link.springer.com/article/10.1007/s10846-013-9907-6}, } |
| [2] | Unterberger, Elif B. and Eichner, Johannes and Wrzodek, Clemens and
Lempiäinen, Harri and Luisier, Rapha\"elle and Terranova, R\'{e}mi
and Metzger, Ute and Plummer, Simon and Knorpp, Thomas and Braeuning,
Albert and Moggs, Jonathan and Templin, Markus and Honndorf, Valerie
and Piotto, Martial and Zell, Andreas and Schwarz, Michael. {Metabolic Programs Orchestrated by the Activated Ha-ras and $\beta$-Catenin
Oncoproteins in Mouse Liver Tumors}. mar, 2014. [url]Bibtex@ARTICLE{Unterberger2014,author = {Unterberger, Elif B. and Eichner, Johannes and Wrzodek, Clemens and Lempiäinen, Harri and Luisier, Rapha\"elle and Terranova, R\'{e}mi and Metzger, Ute and Plummer, Simon and Knorpp, Thomas and Braeuning, Albert and Moggs, Jonathan and Templin, Markus and Honndorf, Valerie and Piotto, Martial and Zell, Andreas and Schwarz, Michael}, title = {{Metabolic Programs Orchestrated by the Activated Ha-ras and $\beta$-Catenin Oncoproteins in Mouse Liver Tumors}}, journal = {International Journal of Cancer}, year = {2014}, month = {mar}, doi = {10.1002/ijc.28798}, issn = {1097-0215}, owner = {eichner}, project = {abt_zell, bioinformatics, MARCAR}, publisher = {Wiley}, timestamp = {2014.02.10}, url = {http://dx.doi.org/10.1002/ijc.28798}, } |
| [3] | Johannes Eichner and Lars Rosenbaum and Clemens Wrzodek and Hans-Ulrich
Häring and Andreas Zell and Rainer Lehmann. {Integrated enrichment analysis and pathway-centered visualization
of metabolomics, proteomics, transcriptomics, and genomics data by
using the InCroMAP software}. may, 2014. [url]Bibtex@ARTICLE{Eichner2014a,author = {Johannes Eichner and Lars Rosenbaum and Clemens Wrzodek and Hans-Ulrich Häring and Andreas Zell and Rainer Lehmann}, title = {{Integrated enrichment analysis and pathway-centered visualization of metabolomics, proteomics, transcriptomics, and genomics data by using the InCroMAP software}}, journal = {Journal of Chromatography B}, year = {2014}, month = {may}, doi = {http://dx.doi.org/10.1016/j.jchromb.2014.04.030}, issn = {1570-0232}, keywords = {Metabolomics}, project = {abt_zell, bioinformatics, MARCAR}, publisher = {Elsevier}, timestamp = {2014.04.18}, url = {http://www.sciencedirect.com/science/article/pii/S1570023214002682}, } |
| [4] | Johannes Eichner and Clemens Wrzodek and Michael Römer and Heidrun
Ellinger-Ziegelbauer and Andreas Zell. {Evaluation of toxicogenomics approaches for assessing the risk of
nongenotoxic carcinogenicity in rat liver}. , pages e97678,may, 2014. [url]Bibtex@ARTICLE{Eichner2014b,author = {Johannes Eichner and Clemens Wrzodek and Michael Römer and Heidrun Ellinger-Ziegelbauer and Andreas Zell}, title = {{Evaluation of toxicogenomics approaches for assessing the risk of nongenotoxic carcinogenicity in rat liver}}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2014}, volume = {9}, pages = {e97678}, number = {5}, month = {may}, doi = {10.1371/journal.pone.0097678}, project = {abt_zell, bioinformatics, MARCAR}, timestamp = {2014.04.24}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0097678}, } |
| [5] | Artur Koch and Andreas Zell. Mapping of Passive {UHF} {RFID} Tags with a Mobile Robot using Outlier
Detection and Negative Information. In IEEE International Conference on Robotics and Automation (ICRA), Hong Kong, China,May, 2014. Bibtex@INPROCEEDINGS{koch2014icra,author = {Artur Koch and Andreas Zell}, title = {Mapping of Passive {UHF} {RFID} Tags with a Mobile Robot using Outlier Detection and Negative Information}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2014}, address = {Hong Kong, China}, month = {May}, publisher = {IEEE}, abstract = {In this paper we propose a novel approach to classify detection events from a stream of radio-frequency identification (RFID) measurements for the purpose of mapping RFID transponders. Since raw readings from RFID readers only provide information on positive read attempts, i.e. the detections of a tag, we propose an outlier filter method solely based on the spatial extent of the sensor model that is used for the mapping process. Furthermore, we use this filter to actually classify detections as well as non-detections of tags into valid and invalid positive as well as negative detection events. We incorporate the different classes into our mapping pipeline and introduce several extensions to improve the mapping accuracy. Experimental results including the classification and mapping accuracy are presented to prove the effectiveness of our approach.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?koch2014icra}, project = {abt_zell, robotics, rfid}, } |
| [6] | Michael Römer and Johannes Eichner and Ute Metzger and Markus F.
