[{"title":"Kernel Methods in Computer Vision","quality_controlled":"1","article_processing_charge":"No","intvolume":"         4","extern":"1","publisher":"now publishers","publication_status":"published","volume":4,"date_updated":"2021-12-21T15:38:43Z","language":[{"iso":"eng"}],"day":"03","type":"book","_id":"3707","publist_id":"2651","page":"112","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"None","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"date_published":"2009-09-03T00:00:00Z","abstract":[{"lang":"eng","text":"Over the last years, kernel methods have established themselves as powerful tools for computer vision researchers as well as for practitioners. In this tutorial, we give an introduction to kernel methods in computer vision from a geometric perspective, introducing not only the ubiquitous support vector machines, but also less known techniques for regression, dimensionality reduction, outlier detection and clustering. Additionally, we give an outlook on very recent, non-classical techniques for the prediction of structure data, for the estimation of statistical dependency and for learning the kernel function itself. All methods are illustrated with examples of successful application from the recent computer vision research literature."}],"year":"2009","alternative_title":["Foundations and Trends® in Computer Graphics and Vision"],"publication_identifier":{"isbn":["978-1-60198-268-1"],"eisbn":["978-1-60198-269-8"]},"status":"public","month":"09","date_created":"2018-12-11T12:04:44Z","doi":"10.1561/0600000027","citation":{"ista":"Lampert C. 2009. Kernel Methods in Computer Vision, now publishers, 112p.","ama":"Lampert C. <i>Kernel Methods in Computer Vision</i>. Vol 4. now publishers; 2009. doi:<a href=\"https://doi.org/10.1561/0600000027\">10.1561/0600000027</a>","apa":"Lampert, C. (2009). <i>Kernel Methods in Computer Vision</i> (Vol. 4). now publishers. <a href=\"https://doi.org/10.1561/0600000027\">https://doi.org/10.1561/0600000027</a>","chicago":"Lampert, Christoph. <i>Kernel Methods in Computer Vision</i>. Vol. 4. now publishers, 2009. <a href=\"https://doi.org/10.1561/0600000027\">https://doi.org/10.1561/0600000027</a>.","mla":"Lampert, Christoph. <i>Kernel Methods in Computer Vision</i>. Vol. 4, now publishers, 2009, doi:<a href=\"https://doi.org/10.1561/0600000027\">10.1561/0600000027</a>.","ieee":"C. Lampert, <i>Kernel Methods in Computer Vision</i>, vol. 4. now publishers, 2009.","short":"C. Lampert, Kernel Methods in Computer Vision, now publishers, 2009."}},{"conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"date_updated":"2021-01-12T07:51:38Z","quality_controlled":0,"title":"Global connectivity potentials for random field models","publication_status":"published","publisher":"IEEE","extern":1,"status":"public","year":"2009","citation":{"ama":"Nowozin S, Lampert C. Global connectivity potentials for random field models. In: IEEE; 2009:818-825. doi:<a href=\"https://doi.org/10.1109/CVPR.2009.5206567\">10.1109/CVPR.2009.5206567</a>","apa":"Nowozin, S., &#38; Lampert, C. (2009). Global connectivity potentials for random field models (pp. 818–825). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPR.2009.5206567\">https://doi.org/10.1109/CVPR.2009.5206567</a>","ista":"Nowozin S, Lampert C. 2009. Global connectivity potentials for random field models. CVPR: Computer Vision and Pattern Recognition, 818–825.","ieee":"S. Nowozin and C. Lampert, “Global connectivity potentials for random field models,” presented at the CVPR: Computer Vision and Pattern Recognition, 2009, pp. 818–825.","short":"S. Nowozin, C. Lampert, in:, IEEE, 2009, pp. 818–825.","mla":"Nowozin, Sebastian, and Christoph Lampert. <i>Global Connectivity Potentials for Random Field Models</i>. IEEE, 2009, pp. 818–25, doi:<a href=\"https://doi.org/10.1109/CVPR.2009.5206567\">10.1109/CVPR.2009.5206567</a>.","chicago":"Nowozin, Sebastian, and Christoph Lampert. “Global Connectivity Potentials for Random Field Models,” 818–25. IEEE, 2009. <a href=\"https://doi.org/10.1109/CVPR.2009.5206567\">https://doi.org/10.1109/CVPR.2009.5206567</a>."},"doi":"10.1109/CVPR.2009.5206567","month":"06","date_created":"2018-12-11T12:04:44Z","page":"818 - 825","type":"conference","_id":"3708","publist_id":"2649","day":"20","abstract":[{"text":"Markov random field (MRF, CRF) models are popular in computer vision. However, in order to be computationally tractable they are limited to incorporate only local interactions and cannot model global properties, such as connectedness, which is a potentially useful high-level prior for object segmentation. In this work, we overcome this limitation by deriving a potential function that enforces the output labeling to be connected and that can naturally be used in the framework of recent MAP-MRF LP relaxations. Using techniques from polyhedral combinatorics, we show that a provably tight approximation to the MAP solution of the resulting MRF can still be found efficiently by solving a sequence of max-flow problems. The efficiency of the inference procedure also allows us to learn the parameters of a MRF with global connectivity potentials by means of a cutting plane algorithm. We experimentally evaluate our algorithm on both synthetic data and on the challenging segmentation task of the PASCAL VOC 2008 data set. We show that in both cases the addition of a connectedness prior significantly reduces the segmentation error.","lang":"eng"}],"acknowledgement":"Conference Information URL:\n\nhttp://www.cvpr2009.org/","date_published":"2009-06-20T00:00:00Z","author":[{"first_name":"Sebastian","full_name":"Nowozin, Sebastian","last_name":"Nowozin"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Christoph Lampert","last_name":"Lampert","orcid":"0000-0001-8622-7887"}]},{"title":"Detecting objects in large image collections and videos by efficient subimage retrieval","quality_controlled":0,"extern":1,"publication_status":"published","publisher":"IEEE","conference":{"name":"ICCV: International Conference on Computer Vision"},"date_updated":"2021-01-12T07:51:38Z","day":"29","_id":"3709","type":"conference","publist_id":"2647","page":"987 - 994","date_published":"2009-09-29T00:00:00Z","author":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"acknowledgement":"Conference Information URL:\n\nhttp://www.iccv2009.org/","abstract":[{"text":"We study the task of detecting the occurrence of objects in large image collections or in videos, a problem that combines aspects of content based image retrieval and object localization. While most previous approaches are either limited to special kinds of queries, or do not scale to large image sets, we propose a new method, efficient subimage retrieval (ESR), which is at the same time very flexible and very efficient. Relying on a two-layered branch-and-bound setup, ESR performs object-based image retrieval in sets of 100,000 or more images within seconds. An extensive evaluation on several datasets shows that ESR is not only very fast, but it also achieves detection accuracies that are on par with or superior to previously published methods for object-based image retrieval.","lang":"eng"}],"year":"2009","status":"public","month":"09","date_created":"2018-12-11T12:04:44Z","citation":{"apa":"Lampert, C. (2009). Detecting objects in large image collections and videos by efficient subimage retrieval (pp. 987–994). Presented at the ICCV: International Conference on Computer Vision, IEEE. <a href=\"https://doi.org/10.1109/ICCV.2009.5459359\">https://doi.org/10.1109/ICCV.2009.5459359</a>","ama":"Lampert C. Detecting objects in large image collections and videos by efficient subimage retrieval. In: IEEE; 2009:987-994. doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459359\">10.1109/ICCV.2009.5459359</a>","ista":"Lampert C. 2009. Detecting objects in large image collections and videos by efficient subimage retrieval. ICCV: International Conference on Computer Vision, 987–994.","short":"C. Lampert, in:, IEEE, 2009, pp. 987–994.","ieee":"C. Lampert, “Detecting objects in large image collections and videos by efficient subimage retrieval,” presented at the ICCV: International Conference on Computer Vision, 2009, pp. 987–994.","mla":"Lampert, Christoph. <i>Detecting Objects in Large Image Collections and Videos by Efficient Subimage Retrieval</i>. IEEE, 2009, pp. 987–94, doi:<a href=\"https://doi.org/10.1109/ICCV.2009.5459359\">10.1109/ICCV.2009.5459359</a>.","chicago":"Lampert, Christoph. “Detecting Objects in Large Image Collections and Videos by Efficient Subimage Retrieval,” 987–94. IEEE, 2009. <a href=\"https://doi.org/10.1109/ICCV.2009.5459359\">https://doi.org/10.1109/ICCV.2009.5459359</a>."