[{"alternative_title":["LNCS"],"type":"conference","extern":1,"abstract":[{"text":"Algorithms for discrete energy minimization play a fundamental role for low-level vision. Known techniques include graph cuts, belief propagation (BP) and recently introduced tree-reweighted message passing (TRW). So far, the standard benchmark for their comparison has been a 4-connected grid-graph arising in pixel-labelling stereo. This minimization problem, however, has been largely solved: recent work shows that for many scenes TRW finds the global optimum. Furthermore, it is known that a 4-connecled grid-graph is a poor stereo model since it does not take occlusions into account. We propose the problem of stereo with occlusions as a new test bed for minimization algorithms. This is a more challenging graph since it has much larger connectivity, and it also serves as a better stereo model. An attractive feature of this problem is that increased connectivity does not result in increased complexity of message passing algorithms. Indeed, one contribution of this paper is to show that sophisticated implementations of BP and TRW have the same time and memory complexity as that of 4-connecled grid-graph stereo. The main conclusion of our experimental study is that for our problem graph cut outperforms both TRW and BP considerably. TRW achieves consistently a lower energy than BP. However, as connectivity increases the speed of convergence of TRW becomes slower. Unlike 4-connected grids, the difference between the energy of the best optimization method and the lower bound of TRW appears significant. This shows the hardness of the problem and motivates future research.","lang":"eng"}],"publist_id":"3498","publication_status":"published","status":"public","title":"Comparison of energy minimization algorithms for highly connected graphs","publisher":"Springer","_id":"3184","year":"2006","date_updated":"2021-01-12T07:41:39Z","date_created":"2018-12-11T12:01:52Z","volume":"3952 LNCS","author":[{"full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"month":"05","day":"03","quality_controlled":0,"page":"1 - 15","citation":{"chicago":"Kolmogorov, Vladimir, and Carsten Rother. “Comparison of Energy Minimization Algorithms for Highly Connected Graphs,” 3952 LNCS:1–15. Springer, 2006. https://doi.org/10.1007/11744047_1.","short":"V. Kolmogorov, C. Rother, in:, Springer, 2006, pp. 1–15.","mla":"Kolmogorov, Vladimir, and Carsten Rother. Comparison of Energy Minimization Algorithms for Highly Connected Graphs. Vol. 3952 LNCS, Springer, 2006, pp. 1–15, doi:10.1007/11744047_1.","ieee":"V. Kolmogorov and C. Rother, “Comparison of energy minimization algorithms for highly connected graphs,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3952 LNCS, pp. 1–15.","apa":"Kolmogorov, V., & Rother, C. (2006). Comparison of energy minimization algorithms for highly connected graphs (Vol. 3952 LNCS, pp. 1–15). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744047_1","ista":"Kolmogorov V, Rother C. 2006. Comparison of energy minimization algorithms for highly connected graphs. ECCV: European Conference on Computer Vision, LNCS, vol. 3952 LNCS, 1–15.","ama":"Kolmogorov V, Rother C. Comparison of energy minimization algorithms for highly connected graphs. In: Vol 3952 LNCS. Springer; 2006:1-15. doi:10.1007/11744047_1"},"main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67889/paper_eccv06-trw.pdf"}],"conference":{"name":"ECCV: European Conference on Computer Vision"},"doi":"10.1007/11744047_1","date_published":"2006-05-03T00:00:00Z"},{"date_updated":"2021-01-12T07:41:39Z","date_created":"2018-12-11T12:01:53Z","volume":28,"author":[{"full_name":"Vladimir Kolmogorov","first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Criminisi, Antonio","last_name":"Criminisi","first_name":"Antonio"},{"full_name":"Blake, Andrew","last_name":"Blake","first_name":"Andrew"},{"full_name":"Cross, Geoffrey","last_name":"Cross","first_name":"Geoffrey"},{"full_name":"Rother, Carsten","first_name":"Carsten","last_name":"Rother"}],"publication_status":"published","status":"public","title":"Probabilistic