Templin and Simon Plummer and Heidrun Ellinger-Ziegelbauer and Andreas
Zell. Cross-Platform Toxicogenomics for the Prediction of Non-Genotoxic
Hepatocarcinogenesis in Rat. , pages e97640,may, 2014. [url]Bibtex@ARTICLE{Roemer2014a,author = {Michael Römer and Johannes Eichner and Ute Metzger and Markus F. Templin and Simon Plummer and Heidrun Ellinger-Ziegelbauer and Andreas Zell}, title = {Cross-Platform Toxicogenomics for the Prediction of Non-Genotoxic Hepatocarcinogenesis in Rat}, journal = {PLoS ONE}, publisher = {Public Library of Science}, year = {2014}, volume = {9}, pages = {e97640}, number = {5}, month = {may}, abstract = {<p>In the area of omics profiling in toxicology, i.e. toxicogenomics, characteristic molecular profiles have previously been incorporated into prediction models for early assessment of a carcinogenic potential and mechanism-based classification of compounds. Traditionally, the biomarker signatures used for model construction were derived from individual high-throughput techniques, such as microarrays designed for monitoring global mRNA expression. In this study, we built predictive models by integrating omics data across complementary microarray platforms and introduced new concepts for modeling of pathway alterations and molecular interactions between multiple biological layers. We trained and evaluated diverse machine learning-based models, differing in the incorporated features and learning algorithms on a cross-omics dataset encompassing mRNA, miRNA, and protein expression profiles obtained from rat liver samples treated with a heterogeneous set of substances. Most of these compounds could be unambiguously classified as genotoxic carcinogens, non-genotoxic carcinogens, or non-hepatocarcinogens based on evidence from published studies. Since mixed characteristics were reported for the compounds Cyproterone acetate, Thioacetamide, and Wy-14643, we reclassified these compounds as either genotoxic or non-genotoxic carcinogens based on their molecular profiles. Evaluating our toxicogenomics models in a repeated external cross-validation procedure, we demonstrated that the prediction accuracy of our models could be increased by joining the biomarker signatures across multiple biological layers and by adding complex features derived from cross-platform integration of the omics data. Furthermore, we found that adding these features resulted in a better separation of the compound classes and a more confident reclassification of the three undefined compounds as non-genotoxic carcinogens.</p>}, doi = {10.1371/journal.pone.0097640}, project = {abt_zell, bioinformatics, MARCAR}, url = {http://dx.doi.org/10.1371%2Fjournal.pone.0097640}, } |
| [7] | Konstantin Schauwecker and Andreas Zell. {Robust and Efficient Volumetric Occupancy Mapping with an Application
to Stereo Vision}. In IEEE International Conference on Robotics and Automation (ICRA), pages 6102--6107,, Hong Kong, China,May, 2014. [pdf]Bibtex@INPROCEEDINGS{Schauwecker2014b,author = {Konstantin Schauwecker and Andreas Zell}, title = {{Robust and Efficient Volumetric Occupancy Mapping with an Application to Stereo Vision}}, booktitle = {IEEE International Conference on Robotics and Automation (ICRA)}, year = {2014}, pages = {6102--6107}, address = {Hong Kong, China}, month = {May}, owner = {schauwecker}, pdf = {http://www.ra.cs.uni-tuebingen.de/publikationen/2014/schauwecker_icra2014.pdf}, project = {abt_zell, robotics, stereo_mav, uav}, } |
| [8] | Eichner, Johannes and Heubach, Yvonne and Ruff, Manuel and Kohlhof,
Hella and Strobl, Stefan and Mayer, Barbara and Pawlak, Michael and Templin,
Markus F. and Zell, Andreas. {RPPApipe: A pipeline for the analysis of reverse-phase protein array
data}. jun, 2014. [pdf , url]Bibtex@ARTICLE{Eichner2014c,author = {Eichner, Johannes and Heubach, Yvonne and Ruff, Manuel and Kohlhof, Hella and Strobl, Stefan and Mayer, Barbara and Pawlak, Michael and Templin, Markus F. and Zell, Andreas}, title = {{RPPApipe: A pipeline for the analysis of reverse-phase protein array data}}, journal = {BioSystems}, year = {2014}, month = {jun}, keywords = {Reverse-phase protein arrays; Web application; Statistical analysis; Clustering; Pathway analysis; Visualization}, abstract = {Background and scope: Today, web-based data analysis pipelines exist for a wide variety of microarray platforms, such as ordinary gene-centered arrays, exon arrays and SNP