},"doi":"10.1109/ICCV.2009.5459359"},{"page":"2129 - 2142","day":"01","publist_id":"2648","_id":"3710","type":"journal_article","abstract":[{"text":"Most successful object recognition systems rely on binary classification, deciding only if an object is present or not, but not providing information on the actual object location. To estimate the object‘s location, one can take a sliding window approach, but this strongly increases the computational cost because the classifier or similarity function has to be evaluated over a large set of candidate subwindows. In this paper, we propose a simple yet powerful branch and bound scheme that allows efficient maximization of a large class of quality functions over all possible subimages. It converges to a globally optimal solution typically in linear or even sublinear time, in contrast to the quadratic scaling of exhaustive or sliding window search. We show how our method is applicable to different object detection and image retrieval scenarios. The achieved speedup allows the use of classifiers for localization that formerly were considered too slow for this task, such as SVMs with a spatial pyramid kernel or nearest-neighbor classifiers based on the chi^2 distance. We demonstrate state-of-the-art localization performance of the resulting systems on the UIUC Cars data set, the PASCAL VOC 2006 data set, and in the PASCAL VOC 2007 competition.","lang":"eng"}],"publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","acknowledgement":"This work was funded in part by the EU projects CLASS, IST 027978, and PerAct, EST 504321. ","author":[{"orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Christoph Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"},{"first_name":"Matthew","full_name":"Blaschko,Matthew B","last_name":"Blaschko"},{"first_name":"Thomas","full_name":"Hofmann,Thomas","last_name":"Hofmann"}],"issue":"12","date_published":"2009-12-01T00:00:00Z","year":"2009","status":"public","citation":{"ista":"Lampert C, Blaschko M, Hofmann T. 2009. Efficient subwindow search: A branch and bound framework for object localization. IEEE Transactions on Pattern Analysis and Machine Intelligence. 31(12), 2129–2142.","apa":"Lampert, C., Blaschko, M., &#38; Hofmann, T. (2009). Efficient subwindow search: A branch and bound framework for object localization. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE. <a href=\"https://doi.org/10.1109/TPAMI.2009.144\">https://doi.org/10.1109/TPAMI.2009.144</a>","ama":"Lampert C, Blaschko M, Hofmann T. Efficient subwindow search: A branch and bound framework for object localization. <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. 2009;31(12):2129-2142. doi:<a href=\"https://doi.org/10.1109/TPAMI.2009.144\">10.1109/TPAMI.2009.144</a>","chicago":"Lampert, Christoph, Matthew Blaschko, and Thomas Hofmann. “Efficient Subwindow Search: A Branch and Bound Framework for Object Localization.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>. IEEE, 2009. <a href=\"https://doi.org/10.1109/TPAMI.2009.144\">https://doi.org/10.1109/TPAMI.2009.144</a>.","mla":"Lampert, Christoph, et al. “Efficient Subwindow Search: A Branch and Bound Framework for Object Localization.” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 31, no. 12, IEEE, 2009, pp. 2129–42, doi:<a href=\"https://doi.org/10.1109/TPAMI.2009.144\">10.1109/TPAMI.2009.144</a>.","short":"C. Lampert, M. Blaschko, T. Hofmann, IEEE Transactions on Pattern Analysis and Machine Intelligence 31 (2009) 2129–2142.","ieee":"C. Lampert, M. Blaschko, and T. Hofmann, “Efficient subwindow search: A branch and bound framework for object localization,” <i>IEEE Transactions on Pattern Analysis and Machine Intelligence</i>, vol. 31, no. 12. IEEE, pp. 2129–2142, 2009."},"doi":"10.1109/TPAMI.2009.144","date_created":"2018-12-11T12:04:45Z","month":"12","title":"Efficient subwindow search: A branch and bound framework for object localization","quality_controlled":0,"main_file_link":[{"open_access":"0","url":"http://www2.computer.org/portal/web/csdl/doi/10.1109/TPAMI.2009.144"}],"publisher":"IEEE","publication_status":"published","extern":1,"intvolume":"        31","date_updated":"2021-01-12T07:51:39Z","volume":31},{"title":"Combining appearance and motion for human action classification in videos","quality_controlled":0,"main_file_link":[{"open_access":"0","url":"http://www.nowozin.net/sebastian/papers/dhillon2008actionclassification.pdf"}],"extern":1,"publication_status":"published","publisher":"IEEE","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"date_updated":"2021-01-12T07:51:39Z","day":"18","publist_id":"2645","_id":"3711","type":"conference","page":"22 - 29","date_published":"2009-08-18T00:00:00Z","author":[{"first_name":"Paramveer","full_name":"Dhillon, Paramveer S","last_name":"Dhillon"},{"first_name":"Sebastian","full_name":"Nowozin, Sebastian","last_name":"Nowozin"},{"orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Christoph Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"An important cue to high level scene understanding is to analyze the objects in the scene and their behavior and interactions. In this paper, we study the problem of classification of activities in videos, as this is an integral component of any scene understanding system, and present a novel approach for recognizing human action categories in videos by combining information from appearance and motion of human body parts. Our approach is based on tracking human body parts by using mixture particle filters and then clustering the particles using local non - parametric clustering, hence associating a local set of particles to each cluster mode. The trajectory of these cluster modes provides the ldquomotionrdquo information and the ldquoappearancerdquo information is provided by the statistical information about the relative motion of these local set of particles over a number of frames. Later we use a ldquoBag of Wordsrdquo model to build one histogram per video sequence from the set of these robust appearance and motion descriptors. These histograms provide us characteristic information which helps us to discriminate among various human actions which ultimately helps us in better understanding of the complete scene. We tested our approach on the standard KTH and Weizmann human action datasets and the results were comparable to the state of the art methods. Additionally our approach is able to distinguish between activities that involve the motion of complete body from those in which only certain body parts move. In other words, our method discriminates well between activities with ldquoglobal body motionrdquo like running, jogging etc. and ldquolocal motionrdquo like waving, boxing etc."}],"year":"2009","status":"public","month":"08","date_created":"2018-12-11T12:04:45Z","doi":"10.1109/CVPRW.2009.5204237","citation":{"ieee":"P. Dhillon, S. Nowozin, and C. Lampert, “Combining appearance and motion for human action classification in videos,” presented at the CVPR: Computer Vision and Pattern Recognition, 2009, pp. 22–29.","short":"P. Dhillon, S. Nowozin, C. Lampert, in:, IEEE, 2009, pp. 22–29.","mla":"Dhillon, Paramveer, et al. <i>Combining Appearance and Motion for Human Action Classification in Videos</i>. IEEE, 2009, pp. 22–29, doi:<a href=\"https://doi.org/10.1109/CVPRW.2009.5204237\">10.1109/CVPRW.2009.5204237</a>.","chicago":"Dhillon, Paramveer, Sebastian Nowozin, and Christoph Lampert. “Combining Appearance and Motion for Human Action Classification in Videos,” 22–29. IEEE, 2009. <a href=\"https://doi.org/10.1109/CVPRW.2009.5204237\">https://doi.org/10.1109/CVPRW.2009.5204237</a>.","apa":"Dhillon, P., Nowozin, S., &#38; Lampert, C. (2009). Combining appearance and motion for human action classification in videos (pp. 22–29). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. <a href=\"https://doi.org/10.1109/CVPRW.2009.5204237\">https://doi.org/10.1109/CVPRW.2009.5204237</a>","ama":"Dhillon P, Nowozin S, Lampert C. Combining appearance and motion for human action classification in videos. In: IEEE; 2009:22-29. doi:<a href=\"https://doi.org/10.1109/CVPRW.2009.5204237\">10.1109/CVPRW.2009.5204237</a>","ista":"Dhillon P, Nowozin S, Lampert C. 2009. Combining appearance and motion for human action classification in videos. CVPR: Computer Vision and Pattern Recognition, 22–29."