fusion of stereo with color and contrast for bilayer segmentation","intvolume":" 28","publisher":"IEEE","_id":"3185","year":"2006","extern":1,"abstract":[{"lang":"eng","text":"This paper describes models and algorithms for the real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from color/contrast or from stereo alone is known to be error-prone. Here, color, contrast, and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended six-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive color model that is learned on-the-fly and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead, the stereo match likelihood is marginalized over disparities to evaluate foreground and background hypotheses and then fused with a contrast-sensitive color model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than either stereo or color/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output."}],"issue":"9","publist_id":"3496","type":"journal_article","date_published":"2006-09-01T00:00:00Z","doi":"10.1109/TPAMI.2006.193","quality_controlled":0,"page":"1480 - 1492","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67414/criminisi_pami2006.pdf"}],"citation":{"chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2006. https://doi.org/10.1109/TPAMI.2006.193.","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 28 (2006) 1480–1492.","mla":"Kolmogorov, Vladimir, et al. “Probabilistic Fusion of Stereo with Color and Contrast for Bilayer Segmentation.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9, IEEE, 2006, pp. 1480–92, doi:10.1109/TPAMI.2006.193.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2006). Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2006.193","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Probabilistic fusion of stereo with color and contrast for bilayer segmentation,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 9. IEEE, pp. 1480–1492, 2006.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2006. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 28(9), 1480–1492.","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Probabilistic fusion of stereo with color and contrast for bilayer segmentation. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2006;28(9):1480-1492. doi:10.1109/TPAMI.2006.193"},"day":"01","month":"09"},{"date_updated":"2021-01-12T07:41:39Z","date_created":"2018-12-11T12:01:53Z","volume":3953,"author":[{"first_name":"Yuri","last_name":"Boykov","full_name":"Boykov, Yuri"},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Vladimir Kolmogorov"},{"full_name":"Cremers, Daniel","first_name":"Daniel","last_name":"Cremers"},{"full_name":"Delong, Andrew","last_name":"Delong","first_name":"Andrew"}],"title":"An integral solution to surface evolution PDEs via geo cuts","publication_status":"published","status":"public","publisher":"Springer","intvolume":" 3953","year":"2006","_id":"3186","extern":1,"abstract":[{"text":"We introduce a new approach to modelling gradient flows of contours and surfaces. While standard variational methods (e.g. level sets) compute local interface motion in a differential fashion by estimating local contour velocity via energy derivatives, we propose to solve surface evolution PDEs by explicitly estimating integral motion of the whole surface. We formulate an optimization problem directly based on an integral characterization of gradient flow as an infinitesimal move of the (whole) surface giving the largest energy decrease among all moves of equal size. We show that this problem can be efficiently solved using recent advances in algorithms for global hypersurface optimization [4, 2, 11]. In particular, we employ the geo-cuts method [4] that uses ideas from integral geometry to represent continuous surfaces as cuts on discrete graphs. The resulting interface evolution