arrays. However, most of the available software tools provide only limited support for reverse-phase protein arrays (RPPA), as relevant inherent properties of the corresponding datasets are not taken into account. Thus, we developed the web-based data analysis pipeline RPPApipe, which was specifically tailored to suit the characteristics of the RPPA platform and encompasses various tools for data preprocessing, statistical analysis, clustering and pathway analysis. Implementation and performance: All tools which are part of the RPPApipe software were implemented using R/Bioconductor. The software was embedded into our web-based ZBIT Bioinformatics Toolbox which is a customized instance of the Galaxy platform. Availability: RPPApipe is freely available under GNU Public License from \url{http://webservices.cs.uni-tuebingen.de}. A full documentation of the tool can be found on the corresponding website \url{http://www.cogsys.cs.uni-tuebingen.de/software/RPPApipe}. \textcopyright{} 2014 Elsevier Ireland Ltd.}, project = {abt_zell, bioinformatics, MARCAR, VLN, Spher4Sys}, doi = {10.1016/j.biosystems.2014.06.009}, url = {http://www.sciencedirect.com/science/article/pii/S0303264714000902}, pdf = {http://www.sciencedirect.com/science/article/pii/S0303264714000902/pdfft?md5=8824813e798bbc740be6b96c29e944e2&pid=1-s2.0-S0303264714000902-main.pdf}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Eichner2014c}, publisher = {Elsevier}, timestamp = {2014.06.12}, } |
| [9] | Shaowu Yang and Sebastian A. Scherer and Andreas Zell. Visual {SLAM} for Autonomous {MAVs} with Dual Cameras. In 2014 International Conference on Robotics and Automation (ICRA'14), Hongkong, China,June, 2014. [pdf]Bibtex@INPROCEEDINGS{Yang14b,author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {Visual {SLAM} for Autonomous {MAVs} with Dual Cameras}, booktitle = {2014 International Conference on Robotics and Automation (ICRA'14)}, year = {2014}, address = {Hongkong, China}, month = {June}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Yang14b}, owner = {yangs}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/ICRA14_yang_final.pdf}, project = {abt_zell, multicamSLAM, uav}, } |
| [10] | My Vo Duc and Andreas Zell. Real time Face Recognition using Local Ternary Patterns with Collaborative
Representation based Classification for Mobile Robots. In International Conference on Intelligent Autonomous Systems (IAS-13), Padova, Italy,July, 2014. [url]Bibtex@INPROCEEDINGS{voduc2014,author = {My Vo Duc and Andreas Zell}, title = {Real time Face Recognition using Local Ternary Patterns with Collaborative Representation based Classification for Mobile Robots}, booktitle = {International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, month = {July}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?voduc2014}, owner = {my}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/voduc2014.pdf}, } |
| [11] | Jiang, Lixing and Koch, Artur and Zell, Andreas. Object Recognition and Tracking for Indoor Robots using an {RGB-D}
Sensor. In International Conference on Intelligent Autonomous Systems (IAS-13), Padova, Italy,July, 2014. [url]Bibtex@INPROCEEDINGS{jiang_IAS13,author = {Jiang, Lixing and Koch, Artur and Zell, Andreas}, title = {Object Recognition and Tracking for Indoor Robots using an {RGB-D} Sensor}, booktitle = {International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, month = {July}, abstract = {In this paper we extend and generalize our previously published approach on RGB-D based fruit recognition to be able to recognize different kinds of objects in front of our mobile system. We therefore firstly extend our segmentation to use depth filtering and clustering with a watershed algorithm on the depth data to detect the target to be recognized. We forward the processed data to extract RGB-D descriptors that are used to recoup complementary object information for the classification and recognition task. After having detected the object once, we apply a simple tracking method to reduce the object search space and the computational load through frequent detection queries. The proposed method is evaluated using the random forest (RF) classifier. Experimental results highlight the effectiveness as well as real time suitability of the proposed extensions for our mobile system based on real RGB-D data.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?jiang_IAS13}, owner = {jiang}, project = {abt_zell, robotics}, timestamp = {2014.06.15}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/IAS14_jiang.pdf}, } |