}},{"day":"07","type":"conference","_id":"3715","publist_id":"2642","page":"221 - 231","date_published":"2009-10-07T00:00:00Z","author":[{"last_name":"Lampert","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Christoph Lampert"},{"last_name":"Peters","full_name":"Peters, Jan","first_name":"Jan"}],"abstract":[{"text":"High-speed smooth and accurate visual tracking of objects in arbitrary, unstructured environments is essential for robotics and human motion analysis. However, building a system that can adapt to arbitrary objects and a wide range of lighting conditions is a challenging problem, especially if hard real-time constraints apply like in robotics scenarios. In this work, we introduce a method for learning a discriminative object tracking system based on the recent structured regression framework for object localization. Using a kernel function that allows fast evaluation on the GPU, the resulting system can process video streams at speed of 100 frames per second or more. Consecutive frames in high speed video sequences are typically very redundant, and for training an object detection system, it is sufficient to have training labels from only a subset of all images. We propose an active learning method that select training examples in a data-driven way, thereby minimizing the required number of training labeling. Experiments on realistic data show that the active learning is superior to previously used methods for dataset subsampling for this task.","lang":"eng"}],"acknowledgement":"This work was funded in part by the EU project CLASS, IST 027978.\nConference Information URL: http://www.optecnet.de/veranstaltungen/2009/09/dagm-2009/","alternative_title":["LNCS"],"year":"2009","status":"public","month":"10","date_created":"2018-12-11T12:04:46Z","citation":{"ista":"Lampert C, Peters J. 2009. Active structured learning for high-speed object detection. DAGM: German Association For Pattern Recognition, LNCS, vol. 5748, 221–231.","apa":"Lampert, C., &#38; Peters, J. (2009). Active structured learning for high-speed object detection (Vol. 5748, pp. 221–231). Presented at the DAGM: German Association For Pattern Recognition, Springer. <a href=\"https://doi.org/10.1007/978-3-642-03798-6_23\">https://doi.org/10.1007/978-3-642-03798-6_23</a>","ama":"Lampert C, Peters J. Active structured learning for high-speed object detection. In: Vol 5748. Springer; 2009:221-231. doi:<a href=\"https://doi.org/10.1007/978-3-642-03798-6_23\">10.1007/978-3-642-03798-6_23</a>","chicago":"Lampert, Christoph, and Jan Peters. “Active Structured Learning for High-Speed Object Detection,” 5748:221–31. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-03798-6_23\">https://doi.org/10.1007/978-3-642-03798-6_23</a>.","mla":"Lampert, Christoph, and Jan Peters. <i>Active Structured Learning for High-Speed Object Detection</i>. Vol. 5748, Springer, 2009, pp. 221–31, doi:<a href=\"https://doi.org/10.1007/978-3-642-03798-6_23\">10.1007/978-3-642-03798-6_23</a>.","short":"C. Lampert, J. Peters, in:, Springer, 2009, pp. 221–231.","ieee":"C. Lampert and J. Peters, “Active structured learning for high-speed object detection,” presented at the DAGM: German Association For Pattern Recognition, 2009, vol. 5748, pp. 221–231."},"doi":"10.1007/978-3-642-03798-6_23","title":"Active structured learning for high-speed object detection","quality_controlled":0,"intvolume":"      5748","extern":1,"publisher":"Springer","publication_status":"published","conference":{"name":"DAGM: German Association For Pattern Recognition"},"volume":5748,"date_updated":"2021-01-12T07:51:41Z"},{"date_updated":"2020-07-14T12:46:14Z","title":"A high-speed object tracker from off-the-shelf components","main_file_link":[{"url":"http://pubman.mpdl.mpg.de/pubman/faces/viewItemOverviewPage.jsp?itemId=escidoc:1789154","open_access":"0"}],"quality_controlled":0,"extern":1,"publication_status":"published","publisher":"IEEE","year":"2009","status":"public","month":"09","date_created":"2018-12-11T12:04:47Z","citation":{"apa":"Lampert, C., &#38; Peters, J. (2009). <i>A high-speed object tracker from off-the-shelf components</i>. <i>ICCV: International Conference on Computer Vision</i>. IEEE.","ama":"Lampert C, Peters J. <i>A High-Speed Object Tracker from off-the-Shelf Components</i>. IEEE; 2009.","ista":"Lampert C, Peters J. 2009. A high-speed object tracker from off-the-shelf components, IEEE,p.","ieee":"C. Lampert and J. Peters, <i>A high-speed object tracker from off-the-shelf components</i>. IEEE, 2009.","short":"C. Lampert, J. Peters, A High-Speed Object Tracker from off-the-Shelf Components, IEEE, 2009.","chicago":"Lampert, Christoph, and Jan Peters. <i>A High-Speed Object Tracker from off-the-Shelf Components</i>. <i>ICCV: International Conference on Computer Vision</i>. IEEE, 2009.","mla":"Lampert, Christoph, and Jan Peters. “A High-Speed Object Tracker from off-the-Shelf Components.” <i>ICCV: International Conference on Computer Vision</i>, IEEE, 2009."},"day":"27","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"conference_poster","_id":"3717","publist_id":"2640","date_published":"2009-09-27T00:00:00Z","author":[{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Christoph Lampert","last_name":"Lampert","orcid":"0000-0001-8622-7887"},{"first_name":"Jan","full_name":"Peters, Jan","last_name":"Peters"}],"acknowledgement":"IEEE Workshop URL:  http://humanoidscv.ime.cmc.osaka-u.ac.jp/","publication":"ICCV: International Conference on Computer Vision","abstract":[{"text":"We introduce RTblob, an open-source real-time vision system for 3D object detection that achieves over 200 Hz tracking speed with only off-the-shelf hardware component. It allows fast and accurate tracking of colored objects in 3D without expensive and often custom-built hardware, instead making use of the PC graphics cards for the necessary image processing operations.","lang":"eng"}]},{"date_updated":"2021-01-12T07:51:48Z","volume":"q-bio.NC","oa":1,"publisher":"ArXiv","publication_status":"published","extern":1,"title":"Spin glass models for a network of real neurons","main_file_link":[{"url":"http://arxiv.org/abs/0912.5409v1","open_access":"1"}],"quality_controlled":0,"citation":{"mla":"Tkačik, Gašper, et al. “Spin Glass Models for a Network of Real Neurons.” <i>ArXiv</i>, vol. q-NC, ArXiv, 2009.","chicago":"Tkačik, Gašper, Elad Schneidman, Michael Berry, and William Bialek. “Spin Glass Models for a Network of Real Neurons.” <i>ArXiv</i>. ArXiv, 2009.","ieee":"G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Spin glass models for a network of real neurons,” <i>ArXiv</i>, vol. q-NC. ArXiv, 2009.","short":"G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv q-NC (2009).","ista":"Tkačik G, Schneidman E, Berry M, Bialek W. 2009. Spin glass models for a network of real neurons. ArXiv, q-NC, .","apa":"Tkačik, G., Schneidman, E., Berry, M., &#38; Bialek, W. (2009). Spin glass models for a network of real neurons. <i>ArXiv</i>. ArXiv.","ama":"Tkačik G, Schneidman E, Berry M, Bialek W. Spin glass models for a network of real neurons. <i>ArXiv</i>. 2009;q-NC."},"month":"01","date_created":"2018-12-11T12:04:52Z","year":"2009","status":"public","abstract":[{"text":"Ising models with pairwise interactions are the least structured, or maximum-entropy, probability distributions that exactly reproduce measured pairwise correlations between spins. Here we use this equivalence to construct Ising models that describe the correlated spiking activity of populations of 40 neurons in the salamander retina responding to natural movies. We show that pairwise interactions between neurons account for observed higher-order correlations, and that for groups of 10 or more neurons pairwise interactions can no longer be regarded as small perturbations in an independent system. We then construct network ensembles that generalize the network instances observed in the experiment, and study their thermodynamic behavior and coding capacity. Based on this construction, we can also create synthetic networks of 120 neurons, and find that with increasing size the networks operate closer to a critical point and start exhibiting collective behaviors reminiscent of spin glasses. We examine closely two such behaviors that could be relevant for neural code: tuning of the network to the critical point to maximize the ability to encode diverse stimuli, and using the metastable states of the Ising Hamiltonian as neural code words.","lang":"eng"}],"publication":"ArXiv","author":[{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Gasper Tkacik"},{"full_name":"Schneidman, Elad","first_name":"Elad","last_name":"Schneidman"},{"last_name":"Berry","full_name":"Berry, Michael J","first_name":"Michael"},{"first_name":"William","full_name":"Bialek, William S","last_name":"Bialek"}],"date_published":"2009-01-01T00:00:00Z","day":"01","type":"preprint","_id":"3732","publist_id":"2496"},{"volume":106,"date_updated":"2021-01-12T07:51:48Z","intvolume":"       106","extern":1,"publication_status":"published","publisher":"National Academy of Sciences","title":"The dynamics of adaptation on correlated fitness landscapes","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767361","open_access":"0"}],"quality_controlled":0,"date_created":"2018-12-11T12:04:52Z","month":"01","citation":{"chicago":"Kryazhimskiy, Sergey, Gašper Tkačik, and Joshua Plotkin. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” <i>PNAS</i>. National Academy of Sciences, 2009. <a href=\"https://doi.org/10.1073/pnas.0905497106\">https://doi.org/10.1073/pnas.0905497106</a>.","mla":"Kryazhimskiy, Sergey, et al. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” <i>PNAS</i>, vol. 106, no. 44, National Academy of Sciences, 2009, pp. 18638–43, doi:<a href=\"https://doi.org/10.1073/pnas.0905497106\">10.1073/pnas.0905497106</a>.","short":"S. Kryazhimskiy, G. Tkačik, J. Plotkin, PNAS 106 (2009) 18638–18643.","ieee":"S. Kryazhimskiy, G. Tkačik, and J. Plotkin, “The dynamics of adaptation on correlated fitness landscapes,” <i>PNAS</i>, vol. 106, no. 44. National Academy of Sciences, pp. 18638–18643, 2009.","ista":"Kryazhimskiy S, Tkačik G, Plotkin J. 2009. The dynamics of adaptation on correlated fitness landscapes. PNAS. 106(44), 18638–18643.","ama":"Kryazhimskiy S, Tkačik G, Plotkin J. The dynamics of adaptation on correlated fitness landscapes. <i>PNAS</i>. 2009;106(44):18638-18643. doi:<a href=\"https://doi.org/10.1073/pnas.0905497106\">10.1073/pnas.0905497106</a>","apa":"Kryazhimskiy, S., Tkačik, G., &#38; Plotkin, J. (2009). The dynamics of adaptation on correlated fitness landscapes. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.0905497106\">https://doi.org/10.1073/pnas.0905497106</a>"},"doi":"10.1073/pnas.0905497106","year":"2009","status":"public","author":[{"last_name":"Kryazhimskiy","first_name":"Sergey","full_name":"Kryazhimskiy,Sergey"},{"last_name":"Tkacik","orcid":"0000-0002-6699-1455","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Gasper Tkacik"},{"last_name":"Plotkin","full_name":"Plotkin,Joshua B","first_name":"Joshua"}],"date_published":"2009-01-01T00:00:00Z","issue":"44","abstract":[{"text":"Evolutionary theory predicts that a population in a new environment will accumulate adaptive substitutions, but precisely how they accumulate is poorly understood. The dynamics of adaptation depend on the underlying fitness landscape. Virtually nothing is known about fitness landscapes in nature, and few methods allow us to infer the landscape from empirical data. With a view toward this inference problem, we have developed a theory that, in the weak-mutation limit, predicts how a population's mean fitness and the number of accumulated substitutions are expected to increase over time, depending on the underlying fitness landscape. We find that fitness and substitution trajectories depend not on the full distribution of fitness effects of available mutations but rather on the expected fixation probability and the expected fitness increment of mutations. We introduce a scheme that classifies landscapes in terms of the qualitative evolutionary dynamics they produce. We show that linear substitution trajectories, long considered the hallmark of neutral evolution, can arise even when mutations are strongly selected. Our results provide a basis for understanding the dynamics of adaptation and for inferring properties of an organism's fitness landscape from temporal data. Applying these methods to data from a long-term experiment, we infer the sign and strength of epistasis among beneficial mutations in the Escherichia coli genome.","lang":"eng"}],"publication":"PNAS","day":"01","type":"journal_article","_id":"3733","publist_id":"2497","page":"18638 - 18643"},{"citation":{"ista":"Tkačik G, Walczak A, Bialek W. 2009. Optimizing information flow in small genetic networks. Physical Review E Statistical Nonlinear and Soft Matter Physics. 80(3).","apa":"Tkačik, G., Walczak, A., &#38; Bialek, W. (2009). Optimizing information flow in small genetic networks. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.80.031920\">https://doi.org/10.1103/PhysRevE.80.031920</a>","ama":"Tkačik G, Walczak A, Bialek W. Optimizing information flow in small genetic networks. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2009;80(3). doi:<a href=\"https://doi.org/10.1103/PhysRevE.80.031920\">10.1103/PhysRevE.80.031920</a>","mla":"Tkačik, Gašper, et al. “Optimizing Information Flow in Small Genetic Networks.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 80, no. 3, American Institute of Physics, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevE.80.031920\">10.1103/PhysRevE.80.031920</a>.","chicago":"Tkačik, Gašper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2009. <a href=\"https://doi.org/10.1103/PhysRevE.80.031920\">https://doi.org/10.1103/PhysRevE.80.031920</a>.","short":"G. Tkačik, A. Walczak, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 80 (2009).","ieee":"G. Tkačik, A. Walczak, and W. Bialek, “Optimizing information flow in small genetic networks,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 80, no. 3. American Institute of Physics, 2009."},"doi":"10.1103/PhysRevE.80.031920","date_created":"2018-12-11T12:04:53Z","month":"09","year":"2009","status":"public","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","abstract":[{"text":"In order to survive, reproduce, and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable randomness of individual molecular events. Here we explore how cells can maximize their control power in the presence of these physical limits; formally, we solve the theoretical problem of maximizing the information transferred from inputs to outputs when the number of available molecules is held fixed. We start with the simplest version of the problem, in which a single transcription factor protein controls the readout of one or more genes by binding to DNA. We further simplify by assuming that this regulatory network operates in steady state, that the noise is small relative to the available dynamic range, and that the target genes do not interact. Even in this simple limit, we find a surprisingly rich set of optimal solutions. Importantly, for each locally optimal regulatory network, all parameters are determined once the physical constraints on the number of available molecules are specified. Although we are solving an oversimplified version of the problem facing real cells, we see parallels between the structure of these optimal solutions and the behavior of actual genetic regulatory networks. Subsequent papers will discuss more complete versions of the problem.","lang":"eng"}],"date_published":"2009-09-29T00:00:00Z","issue":"3 ","author":[{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Gasper Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Walczak","full_name":"Walczak, Aleksandra M","first_name":"Aleksandra"},{"full_name":"Bialek, William S","first_name":"William","last_name":"Bialek"}],"day":"29","publist_id":"2493","_id":"3737","type":"journal_article","date_updated":"2021-01-12T07:51:50Z","volume":80,"publication_status":"published","publisher":"American Institute of Physics","intvolume":"        80","extern":1,"title":"Optimizing information flow in small genetic networks","main_file_link":[{"open_access":"0","url":"http://arxiv.org/abs/0903.4491"}],"quality_controlled":0},{"publisher":"American Institute of Physics","publication_status":"published","extern":1,"intvolume":"        79","title":"Diffusion, dimensionality, and noise in transcriptional regulation","quality_controlled":0,"date_updated":"2021-01-12T07:51:54Z","volume":79,"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","abstract":[{"text":"The precision of biochemical signaling is limited by randomness in the diffusive arrival of molecules at their targets. For proteins binding to specific sites on DNA and regulating transcription, the ability of the proteins to diffuse in one dimension by sliding along the length of the DNA, in addition to their diffusion in bulk solution, would seem to generate a larger target for DNA binding, consequently reducing the noise in the occupancy of the regulatory site. Here we show that this effect is largely canceled by the enhanced temporal correlations in one-dimensional diffusion. With realistic parameters, sliding along DNA has surprisingly little effect on the physical limits to the precision of transcriptional regulation.","lang":"eng"}],"date_published":"2009-05-04T00:00:00Z","issue":"5","author":[{"full_name":"Gasper Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"last_name":"Bialek","full_name":"Bialek, William S","first_name":"William"}],"day":"04","publist_id":"2483","_id":"3745","type":"journal_article","doi":"10.1103/PhysRevE.79.051901","citation":{"short":"G. Tkačik, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 79 (2009).","ieee":"G. Tkačik and W. Bialek, “Diffusion, dimensionality, and noise in transcriptional regulation,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 79, no. 5. American Institute of Physics, 2009.","mla":"Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 79, no. 5, American Institute of Physics, 2009, doi:<a href=\"https://doi.org/10.1103/PhysRevE.79.051901\">10.1103/PhysRevE.79.051901</a>.","chicago":"Tkačik, Gašper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2009. <a href=\"https://doi.org/10.1103/PhysRevE.79.051901\">https://doi.org/10.1103/PhysRevE.79.051901</a>.","apa":"Tkačik, G., &#38; Bialek, W. (2009). Diffusion, dimensionality, and noise in transcriptional regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.79.051901\">https://doi.org/10.1103/PhysRevE.79.051901</a>","ama":"Tkačik G, Bialek W. Diffusion, dimensionality, and noise in transcriptional regulation. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2009;79(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.79.051901\">10.1103/PhysRevE.79.051901</a>","ista":"Tkačik G, Bialek W. 2009. Diffusion, dimensionality, and noise in transcriptional regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 79(5)."},"month":"05","date_created":"2018-12-11T12:04:56Z","year":"2009","status":"public"},{"publication":"Encyclopedia of Complexity and Systems Science","author":[{"full_name":"Gasper Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"},{"last_name":"Bialek","full_name":"Bialek, William S","first_name":"William"}],"date_published":"2009-01-01T00:00:00Z","page":"719 - 741","publist_id":"2481","_id":"3747","type":"book_chapter","day":"01","doi":"10.1007/978-0-387-30440-3_48","citation":{"ama":"Tkačik G, Bialek W. Cell Biology: Networks, regulation, pathways. In: Meyers R, ed. <i>Encyclopedia of Complexity and Systems Science</i>. Springer; 2009:719-741. doi:<a href=\"https://doi.org/10.1007/978-0-387-30440-3_48\">10.1007/978-0-387-30440-3_48</a>","apa":"Tkačik, G., &#38; Bialek, W. (2009). Cell Biology: Networks, regulation, pathways. In R. Meyers (Ed.), <i>Encyclopedia of Complexity and Systems Science</i> (pp. 719–741). Springer. <a href=\"https://doi.org/10.1007/978-0-387-30440-3_48\">https://doi.org/10.1007/978-0-387-30440-3_48</a>","ista":"Tkačik G, Bialek W. 2009.Cell Biology: Networks, regulation, pathways. In: Encyclopedia of Complexity and Systems Science. , 719–741.","short":"G. Tkačik, W. Bialek, in:, R. Meyers (Ed.), Encyclopedia of Complexity and Systems Science, Springer, 2009, pp. 719–741.","ieee":"G. Tkačik and W. Bialek, “Cell Biology: Networks, regulation, pathways,” in <i>Encyclopedia of Complexity and Systems Science</i>, R. Meyers, Ed. Springer, 2009, pp. 719–741.","chicago":"Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” In <i>Encyclopedia of Complexity and Systems Science</i>, edited by R. Meyers, 719–41. Springer, 2009. <a href=\"https://doi.org/10.1007/978-0-387-30440-3_48\">https://doi.org/10.1007/978-0-387-30440-3_48</a>.","mla":"Tkačik, Gašper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” <i>Encyclopedia of Complexity and Systems Science</i>, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:<a href=\"https://doi.org/10.1007/978-0-387-30440-3_48\">10.1007/978-0-387-30440-3_48</a>."},"date_created":"2018-12-11T12:04:56Z","month":"01","editor":[{"last_name":"Meyers","first_name":"R.","full_name":"Meyers,R. A."}],"status":"public","year":"2009","publication_status":"published","publisher":"Springer","extern":1,"quality_controlled":0,"title":"Cell Biology: Networks, regulation, pathways","date_updated":"2021-01-12T07:51:54Z"},{"status":"public","year":"2009","doi":"10.1145/1531326.1531382","citation":{"mla":"Wojtan, Chris, et al. “Deforming Meshes That Split and Merge.” <i>ACM Transactions on Graphics</i>, vol. 28, no. 3, ACM, 2009, doi:<a href=\"https://doi.org/10.1145/1531326.1531382\">10.1145/1531326.1531382</a>.","chicago":"Wojtan, Chris, Nils Thürey, Markus Gross, and Greg Turk. “Deforming Meshes That Split and Merge.” <i>ACM Transactions on Graphics</i>. ACM, 2009. <a href=\"https://doi.org/10.1145/1531326.1531382\">https://doi.org/10.1145/1531326.1531382</a>.","ieee":"C. Wojtan, N. Thürey, M. Gross, and G. Turk, “Deforming meshes that split and merge,” <i>ACM Transactions on Graphics</i>, vol. 28, no. 3. ACM, 2009.","short":"C. Wojtan, N. Thürey, M. Gross, G. Turk, ACM Transactions on Graphics 28 (2009).","ista":"Wojtan C, Thürey N, Gross M, Turk G. 2009. Deforming meshes that split and merge. ACM Transactions on Graphics. 28(3).","apa":"Wojtan, C., Thürey, N., Gross, M., &#38; Turk, G. (2009). Deforming meshes that split and merge. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/1531326.1531382\">https://doi.org/10.1145/1531326.1531382</a>","ama":"Wojtan C, Thürey N, Gross M, Turk G. Deforming meshes that split and merge. <i>ACM Transactions on Graphics</i>. 2009;28(3). doi:<a href=\"https://doi.org/10.1145/1531326.1531382\">10.1145/1531326.1531382</a>"},"month":"08","date_created":"2018-12-11T12:05:02Z","publist_id":"2466","_id":"3764","type":"journal_article","day":"01","publication":"ACM Transactions on Graphics","abstract":[{"text":"We present a method for accurately tracking the moving surface of deformable materials in a manner that gracefully handles topological changes. We employ a Lagrangian surface tracking method, and we use a triangle mesh for our surface representation so that fine features can be retained. We make topological changes to the mesh by first identifying merging or splitting events at a particular grid resolution, and then locally creating new pieces of the mesh in the affected cells using a standard isosurface creation method. We stitch the new, topologically simplified portion of the mesh to the rest of the mesh at the cell boundaries. Our method detects and treats topological events with an emphasis on the preservation of detailed features, while simultaneously simplifying those portions of the material that are not visible. Our surface tracker is not tied to a particular method for simulating deformable materials. In particular, we show results from two significantly different simulators: a Lagrangian FEM simulator with tetrahedral elements, and an Eulerian grid-based fluid simulator. Although our surface tracking method is generic, it is particularly well-suited for simulations that exhibit fine surface details and numerous topological events. Highlights of our results include merging of viscoplastic materials with complex geometry, a taffy-pulling animation with many fold and merge events, and stretching and slicing of stiff plastic material.","lang":"eng"}],"oa_version":"None","issue":"3","date_published":"2009-08-01T00:00:00Z","author":[{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"last_name":"Thürey","full_name":"Thürey, Nils","first_name":"Nils"},{"full_name":"Gross, Markus","first_name":"Markus","last_name":"Gross"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"date_updated":"2023-02-23T11:41:39Z","volume":28,"article_processing_charge":"No","title":"Deforming meshes that split and merge","publisher":"ACM","publication_status":"published","extern":"1","intvolume":"        28"},{"intvolume":"        25","extern":1,"publisher":"Oxford University Press","publication_status":"published","title":"Comment on '{A} congruence index for testing topological similarity between trees'.","quality_controlled":0,"volume":25,"date_updated":"2021-01-12T07:52:03Z","author":[{"first_name":"Anne","id":"2BB22BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Anne Kupczok","last_name":"Kupczok"},{"last_name":"Von Haeseler","full_name":"von Haeseler,Arndt","first_name":"Arndt"}],"date_published":"2009-01-01T00:00:00Z","issue":"1","acknowledgement":"10.1093/bioinformatics/btn539","publication":"Bioinformatics","day":"01","type":"journal_article","_id":"3768","publist_id":"2459","page":"147 - 149","date_created":"2018-12-11T12:05:04Z","month":"01","citation":{"ieee":"A. Kupczok and A. Von Haeseler, “Comment on ‘{A} congruence index for testing topological similarity between trees’.,” <i>Bioinformatics</i>, vol. 25, no. 1. Oxford University Press, pp. 147–149, 2009.","short":"A. Kupczok, A. Von Haeseler, Bioinformatics 25 (2009) 147–149.","chicago":"Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘{A} Congruence Index for Testing Topological Similarity between Trees’.” <i>Bioinformatics</i>. Oxford University Press, 2009. <a href=\"https://doi.org/4199\">https://doi.org/4199</a>.","mla":"Kupczok, Anne, and Arndt Von Haeseler. “Comment on ‘{A} Congruence Index for Testing Topological Similarity between Trees’.” <i>Bioinformatics</i>, vol. 25, no. 1, Oxford University Press, 2009, pp. 147–49, doi:<a href=\"https://doi.org/4199\">4199</a>.","apa":"Kupczok, A., &#38; Von Haeseler, A. (2009). Comment on “{A} congruence index for testing topological similarity between trees”. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/4199\">https://doi.org/4199</a>","ama":"Kupczok A, Von Haeseler A. Comment on “{A} congruence index for testing topological similarity between trees”. <i>Bioinformatics</i>. 2009;25(1):147-149. doi:<a href=\"https://doi.org/4199\">4199</a>","ista":"Kupczok A, Von Haeseler A. 2009. Comment on ‘{A} congruence index for testing topological similarity between trees’. Bioinformatics. 25(1), 147–149."},"doi":"4199","year":"2009","status":"public"},{"date_updated":"2021-01-12T07:52:06Z","language":[{"iso":"eng"}],"title":"On the application of statistical physics to evolutionary biology","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-00554594/document"}],"department":[{"_id":"NiBa"}],"year":"2009","type":"journal_article","page":"317 - 324","oa_version":"Submitted Version","oa":1,"volume":259,"scopus_import":1,"quality_controlled":"1","intvolume":"       259","publisher":"Elsevier","publication_status":"published","status":"public","date_created":"2018-12-11T12:05:06Z","month":"07","doi":"10.1016/j.jtbi.2009.03.019","citation":{"chicago":"Barton, Nicholas H, and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>. Elsevier, 2009. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>.","mla":"Barton, Nicholas H., and Jason Coe. “On the Application of Statistical Physics to Evolutionary Biology.” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2, Elsevier, 2009, pp. 317–24, doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>.","short":"N.H. Barton, J. Coe, Journal of Theoretical Biology 259 (2009) 317–324.","ieee":"N. H. Barton and J. Coe, “On the application of statistical physics to evolutionary biology,” <i>Journal of Theoretical Biology</i>, vol. 259, no. 2. Elsevier, pp. 317–324, 2009.","ista":"Barton NH, Coe J. 2009. On the application of statistical physics to evolutionary biology. Journal of Theoretical Biology. 259(2), 317–324.","apa":"Barton, N. H., &#38; Coe, J. (2009). On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">https://doi.org/10.1016/j.jtbi.2009.03.019</a>","ama":"Barton NH, Coe J. On the application of statistical physics to evolutionary biology. <i>Journal of Theoretical Biology</i>. 2009;259(2):317-324. doi:<a href=\"https://doi.org/10.1016/j.jtbi.2009.03.019\">10.1016/j.jtbi.2009.03.019</a>"},"day":"21","_id":"3775","publist_id":"2452","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H"},{"last_name":"Coe","first_name":"Jason","full_name":"Coe, Jason"}],"issue":"2","date_published":"2009-07-21T00:00:00Z","acknowledgement":"This work was supported by a Royal Society/Wolfson Award, and by grants EP/T11753/01, EP/C546318/01 from the EPSRC.\r\nWe are grateful to M. Cates, H.P. de Vladar and G. Sella, and to two anonymous referees, for their helpful comments.","publication":"Journal of Theoretical Biology","abstract":[{"lang":"eng","text":"There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. Wright's formula for the stationary distribution of allele frequencies is analogous to the Boltzmann distribution in statistical physics. Population size, 2N, plays the role of the inverse temperature, 1/kT, and determines the magnitude of random fluctuations. Log mean fitness, View the MathML source, tends to increase under selection, and is analogous to a (negative) energy; a potential function, U, increases under mutation in a similar way. An entropy, SH, can be defined which measures the deviation from the distribution of allele frequencies expected under random drift alone; the sum View the MathML source gives a free fitness that increases as the population evolves towards its stationary distribution. Usually, we observe the distribution of a few quantitative traits that depend on the frequencies of very many alleles. The mean and variance of such traits are analogous to observable quantities in statistical thermodynamics. Thus, we can define an entropy, SΩ, which measures the volume of allele frequency space that is consistent with the observed trait distribution. The stationary distribution of the traits is View the MathML source; this applies with arbitrary epistasis and dominance. The entropies SΩ, SH are distinct, but converge when there are so many alleles that traits fluctuate close to their expectations. Populations tend to evolve towards states that can be realised in many ways (i.e., large SΩ), which may lead to a substantial drop below the adaptive peak; we illustrate this point with a simple model of genetic redundancy. This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits."}]},{"language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:52:09Z","title":"The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails","department":[{"_id":"NiBa"}],"year":"2009","type":"journal_article","page":"1624 - 1635","pubrep_id":"553","oa_version":"Submitted Version","ddc":["570"],"file_date_updated":"2020-07-14T12:46:15Z","oa":1,"volume":22,"file":[{"content_type":"application/pdf","file_name":"Davison_JEB_v31_2009.pdf","date_created":"2019-02-22T09:21:44Z","date_updated":"2020-07-14T12:46:15Z","relation":"main_file","access_level":"open_access","file_size":2583812,"creator":"dernst","checksum":"f70c15c6ab9306121d4153a3be0d2346","file_id":"6044"}],"quality_controlled":"1","scopus_import":1,"intvolume":"        22","publication_status":"published","publisher":"Wiley","has_accepted_license":"1","status":"public","date_created":"2018-12-11T12:05:08Z","month":"08","citation":{"ista":"Davison A, Barton NH, Clarke B. 2009. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. Journal of Evolutionary Biology. 22(8), 1624–1635.","apa":"Davison, A., Barton, N. H., &#38; Clarke, B. (2009). The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>","ama":"Davison A, Barton NH, Clarke B. The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails. <i>Journal of Evolutionary Biology</i>. 2009;22(8):1624-1635. doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>","mla":"Davison, Angus, et al. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8, Wiley, 2009, pp. 1624–35, doi:<a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">10.1111/j.1420-9101.2009.01770.x</a>.","chicago":"Davison, Angus, Nicholas H Barton, and Bryan Clarke. “The Effect of Chirality Phenotype and Genotype on the Fecundity and Viability of Partula Suturalis and Lymnaea Stagnalis: Implications for the Evolution of Sinistral Snails.” <i>Journal of Evolutionary Biology</i>. Wiley, 2009. <a href=\"https://doi.org/10.1111/j.1420-9101.2009.01770.x\">https://doi.org/10.1111/j.1420-9101.2009.01770.x</a>.","short":"A. Davison, N.H. Barton, B. Clarke, Journal of Evolutionary Biology 22 (2009) 1624–1635.","ieee":"A. Davison, N. H. Barton, and B. Clarke, “The effect of chirality phenotype and genotype on the fecundity and viability of Partula suturalis and Lymnaea stagnalis: Implications for the evolution of sinistral snails,” <i>Journal of Evolutionary Biology</i>, vol. 22, no. 8. Wiley, pp. 1624–1635, 2009."