algorithm is validated on some 2D and 3D examples similar to typical demonstrations of level-set methods. Our method can compute gradient flows of hypersurfaces with respect to a fairly general class of continuous functional and it is flexible with respect to distance metrics on the space of contours/surfaces. Preliminary tests for standard L2 distance metric demonstrate numerical stability, topological changes and an absence of any oscillatory motion.","lang":"eng"}],"publist_id":"3497","alternative_title":["LNCS"],"type":"conference","conference":{"name":"ECCV: European Conference on Computer Vision"},"doi":"10.1007/11744078_32","date_published":"2006-04-28T00:00:00Z","quality_controlled":0,"page":"409 - 422","citation":{"chicago":"Boykov, Yuri, Vladimir Kolmogorov, Daniel Cremers, and Andrew Delong. “An Integral Solution to Surface Evolution PDEs via Geo Cuts,” 3953:409–22. Springer, 2006. https://doi.org/10.1007/11744078_32.","mla":"Boykov, Yuri, et al. An Integral Solution to Surface Evolution PDEs via Geo Cuts. Vol. 3953, Springer, 2006, pp. 409–22, doi:10.1007/11744078_32.","short":"Y. Boykov, V. Kolmogorov, D. Cremers, A. Delong, in:, Springer, 2006, pp. 409–422.","ista":"Boykov Y, Kolmogorov V, Cremers D, Delong A. 2006. An integral solution to surface evolution PDEs via geo cuts. ECCV: European Conference on Computer Vision, LNCS, vol. 3953, 409–422.","apa":"Boykov, Y., Kolmogorov, V., Cremers, D., & Delong, A. (2006). An integral solution to surface evolution PDEs via geo cuts (Vol. 3953, pp. 409–422). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/11744078_32","ieee":"Y. Boykov, V. Kolmogorov, D. Cremers, and A. Delong, “An integral solution to surface evolution PDEs via geo cuts,” presented at the ECCV: European Conference on Computer Vision, 2006, vol. 3953, pp. 409–422.","ama":"Boykov Y, Kolmogorov V, Cremers D, Delong A. An integral solution to surface evolution PDEs via geo cuts. In: Vol 3953. Springer; 2006:409-422. doi:10.1007/11744078_32"},"month":"04","day":"28"},{"date_published":"2006-09-28T00:00:00Z","citation":{"short":"H.L. Janovjak, R. Sawhney, M. Stark, D. Mueller, in:, Techniques in Microscopy for Biomedical Applications, World Scientific Publishing, 2006, pp. 213–284.","mla":"Janovjak, Harald L., et al. “Atomic Force Microscopy.” Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–84.","chicago":"Janovjak, Harald L, Ravi Sawhney, Martin Stark, and Daniel Mueller. “Atomic Force Microscopy.” In Techniques in Microscopy for Biomedical Applications, 2:213–84. World Scientific Publishing, 2006.","ama":"Janovjak HL, Sawhney R, Stark M, Mueller D. Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Vol 2. World Scientific Publishing; 2006:213-284.","apa":"Janovjak, H. L., Sawhney, R., Stark, M., & Mueller, D. (2006). Atomic force microscopy. In Techniques in Microscopy for Biomedical Applications (Vol. 2, pp. 213–284). World Scientific Publishing.","ieee":"H. L. Janovjak, R. Sawhney, M. Stark, and D. Mueller, “Atomic force microscopy,” in Techniques in Microscopy for Biomedical Applications, vol. 2, World Scientific Publishing, 2006, pp. 213–284.","ista":"Janovjak HL, Sawhney R, Stark M, Mueller D. 2006.Atomic force microscopy. In: Techniques in Microscopy for Biomedical Applications. Manuals in Biomedical Research, vol. 2, 213–284."},"publication":"Techniques in Microscopy for Biomedical Applications","page":"213 - 284","quality_controlled":0,"day":"28","month":"09","author":[{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Harald Janovjak"},{"first_name":"Ravi","last_name":"Sawhney","full_name":"Sawhney, Ravi K"},{"first_name":"Martin","last_name":"Stark","full_name":"Stark, Martin"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel J"}],"volume":2,"date_created":"2018-12-11T12:03:09Z","date_updated":"2021-01-12T07:43:15Z","year":"2006","_id":"3404","intvolume":" 2","publisher":"World Scientific Publishing","status":"public","publication_status":"published","title":"Atomic force microscopy","publist_id":"2998","extern":1,"type":"book_chapter","alternative_title":["Manuals in Biomedical Research"]},{"citation":{"apa":"Kessler, M., Gottschalk, K., Janovjak, H. L., Mueller, D., & Gaub, H. (2006). Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.12.065","ieee":"M. Kessler, K. Gottschalk, H. L. Janovjak, D. Mueller, and H. Gaub, “Bacteriorhodopsin folds into the membrane against an external force,” Journal of Molecular Biology, vol. 357, no. 2. Elsevier, pp. 644–654, 2006.","ista":"Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. 2006. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 357(2), 644–654.","ama":"Kessler M, Gottschalk K, Janovjak HL, Mueller D, Gaub H. Bacteriorhodopsin folds into the membrane against an external force. Journal of Molecular Biology. 2006;357(2):644-654. doi:10.1016/j.jmb.2005.12.065","chicago":"Kessler, Max, Kay Gottschalk, Harald L Janovjak, Daniel Mueller, and Hermann Gaub. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.12.065.","short":"M. Kessler, K. Gottschalk, H.L. Janovjak, D. Mueller, H. Gaub, Journal of Molecular Biology 357 (2006) 644–654.","mla":"Kessler, Max, et al. “Bacteriorhodopsin Folds into the Membrane against an External Force.” Journal of Molecular Biology, vol. 357, no. 2, Elsevier, 2006, pp. 644–54, doi:10.1016/j.jmb.2005.12.065."},"publication":"Journal of Molecular Biology","page":"644 - 654","quality_controlled":0,"doi":"10.1016/j.jmb.2005.12.065","date_published":"2006-03-24T00:00:00Z","day":"24","month":"03","year":"2006","_id":"3413","intvolume":" 357","publisher":"Elsevier","status":"public","publication_status":"published","title":"Bacteriorhodopsin folds into the membrane against an external force","author":[{"first_name":"Max","last_name":"Kessler","full_name":"Kessler, Max"},{"full_name":"Gottschalk, Kay E","last_name":"Gottschalk","first_name":"Kay"},{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Harald Janovjak"},{"first_name":"Daniel","last_name":"Mueller","full_name":"Mueller, Daniel J"},{"first_name":"Hermann","last_name":"Gaub","full_name":"Gaub, Hermann"}],"volume":357,"date_updated":"2021-01-12T07:43:18Z","date_created":"2018-12-11T12:03:12Z","type":"journal_article","publist_id":"2988","issue":"2","abstract":[{"lang":"eng","text":"Despite their crucial importance for cellular function, little is known about the folding mechanisms of membrane proteins. Recently details of the folding energy landscape were elucidated by atomic force microscope (AFM)-based single molecule force spectroscopy. Upon unfolding and extraction of individual membrane proteins energy barriers in structural elements such as loops and helices were mapped and quantified with the precision of a few amino acids.\n\nHere we report on the next logical step: controlled refolding of single proteins into the membrane. First individual bacteriorhodopsin monomers were partially unfolded and extracted from the purple membrane by pulling at the C-terminal end with an AFM tip. Then by gradually lowering the tip, the protein was allowed to refold into the membrane while the folding force was recorded.\n\nWe discovered that upon refolding certain helices are pulled into the membraneagainst a sizable externalforce of several tens of picoNewton. From the mechanical work, which the helix performs on the AFM cantilever, we derive an upper limit for the Gibbs free folding energy. Subsequent unfolding allowed us to analyze the pattern of unfolding barriers and corroborate that the protein had refolded into the native state."}],"extern":1},{"day":"06","month":"01","date_published":"2006-01-06T00:00:00Z","doi":"10.1016/j.jmb.2005.10.028","publication":"Journal of Molecular Biology","citation":{"ista":"Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. 2006. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 355(1), 2–8.","apa":"Kedrov, A., Janovjak, H. L., Ziegler, C., Kühlbrandt, W., & Mueller, D. (2006). Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2005.10.028","ieee":"A. Kedrov, H. L. Janovjak, C. Ziegler, W. Kühlbrandt, and D. Mueller, “Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli,” Journal of Molecular Biology, vol. 355, no. 1. Elsevier, pp. 2–8, 2006.","ama":"Kedrov A, Janovjak HL, Ziegler C, Kühlbrandt W, Mueller D. Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli. Journal of Molecular Biology. 2006;355(1):2-8. doi:10.1016/j.jmb.2005.10.028","chicago":"Kedrov, Alexej, Harald L Janovjak, Christine Ziegler, Werner Kühlbrandt, and Daniel Mueller. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology. Elsevier, 2006. https://doi.org/10.1016/j.jmb.2005.10.028.","mla":"Kedrov, Alexej, et al. “Observing Folding Pathways and Kinetics of a Single Sodium-Proton Antiporter from Escherichia Coli.” Journal of Molecular Biology, vol. 355, no. 1, Elsevier, 2006, pp. 2–8, doi:10.1016/j.jmb.2005.10.028.","short":"A. Kedrov, H.L. Janovjak, C. Ziegler, W. Kühlbrandt, D. Mueller, Journal of Molecular Biology 355 (2006) 2–8."},"quality_controlled":0,"page":"2 - 8","abstract":[{"lang":"eng","text":"Mechanisms of folding and misfolding of membrane proteins are of interest in cell biology. Recently, we have established single-molecule force spectroscopy to observe directly the stepwise folding of the Na+/H+antiporter NhaA from Escherichia coli in vitro. Here, we improved this approach significantly to track the folding intermediates of asingle NhaA polypeptide forming structural segments such as the Na+-binding site, transmembrane α-helices, and helical pairs. The folding rates of structural segments ranged from 0.31 s−1 to 47 s−1, providing detailed insight into a distinct folding hierarchy of an unfolded polypeptide into the native membrane protein structure. In some cases, however, the folding chain formed stable and kinetically trapped non-native structures, which could be assigned to misfolding events of the antiporter."}],"issue":"1","publist_id":"2987","extern":1,"type":"journal_article","author":[{"first_name":"Alexej","last_name":"Kedrov","full_name":"Kedrov, Alexej"},{"first_name":"Harald L","last_name":"Janovjak","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","full_name":"Harald Janovjak"},{"first_name":"Christine","last_name":"Ziegler","full_name":"Ziegler, Christine"},{"full_name":"Kühlbrandt, Werner","first_name":"Werner","last_name":"Kühlbrandt"},{"last_name":"Mueller","first_name":"Daniel","full_name":"Mueller, Daniel J"}],"date_created":"2018-12-11T12:03:12Z","date_updated":"2021-01-12T07:43:19Z","volume":355,"year":"2006","_id":"3414","title":"Observing folding pathways and kinetics of a single sodium-proton antiporter from Escherichia coli","publication_status":"published","status":"public","intvolume":" 355","publisher":"Elsevier"},{"month":"01","day":"01","quality_controlled":0,"page":"546 - 561","publication":"Neurobiology of Aging","citation":{"mla":"Janovjak, Harald L., et al. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging, vol. 27, Elsevier, 2006, pp. 546–61, doi:10.1016/j.neurobiolaging.2005.03.031.","short":"H.L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, D. Mueller, Neurobiology of Aging 27 (2006) 546–561.","chicago":"Janovjak, Harald L, Alexej Kedrov, David Cisneros, Tanuj Sapra, Jens Struckmeier, and Daniel Mueller. “Imaging and Detecting Molecular Interactions of Single Membrane Proteins.” Neurobiology of Aging. Elsevier, 2006. https://doi.org/10.1016/j.neurobiolaging.2005.03.031.","ama":"Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 2006;27:546-561. doi:10.1016/j.neurobiolaging.2005.03.031","ista":"Janovjak HL, Kedrov A, Cisneros D, Sapra T, Struckmeier J, Mueller D. 2006. Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. 