| [12] | Andreas Masselli and Richard Hanten and Andreas Zell. Localization of Unmanned Aerial Vehicles Using Terrain Classification
from Aerial Images. In 2014 International Conference on Intelligent Autonomous Systems (IAS-13), Padova, Italy,July, 2014. Bibtex@INPROCEEDINGS{Masselli2014IAS,author = {Andreas Masselli and Richard Hanten and Andreas Zell}, title = {Localization of Unmanned Aerial Vehicles Using Terrain Classification from Aerial Images}, booktitle = {2014 International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, month = {July}, abstract = {In this paper we investigate the benefit of terrain classification for self-localization of a flying robot. The key idea is to use aerial images, which are already available from online databases such as GoogleMaps TM , as reference map and to match images taken with a downward looking camera with this map. Using different terrain classes as features, we can make sure that our method is invariant to lighting/weather changes as well as seasonal variations or minor changes in the environment. A particle filter is used to register the query image with parts of the map. The proposed method has shown to work on image data from both simulated and real flights.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Masselli2014IAS}, project = {abt_zell, uav}, } |
| [13] | Gerald Rauscher and Daniel Dube and Andreas Zell. A Comparison of 3D Sensors for Wheeled Mobile Robots. In 2014 International Conference on Intelligent Autonomous Systems (IAS-13), Padova, Italy,July, 2014. [pdf]Bibtex@INPROCEEDINGS{Rauscher2014IAS,author = {Gerald Rauscher and Daniel Dube and Andreas Zell}, title = {A Comparison of 3D Sensors for Wheeled Mobile Robots}, booktitle = {2014 International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, month = {July}, abstract = {<p>3D Sensors are used for many different applications, e.g. scene reconstruction, object detection and mobile robots, etc. Several studies on usability and accuracy have been done for different sensors. However, all these studies have used different settings for the different sensors. For this reason we compare five 3D sensors, including the structured light sensors Microsoft Kinect and ASUS Xtion Pro Live and the time of flight sensors Fotonic E70P, IFM O3D200 and Nippon Signal FX6, using the same settings. The sensor noise, absolute error and point detection rates are compared for different depth values, environmental illumination and different surfaces. Also simple models of the noise depending on the measured depth are proposed. It is found that the structured light sensors are very accurate for close ranges. The time of flight sensors have more noise, but the noise does not increase as strongly with the measured distance. Further, it is found that these sensors can be used for outdoor applications.</p>}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Rauscher2014IAS}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/rauscher2014ias.pdf}, project = {abt_zell, robotics}, } |
| [14] | Shaowu Yang and Sebastian A. Scherer and Andreas Zell. Robust Onboard Visual {SLAM} for Autonomous {MAVs}. In 2014 International Conference on Intelligent Autonomous Systems (IAS-13), Padova, Italy,July, 2014. [pdf]Bibtex@INPROCEEDINGS{Yang14c,author = {Shaowu Yang and Sebastian A. Scherer and Andreas Zell}, title = {Robust Onboard Visual {SLAM} for Autonomous {MAVs}}, booktitle = {2014 International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, month = {July}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Yang14c}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/ias14_yang.pdf}, project = {abt_zell, multicamSLAM, uav}, } |
| [15] | Andreas Masselli and Andreas Zell. A New Method for Solving the Perspective-Three-Point Problem. In International Conference on Pattern Recognition (ICPR 2014), Stockholm, Sweden,August, 2014. Bibtex@INPROCEEDINGS{Masselli2014ICPR,author = {Andreas Masselli and Andreas Zell}, title = {A New Method for Solving the Perspective-Three-Point Problem}, booktitle = {International Conference on Pattern Recognition (ICPR 2014)}, year = {2014}, address = {Stockholm, Sweden}, month = {August}, note = {Accepted for publication}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Masselli2014ICPR}, owner = {masselli}, project = {abt_zell, robotics, p3p, passivemarkers}, } |