},"doi":"10.1111/j.1420-9101.2009.01770.x","_id":"3780","publist_id":"2447","day":"01","issue":"8","author":[{"first_name":"Angus","full_name":"Davison, Angus","last_name":"Davison"},{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"},{"full_name":"Clarke, Bryan","first_name":"Bryan","last_name":"Clarke"}],"date_published":"2009-08-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Why are sinistral snails so rare? Two main hypotheses are that selection acts against the establishment of new coiling morphs, because dextral and sinistral snails have trouble mating, or else a developmental constraint prevents the establishment of sinistrals. We therefore used an isolate of the snail Lymnaea stagnalis, in which sinistrals are rare, and populations of Partula suturalis, in which sinistrals are common, as well as a mathematical model, to understand the circumstances by which new morphs evolve. The main finding is that the sinistral genotype is associated with reduced egg viability in L. stagnalis, but in P. suturalis individuals of sinistral and dextral genotype appear equally fecund, implying a lack of a constraint. As positive frequency-dependent selection against the rare chiral morph in P. suturalis also operates over a narrow range (&lt; 3%), the results suggest a model for chiral evolution in snails in which weak positive frequency-dependent selection may be overcome by a negative frequency-dependent selection, such as reproductive character displacement. In snails, there is not always a developmental constraint. As the direction of cleavage, and thus the directional asymmetry of the entire body, does not generally vary in other Spiralia (annelids, echiurans, vestimentiferans, sipunculids and nemerteans), it remains an open question as to whether this is because of a constraint and/or because most taxa do not have a conspicuous external asymmetry (like a shell) upon which selection can act.","lang":"eng"}],"publication":"Journal of Evolutionary Biology","acknowledgement":"We owe a great debt to Jim Murray for his many contributions to the study of Partula, in the field, in the laboratory, in the interpretation of data, and in generating new ideas about evolution. With pleasure and respect we dedicate this paper to him. Jim Murray played a leading role in making the collections used here. We are very grateful also to Ann Clarke and Elizabeth Murray for help with collecting, to Lorna Stewart for snail dissections, to Joris Koene for the gift of snails, to Natasha Constant for entering the data, and Takahiro Asami, Edmund Gittenberger and Gerhard Falkner for establishing the sinistral stock of L. stagnalis. Comments from an anonymous referee, A. Richard Palmer and the editorial board improved the manuscript. Work in the field was supported by the Royal Society, The Carnegie Trust, the Percy Sladen Trust and the National Science Foundation. The Science Research Council (B/SR/4144), the National Science Foundation (GB-4188), the Royal Society and the University of Nottingham supported work in the laboratory."},{"publication":"Science","abstract":[{"text":"Glutamate receptors of the AMPA-subtype (AMPARs), together with the transmembrane AMPAR regulatory proteins (TARPs), mediate fast excitatory synaptic transmission in the mammalian brain. Here, we show by proteomic analysis that the majority of AMPARs in the rat brain are coassembled with two members of the cornichon family of transmembrane proteins, rather than with the TARPs. Coassembly with cornichon homologs 2 and 3 affects AMPARs in two ways: Cornichons increase surface expression of AMPARs, and they alter channel gating by markedly slowing deactivation and desensitization kinetics. These results demonstrate that cornichons are intrinsic auxiliary subunits of native AMPARs and provide previously unknown molecular determinants for glutamatergic neurotransmission in the central nervous system.","lang":"eng"}],"issue":"5919","date_published":"2009-01-01T00:00:00Z","author":[{"full_name":"Schwenk, Jochen","first_name":"Jochen","last_name":"Schwenk"},{"first_name":"Nadine","full_name":"Harmel, Nadine","last_name":"Harmel"},{"last_name":"Zolles","full_name":"Zolles, Gerd","first_name":"Gerd"},{"full_name":"Bildl, Wolfgang","first_name":"Wolfgang","last_name":"Bildl"},{"full_name":"Kulik, Ákos","first_name":"Ákos","last_name":"Kulik"},{"first_name":"Bernd","full_name":"Heimrich, Bernd","last_name":"Heimrich"},{"last_name":"Chisaka","first_name":"Osamu","full_name":"Chisaka, Osamu"},{"orcid":"0000-0001-5001-4804","last_name":"Jonas","full_name":"Peter Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"full_name":"Schulte, Uwe","first_name":"Uwe","last_name":"Schulte"},{"last_name":"Fakler","first_name":"Bernd","full_name":"Fakler, Bernd"},{"last_name":"Klocker","full_name":"Klocker, Nikolaj","first_name":"Nikolaj"}],"page":"1313 - 9","_id":"3828","type":"journal_article","publist_id":"2382","day":"01","citation":{"apa":"Schwenk, J., Harmel, N., Zolles, G., Bildl, W., Kulik, Á., Heimrich, B., … Klocker, N. (2009). Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1167852\">https://doi.org/10.1126/science.1167852</a>","ama":"Schwenk J, Harmel N, Zolles G, et al. Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors. <i>Science</i>. 2009;323(5919):1313-1319. doi:<a href=\"https://doi.org/10.1126/science.1167852\">10.1126/science.1167852</a>","ista":"Schwenk J, Harmel N, Zolles G, Bildl W, Kulik Á, Heimrich B, Chisaka O, Jonas PM, Schulte U, Fakler B, Klocker N. 2009. Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors. Science. 323(5919), 1313–9.","ieee":"J. Schwenk <i>et al.</i>, “Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors,” <i>Science</i>, vol. 323, no. 5919. American Association for the Advancement of Science, pp. 1313–9, 2009.","short":"J. Schwenk, N. Harmel, G. Zolles, W. Bildl, Á. Kulik, B. Heimrich, O. Chisaka, P.M. Jonas, U. Schulte, B. Fakler, N. Klocker, Science 323 (2009) 1313–9.","chicago":"Schwenk, Jochen, Nadine Harmel, Gerd Zolles, Wolfgang Bildl, Ákos Kulik, Bernd Heimrich, Osamu Chisaka, et al. “Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors.” <i>Science</i>. American Association for the Advancement of Science, 2009. <a href=\"https://doi.org/10.1126/science.1167852\">https://doi.org/10.1126/science.1167852</a>.","mla":"Schwenk, Jochen, et al. “Functional Proteomics Identify Cornichon Proteins as Auxiliary Subunits of AMPA Receptors.” <i>Science</i>, vol. 323, no. 5919, American Association for the Advancement of Science, 2009, pp. 1313–19, doi:<a href=\"https://doi.org/10.1126/science.1167852\">10.1126/science.1167852</a>."},"doi":"10.1126/science.1167852","month":"01","date_created":"2018-12-11T12:05:23Z","status":"public","year":"2009","publisher":"American Association for the Advancement of Science","publication_status":"published","extern":1,"intvolume":"       323","quality_controlled":0,"title":"Functional proteomics identify cornichon proteins as auxiliary subunits of AMPA receptors","date_updated":"2021-01-12T07:52:29Z","volume":323},{"page":"85 - 92","day":"11","publist_id":"2373","_id":"3835","type":"conference","acknowledgement":"This research was supported in part by the Swiss National Science Foundation under the Indo-Swiss Joint Research Programme, by the European Network of Excellence on Embedded Systems Design (ArtistDesign), by the European Combest, Quasimodo, and Gasics projects, by the PAI program Moves funded by the Belgian Federal Government, and by the CFV (Federated Center in Verification) funded by the F.R.S.-FNRS.","abstract":[{"text":"Many specifications include assumptions on the environment. If the environment satisfies the assumptions then a correct system reacts as intended. However, when the environment deviates from its expected behavior, a correct system can behave arbitrarily. We want to synthesize robust systems that degrade gracefully, i.e., a small number of environment failures should induce a small number of system failures. We define ratio games and show that an optimal robust system corresponds to the winning strategy of a ratio game, where the system minimizes the ratio of system errors to environment errors. We show that ratio games can be solved in pseudopolynomial time.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2009-12-11T00:00:00Z","author":[{"last_name":"Bloem","first_name":"Roderick","full_name":"Bloem, Roderick"},{"first_name":"Karin","full_name":"Greimel, Karin","last_name":"Greimel"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"}],"oa_version":"None","year":"2009","status":"public","citation":{"short":"R. Bloem, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, Springer, 2009, pp. 85–92.","ieee":"R. Bloem, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Synthesizing robust systems,” presented at the FMCAD: Formal Methods in Computer-Aided Design, 2009, pp. 85–92.","mla":"Bloem, Roderick, et al. <i>Synthesizing Robust Systems</i>. Springer, 2009, pp. 85–92, doi:<a href=\"https://doi.org/10.1109/FMCAD.2009.5351139\">10.1109/FMCAD.2009.5351139</a>.","chicago":"Bloem, Roderick, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Synthesizing Robust Systems,” 85–92. Springer, 2009. <a href=\"https://doi.org/10.1109/FMCAD.2009.5351139\">https://doi.org/10.1109/FMCAD.2009.5351139</a>.","apa":"Bloem, R., Greimel, K., Henzinger, T. A., &#38; Jobstmann, B. (2009). Synthesizing robust systems (pp. 85–92). Presented at the FMCAD: Formal Methods in Computer-Aided Design, Springer. <a href=\"https://doi.org/10.1109/FMCAD.2009.5351139\">https://doi.org/10.1109/FMCAD.2009.5351139</a>","ama":"Bloem R, Greimel K, Henzinger TA, Jobstmann B. Synthesizing robust systems. In: Springer; 2009:85-92. doi:<a href=\"https://doi.org/10.1109/FMCAD.2009.5351139\">10.1109/FMCAD.2009.5351139</a>","ista":"Bloem R, Greimel K, Henzinger TA, Jobstmann B. 2009. Synthesizing robust systems. FMCAD: Formal Methods in Computer-Aided Design, 85–92."