| [16] | Otte, Sebastian and Schwanecke, Ulrich and Zell, Andreas. {ANTSAC}: {A} {Generic} {RANSAC} {Variant} {Using} {Principles} of {Ant} {Colony} {Algorithms}. In 2014 22nd {International} {Conference} on {Pattern} {Recognition} ({ICPR}), pages 3558--3563,aug, 2014. Bibtex@inproceedings{otte_antsac_2014,title = {{ANTSAC}: {A} {Generic} {RANSAC} {Variant} {Using} {Principles} of {Ant} {Colony} {Algorithms}}, shorttitle = {{ANTSAC}}, doi = {10.1109/ICPR.2014.612}, abstract = {In this paper, we present a new variant of the well-known Random Sample Consensus (RANSAC) algorithm for robust estimation of model parameters. The idea of our method is based on a kind of volatile memory which is similar to the pheromone evaporation in the ant colony optimization algorithm. Therefore, we call our improved RANSAC like algorithm ANTSAC. We describe our new approach and the influence of its relevant parameters to the achieved performance in detail. ANTSAC is computationally efficient and convincingly easy to implement. It turns out that ANTSAC significantly outperforms RANSAC regarding the number of inliers after a given number of iterations. Further, we show that the advantage of ANTSAC increases with the complexity of the problem, i.e., with the number of model parameters, as well as with the relative number of outliers. ANTSAC is entirely generic, such that no further domain knowledge is required, as it is for many other RANSAC extensions. Nevertheless, we show that it is competitive to state-of-the-art methods even in domain specific scenarios.}, booktitle = {2014 22nd {International} {Conference} on {Pattern} {Recognition} ({ICPR})}, author = {Otte, Sebastian and Schwanecke, Ulrich and Zell, Andreas}, month = {aug}, year = {2014}, pages = {3558--3563}, project = {abt_zell, antsac}, } |
| [17] | Stefan Laible and Andreas Zell. Building Local Terrain Maps Using Spatio-Temporal Classification
for Semantic Robot Localization. In Intelligent Robots and Systems (IROS 2014), 2014 IEEE/RSJ International
Conference on, pages 4591--4597,, Chicago, IL,September, 2014. [pdf]Bibtex@INPROCEEDINGS{laible2014iros,author = {Stefan Laible and Andreas Zell}, title = {Building Local Terrain Maps Using Spatio-Temporal Classification for Semantic Robot Localization}, booktitle = {Intelligent Robots and Systems (IROS 2014), 2014 IEEE/RSJ International Conference on}, year = {2014}, pages = {4591--4597}, address = {Chicago, IL}, month = {September}, organization = {IEEE}, publisher = {IEEE}, abstract = {The correct classification of the surrounding terrain is an important ability of a mobile robot that drives in outdoor environments. Our robot uses a 3D LIDAR and a camera to classify terrain as either asphalt, cobblestones, grass, or gravel. We build on previous work where we modeled the terrain as a Conditional random field to account for spatial dependencies, which improved results substantially. We now show how to speed up the spatial classification by defining a new energy term for neighborhood relations. Moreover, we now also consider temporal dependencies as the robot moves. This not only further improves the results, but makes it possible to build local terrain maps of the environment. We describe how to efficiently integrate the classification results of each time step into the map in a probabilistic manner. By also detecting obstacles with the LIDAR, the robot can build combined terrain and elevation maps. We show that these maps can be used for semantic robot localization.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?laible2014iros}, doi = {10.1109/IROS.2014.6943213}, owner = {laible}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/laible2014iros.pdf}, project = {abt_zell, robotics, terrain_classification}, timestamp = {2014.05.25}, } |
| [18] | Otte, Sebastian and Liwicki, Marcus and Zell, Andreas. Dynamic {Cortex} {Memory}: {Enhancing} {Recurrent} {Neural} {Networks} for {Gradient}-{Based} {Sequence} {Learning}. In Artificial {Neural} {Networks} and {Machine} {Learning} -- {ICANN} 2014, pages 1--8,sep, 2014. Bibtex@incollection{otte_dcm_2014,series = {Lecture {Notes} in {Computer} {Science}}, title = {Dynamic {Cortex} {Memory}: {Enhancing} {Recurrent} {Neural} {Networks} for {Gradient}-{Based} {Sequence} {Learning}}, isbn = {978-3-319-11178-0, 978-3-319-11179-7}, shorttitle = {Dynamic {Cortex} {Memory}}, abstract = {In this paper a novel recurrent neural network (RNN) model for gradient-based sequence learning is introduced. The presented dynamic cortex memory (DCM) is an extension of the well-known long short term memory (LSTM) model. The main innovation of the DCM is the enhancement of the inner interplay of the gates and the error carousel due to several new and trainable connections. These connections enable a direct signal transfer from the gates to one another. With this novel enhancement the networks are able to converge faster during training with back-propagation through time (BPTT) than LSTM under the same training conditions. Furthermore, DCMs yield better generalization results than LSTMs. This behaviour is shown for different supervised problem scenarios, including storing precise values, adding and learning a context-sensitive grammar.}, language = {en}, number = {8681}, booktitle = {Artificial {Neural} {Networks} and {Machine} {Learning} -- {ICANN} 2014}, publisher = {Springer International Publishing}, author = {Otte, Sebastian and Liwicki, Marcus and Zell, Andreas}, editor = {Stefan Wermter et al}, month = {sep}, year = {2014}, pages = {1--8}, project = {abt_zell, rnn}, } |
| [19] | Römer, Michael and Backert, Linus and Eichner, Johannes and Zell,
Andreas. ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases
for Drug Candidates. , pages 19037--19055,October, 2014. [url]Bibtex@ARTICLE{Roemer2014b,author = {Römer, Michael and Backert, Linus and Eichner, Johannes and Zell, Andreas}, title = {ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates}, journal = {International Journal of Molecular Sciences}, year = {2014}, volume = {15}, pages = {19037--19055}, number = {10}, month = {October}, doi = {10.3390/ijms151019037}, issn = {1422-0067}, project = {abt_zell, bioinformatics, MARCAR}, url = {http://www.mdpi.com/1422-0067/15/10/19037}, } |
| [20] | Dörr, Alexander and Keller, Roland and Zell, Andreas and Dräger,
Andreas. {SBMLsimulator: a Java tool for model simulation and parameter estimation
in systems biology}. , pages 246--257,dec, 2014. [pdf , url]Bibtex@ARTICLE{Doerr2014a,author = {Dörr, Alexander and Keller, Roland and Zell, Andreas and Dräger, Andreas}, title = {{SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology}}, journal = {Computation}, year = {2014}, volume = {2}, pages = {246--257}, number = {4}, month = {dec}, abstract = {The identification of suitable model parameters for biochemical reactions has been recognized as a quite difficult endeavor. Parameter values from literature or experiments can often not directly be combined in complex reaction systems. Nature-inspired optimization techniques can find appropriate sets of parameters that calibrate a model to experimentally obtained time series data. We present SBMLsimulator, a tool that combines the Systems Biology Simulation Core Library for dynamic simulation of biochemical models with the heuristic optimization framework EvA2. SBMLsimulator provides an intuitive graphical user interface with various options as well as a fully-featured command-line interface for large-scale and script-based model simulation and calibration. In a parameter estimation study based on a published model and artificial data we demonstrate the capability of SBMLsimulator to identify parameters. SBMLsimulator is useful for both, the interactive simulation and exploration of the parameter space and for the large-scale model calibration and estimation of uncertain parameter values.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Doerr2014a.html}, doi = {10.3390/computation2040246}, issn = {2079-3197}, keywords = {SBML; ODE modeling; Simulation; Parameter estimation}, pdf = {http://www.mdpi.com/2079-3197/2/4/246/pdf}, project = {abt_zell, bioinformatics, SBMLsimulator, VLN, AMBiCon, NIH_JSBML}, url = {http://www.mdpi.com/2079-3197/2/4/246}, } |