},"doi":"10.1109/FMCAD.2009.5351139","date_created":"2018-12-11T12:05:26Z","month":"12","article_processing_charge":"No","title":"Synthesizing robust systems","scopus_import":"1","quality_controlled":"1","publisher":"Springer","publication_status":"published","extern":"1","conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design"},"date_updated":"2022-03-21T08:25:44Z","language":[{"iso":"eng"}]},{"citation":{"ama":"Tripakis S, Lickly B, Henzinger TA, Lee E. On relational interfaces. In: <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>. ACM; 2009:67-76. doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>","apa":"Tripakis, S., Lickly, B., Henzinger, T. A., &#38; Lee, E. (2009). On relational interfaces. In <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i> (pp. 67–76). Grenoble, France: ACM. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>","ista":"Tripakis S, Lickly B, Henzinger TA, Lee E. 2009. On relational interfaces. EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software. EMSOFT: Embedded Software , 67–76.","short":"S. Tripakis, B. Lickly, T.A. Henzinger, E. Lee, in:, EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software, ACM, 2009, pp. 67–76.","ieee":"S. Tripakis, B. Lickly, T. A. Henzinger, and E. Lee, “On relational interfaces,” in <i>EMSOFT ’09 Proceedings of the seventh ACM international conference on Embedded software</i>, Grenoble, France, 2009, pp. 67–76.","chicago":"Tripakis, Stavros, Ben Lickly, Thomas A Henzinger, and Edward Lee. “On Relational Interfaces.” In <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, 67–76. ACM, 2009. <a href=\"https://doi.org/10.1145/1629335.1629346\">https://doi.org/10.1145/1629335.1629346</a>.","mla":"Tripakis, Stavros, et al. “On Relational Interfaces.” <i>EMSOFT ’09 Proceedings of the Seventh ACM International Conference on Embedded Software</i>, ACM, 2009, pp. 67–76, doi:<a href=\"https://doi.org/10.1145/1629335.1629346\">10.1145/1629335.1629346</a>."},"doi":"10.1145/1629335.1629346","date_created":"2018-12-11T12:05:26Z","month":"01","status":"public","abstract":[{"text":"In this paper we extend the work of Alfaro, Henzinger et al. on interface theories for component-based design. Existing interface theories often fail to capture functional relations between the inputs and outputs of an interface. For example, a simple synchronous interface that takes as input a number n ≥ 0 and returns, at the same time, as output n + 1, cannot be expressed in existing theories. In this paper we provide a theory of relational interfaces, where such input-output relations can be captured. Our theory supports synchronous interfaces, both stateless and stateful. It includes explicit notions of environments and pluggability, and satisfies fundamental properties such as preservation of refinement by composition, and characterization of pluggability by refinement. We achieve these properties by making reasonable restrictions on feedback loops in interface compositions.","lang":"eng"}],"acknowledgement":"This work is supported by the Center for Hybrid and Embedded Software Systems (CHESS) at UC Berkeley, which receives support from the National Science Foundation (NSF awards #0720882 (CSR-EHS: PRET) and #0720841 (CSR-CPS)), the U.S. Army Research Office (ARO #W911NF-07-2-0019), the U.S. Air Force Office of Scientific Research (MURI #FA9550-06-0312), the Air Force Research Lab (AFRL), the State of California Micro Program, and the following companies: Agilent, Bosch, Lockheed-Martin, National Instruments, Thales and Toyota. This work is also supported by the COMBEST and ArtistDesign projects of the European Union, and the Swiss National Science Foundation. ","publication":"EMSOFT '09 Proceedings of the seventh ACM international conference on Embedded software","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Stavros","full_name":"Tripakis, Stavros","last_name":"Tripakis"},{"full_name":"Lickly, Ben","first_name":"Ben","last_name":"Lickly"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Edward","full_name":"Lee, Edward","last_name":"Lee"}],"date_published":"2009-01-01T00:00:00Z","day":"01","publist_id":"2360","_id":"3837","file":[{"content_type":"application/pdf","file_name":"IST-2012-70-v1+1_On_Relational_Interfaces.pdf","date_created":"2018-12-12T10:13:57Z","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:16Z","creator":"system","file_size":310902,"checksum":"3a70e21527dfaad2f198549ae5710786","file_id":"5045"}],"project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques"},{"call_identifier":"FP7","name":"Design for Embedded Systems","grant_number":"214373","_id":"25F1337C-B435-11E9-9278-68D0E5697425"}],"oa":1,"file_date_updated":"2020-07-14T12:46:16Z","publication_status":"published","publisher":"ACM","has_accepted_license":"1","ec_funded":1,"quality_controlled":"1","year":"2009","ddc":["004"],"oa_version":"Submitted Version","pubrep_id":"70","page":"67 - 76","type":"conference","date_updated":"2021-01-12T07:52:33Z","language":[{"iso":"eng"}],"conference":{"name":"EMSOFT: Embedded Software ","start_date":"2009-10-12","location":"Grenoble, France","end_date":"2009-10-16"},"department":[{"_id":"ToHe"}],"title":"On relational interfaces"},{"oa_version":"Submitted Version","ddc":["005"],"type":"conference","page":"3 - 23","pubrep_id":"67","year":"2009","title":"Formalisms for specifying Markovian population models","department":[{"_id":"ToHe"}],"related_material":{"record":[{"relation":"later_version","id":"3381","status":"public"}]},"language":[{"iso":"eng"}],"date_updated":"2023-02-23T11:24:49Z","conference":{"start_date":"2009-09-23","name":"RP: Reachability Problems","end_date":"2009-09-25","location":"Palaiseau, France"},"date_published":"2009-09-07T00:00:00Z","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"},{"first_name":"Verena","full_name":"Wolf, Verena","last_name":"Wolf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages —matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models— all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model. ","lang":"eng"}],"acknowledgement":"This research was supported in part by the Excellence Cluster on Multimodal Computing and Interaction and the Swiss National Science Foundation.","publist_id":"2352","_id":"3841","day":"07","month":"09","date_created":"2018-12-11T12:05:28Z","citation":{"ista":"Henzinger TA, Jobstmann B, Wolf V. 2009. Formalisms for specifying Markovian population models. RP: Reachability Problems, LNCS, vol. 5797, 3–23.","apa":"Henzinger, T. A., Jobstmann, B., &#38; Wolf, V. (2009). Formalisms for specifying Markovian population models (Vol. 5797, pp. 3–23). Presented at the RP: Reachability Problems, Palaiseau, France: Springer. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>","ama":"Henzinger TA, Jobstmann B, Wolf V. Formalisms for specifying Markovian population models. In: Vol 5797. Springer; 2009:3-23. doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>","mla":"Henzinger, Thomas A., et al. <i>Formalisms for Specifying Markovian Population Models</i>. Vol. 5797, Springer, 2009, pp. 3–23, doi:<a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">10.1007/978-3-642-04420-5_2</a>.","chicago":"Henzinger, Thomas A, Barbara Jobstmann, and Verena Wolf. “Formalisms for Specifying Markovian Population Models,” 5797:3–23. Springer, 2009. <a href=\"https://doi.org/10.1007/978-3-642-04420-5_2\">https://doi.org/10.1007/978-3-642-04420-5_2</a>.","short":"T.A. Henzinger, B. Jobstmann, V. Wolf, in:, Springer, 2009, pp. 3–23.","ieee":"T. A. Henzinger, B. Jobstmann, and V. Wolf, “Formalisms for specifying Markovian population models,” presented at the RP: Reachability Problems, Palaiseau, France, 2009, vol. 5797, pp. 3–23."},"doi":"10.1007/978-3-642-04420-5_2","status":"public","alternative_title":["LNCS"],"intvolume":"      5797","has_accepted_license":"1","publisher":"Springer","publication_status":"published","quality_controlled":"1","scopus_import":1,"volume":5797,"file":[{"date_created":"2018-12-12T10:08:41Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:16Z","content_type":"application/pdf","file_name":"IST-2012-67-v1+1_Formalisms_for_specifying_Markovian_population_models.pdf","creator":"system","file_size":222840,"file_id":"4702","checksum":"df88431872586c773fbcfea37d7b36a2"}],"oa":1,"file_date_updated":"2020-07-14T12:46:16Z"}]