| [21] | Dräger, Andreas and Palsson, Bernhard {\O}.. Improving collaboration by standardization efforts in systems biology. dec, 2014. [pdf , url]Bibtex@ARTICLE{Draeger2014,author = {Dräger, Andreas and Palsson, Bernhard {\O}.}, title = {Improving collaboration by standardization efforts in systems biology}, journal = {Frontiers in Bioengineering}, year = {2014}, volume = {2}, number = {61}, month = {dec}, abstract = {Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to on-line resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programming languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, markup languages, graphical descriptions, and fundamental software support with relevance to systems biology.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/mitarb/draeger/publications/Draeger2014.html}, doi = {10.3389/fbioe.2014.00061}, issn = {2296-4185}, keywords = {model formats, modeling guidelines, ontologies, model databases, network visualization, software support}, pdf = {http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00061/pdf}, project = {extern, bioinformatics, AMBiCon, NIH_JSBML}, url = {http://journal.frontiersin.org/Journal/10.3389/fbioe.2014.00061/}, } |
| [22] | My Vo Duc and Lixing Jiang and Andreas Zell. Real time Multiple Person Detection and Tracking Using {RGB-D} Images
for Mobile Robots. In IEEE International Conference on Robotics and Biomimetics 2014, Bali, Indonesia,December, 2014. [url]Bibtex@INPROCEEDINGS{voduc2014_2,author = {My Vo Duc and Lixing Jiang and Andreas Zell}, title = {Real time Multiple Person Detection and Tracking Using {RGB-D} Images for Mobile Robots}, booktitle = {IEEE International Conference on Robotics and Biomimetics 2014}, year = {2014}, address = {Bali, Indonesia}, month = {December}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?voduc2014_2}, owner = {my}, project = {abt_zell, robotics}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2014/voduc2014_robio.pdf}, } |
| [23] | Kenar, Erhan and Franken, Holger and Forcisi, Sara and W\F6rmann,
Kilian and H\E4ring, Hans-Ulrich and Lehmann, Rainer and Schmitt-Kopplin,
Philippe and Zell, Andreas and Kohlbacher, Oliver. Automated Label-free Quantification of Metabolites from Liquid Chromatography-Mass
Spectrometry Data. , pages 348-359,2014. [url]Bibtex@ARTICLE{Kenar2014,author = {Kenar, Erhan and Franken, Holger and Forcisi, Sara and W\F6rmann, Kilian and H\E4ring, Hans-Ulrich and Lehmann, Rainer and Schmitt-Kopplin, Philippe and Zell, Andreas and Kohlbacher, Oliver}, title = {Automated Label-free Quantification of Metabolites from Liquid Chromatography-Mass Spectrometry Data}, journal = {Molecular \& Cellular Proteomics}, year = {2014}, volume = {13}, pages = {348-359}, number = {1}, abstract = {Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require automated processing of the large and complex LC-MS datasets.We present a novel algorithm for the detection of mass traces and their aggregation into features (i.e. all signals caused by the same analyte species) that is computationally efficient and sensitive and that leads to reproducible quantification results. The algorithm is based on a sensitive detection of mass traces, which are then assembled into features based on mass-to-charge spacing, co-elution information, and a support vector machine-based classifier able to identify potential metabolite isotope patterns. The algorithm is not limited to metabolites but is applicable to a wide range of small molecules (e.g. lipidomics, peptidomics), as well as to other separation technologies.We assessed the algorithm's robustness with regard to varying noise levels on synthetic data and then validated the approach on experimental data investigating human plasma samples. We obtained excellent results in a fully automated data-processing pipeline with respect to both accuracy and reproducibility. Relative to state-of-the art algorithms, ours demonstrated increased precision and recall of the method. The algorithm is available as part of the open-source software package OpenMS and runs on all major operating systems.}, doi = {10.1074/mcp.M113.031278}, eprint = {http://www.mcponline.org/content/13/1/348.full.pdf+html}, project = {diabetes, abt_zell, bioinformatics}, url = {http://www.mcponline.org/content/13/1/348.abstract}, } |
| [24] | Ran Liu and Goran Huski\'{c} and Andreas Zell. {Dynamic Objects Tracking with a Mobile Robot using Passive UHF RFID
Tags}. In IEEE/RSJ International Conference on Intelligent Robots and Systems
(IROS 2014), Chicago, Illinois, USA,2014. Bibtex@INPROCEEDINGS{Ran_IROS_2014,author = {Ran Liu and Goran Huski\'{c} and Andreas Zell}, title = {{Dynamic Objects Tracking with a Mobile Robot using Passive UHF RFID Tags}}, booktitle = {IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS 2014)}, year = {2014}, address = {Chicago, Illinois, USA}, days = {September 14--18}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Ran_IROS_2014}, project = {abt_zell, robotics, rfid, Ran_IROS_2014}, } |
| [25] | Ran Liu and Andreas Zell. {Towards Localizing Both Static and Non-static RFID Tags with a Mobile
Robot}. In International Conference on Intelligent Autonomous Systems (IAS-13), Padova, Italy,2014. Bibtex@INPROCEEDINGS{Ran_IAS_2014,author = {Ran Liu and Andreas Zell}, title = {{Towards Localizing Both Static and Non-static RFID Tags with a Mobile Robot}}, booktitle = {International Conference on Intelligent Autonomous Systems (IAS-13)}, year = {2014}, address = {Padova, Italy}, days = {July 15-July 19}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Ran_IAS_2014}, project = {abt_zell, robotics, rfid, Ran_IAS_2014}, } |
| [26] | Andreas Masselli and Shaowu Yang and Karl Engelbert Wenzel and Andreas
Zell. A Cross-Platform Comparison of Visual Marker Based Approaches for
Autonomous Flight of Quadrocopters. , pages 349--359,2014. [url]Bibtex@ARTICLE{Masselli2014JINT,author = {Andreas Masselli and Shaowu Yang and Karl Engelbert Wenzel and Andreas Zell}, title = {A Cross-Platform Comparison of Visual Marker Based Approaches for Autonomous Flight of Quadrocopters}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2014}, volume = {73}, pages = {349--359}, number = {1-4}, abstract = {In this paper, we compare three different marker based approaches for six degrees of freedom (6DOF) pose estimation, which can be used for position and attitude control of micro aerial vehicles (MAV). All methods are able to achieve real time pose estimation onboard without assistance of any external metric sensor. Since these methods can be used in various working environments, we compare their performance by carrying out experiments across two different platforms: an AscTec Hummingbird and a Pixhawk quadrocopter. We evaluate each method's accuracy by using an external tracking system and compare the methods with respect to their operating ranges and processing time. We also compare each method's performance during autonomous takeoff, hovering and landing of a quadrocopter. Finally we show how the methods perform in an outdoor environment. The paper is an extended version of the one with the same title published at the ICUAS Conference 2013.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?Masselli2014JINT}, doi = {10.1007/s10846-013-9925-4}, owner = {masselli}, project = {abt_zell, robotics, uav, passivemarkers}, publisher = {Springer}, url = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/masselli2013JINT.pdf}, } |
| [27] | Shaowu Yang and Sebastian A. Scherer and Konstantin Schauwecker and
Andreas Zell. {Autonomous Landing of MAVs on Arbitrarily Textured Landing Sites
using Onboard Monocular Vision}. , pages 27-43,2014. [pdf , url]Bibtex@ARTICLE{YangsJINT13,author = {Shaowu Yang and Sebastian A. Scherer and Konstantin Schauwecker and Andreas Zell}, title = {{Autonomous Landing of MAVs on Arbitrarily Textured Landing Sites using Onboard Monocular Vision}}, journal = {Journal of Intelligent \& Robotic Systems}, year = {2014}, volume = {74}, pages = {27-43}, number = {1-2}, abstract = {This paper presents a novel solution for micro aerial vehicles (MAVs) to autonomously search for and land on an arbitrary landing site using real-time monocular vision. The autonomous MAV is provided with only one single reference image of the landing site with an unknown size before initiating this task. We extend a well-known monocular visual SLAM algorithm that enables autonomous navigation of the MAV in unknown environments, in order to search for such landing sites. Furthermore, a multi-scale ORB feature based method is implemented and integrated into the SLAM framework for landing site detection. We use a RANSAC-based method to locate the landing site within the map of the SLAM system, taking advantage of those map points associated with the detected landing site. We demonstrate the efficiency of the presented vision system in autonomous flights, both indoor and in challenging outdoor environment.}, detailspage = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/LiteraturDB/details.html?YangsJINT13}, doi = {10.1007/s10846-013-9906-7}, issn = {0921-0296}, language = {English}, owner = {yangs}, pdf = {http://www.cogsys.cs.uni-tuebingen.de/publikationen/2013/JINT13_yangs.pdf}, project = {abt_zell, multicamSLAM, uav}, publisher = {Springer}, url = {http://link.springer.com/article/10.1007/s10846-013-9906-7}, } |