27, 546–561.","ieee":"H. L. Janovjak, A. Kedrov, D. Cisneros, T. Sapra, J. Struckmeier, and D. Mueller, “Imaging and detecting molecular interactions of single membrane proteins,” Neurobiology of Aging, vol. 27. Elsevier, pp. 546–561, 2006.","apa":"Janovjak, H. L., Kedrov, A., Cisneros, D., Sapra, T., Struckmeier, J., & Mueller, D. (2006). Imaging and detecting molecular interactions of single membrane proteins. Neurobiology of Aging. Elsevier. https://doi.org/10.1016/j.neurobiolaging.2005.03.031"},"doi":"10.1016/j.neurobiolaging.2005.03.031","date_published":"2006-01-01T00:00:00Z","type":"review","extern":1,"publist_id":"2986","publication_status":"published","title":"Imaging and detecting molecular interactions of single membrane proteins","status":"public","intvolume":" 27","publisher":"Elsevier","year":"2006","_id":"3415","date_created":"2018-12-11T12:03:12Z","date_updated":"2019-04-26T07:22:27Z","volume":27,"author":[{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","full_name":"Harald Janovjak"},{"full_name":"Kedrov, Alexej","first_name":"Alexej","last_name":"Kedrov"},{"last_name":"Cisneros","first_name":"David","full_name":"Cisneros, David"},{"full_name":"Sapra, Tanuj K","last_name":"Sapra","first_name":"Tanuj"},{"full_name":"Struckmeier, Jens","first_name":"Jens","last_name":"Struckmeier"},{"full_name":"Mueller, Daniel J","first_name":"Daniel","last_name":"Mueller"}]},{"issue":"6","publist_id":"2963","abstract":[{"text":"The mutational landscape model is a theoretical model describing sequence evolution in natural populations. However, recent experimental work has begun to test its predictions in laboratory populations of microbes. Several of these studies have focused on testing the prediction that the effects of beneficial mutations should be roughly exponentially distributed. The prediction appears to be borne out by most of these studies, at least qualitatively. Another study showed that a modified version of the model was able to predict, with reasonable accuracy, which of a ranked set of beneficial alleles will be fixed next. Although it remains to be seen whether the mutational landscape model adequately describes adaptation in organisms other than microbes, together these studies suggest that adaptive evolution has surprisingly general properties that can be successfully captured by theoretical models.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"first_name":"Andrea","last_name":"Betancourt","full_name":"Betancourt, Andrea J"},{"full_name":"Jonathan Bollback","orcid":"0000-0002-4624-4612","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","last_name":"Bollback","first_name":"Jonathan P"}],"volume":16,"date_created":"2018-12-11T12:03:19Z","date_updated":"2021-01-12T07:43:27Z","_id":"3437","year":"2006","intvolume":" 16","publisher":"Elsevier","publication_status":"published","title":"Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution","status":"public","day":"01","month":"12","date_published":"2006-12-01T00:00:00Z","doi":"10.1016/j.gde.2006.10.006","citation":{"ista":"Betancourt A, Bollback JP. 2006. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 16(6), 618–623.","apa":"Betancourt, A., & Bollback, J. P. (2006). Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2006.10.006","ieee":"A. Betancourt and J. P. Bollback, “Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution,” Current Opinion in Genetics & Development, vol. 16, no. 6. Elsevier, pp. 618–623, 2006.","ama":"Betancourt A, Bollback JP. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Current Opinion in Genetics & Development. 2006;16(6):618-623. doi:10.1016/j.gde.2006.10.006","chicago":"Betancourt, Andrea, and Jonathan P Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development. Elsevier, 2006. https://doi.org/10.1016/j.gde.2006.10.006.","mla":"Betancourt, Andrea, and Jonathan P. Bollback. “Fitness Effects of Beneficial Mutations: The Mutational Landscape Model in Experimental Evolution.” Current Opinion in Genetics & Development, vol. 16, no. 6, Elsevier, 2006, pp. 618–23, doi:10.1016/j.gde.2006.10.006.","short":"A. Betancourt, J.P. Bollback, Current Opinion in Genetics & Development 16 (2006) 618–623."},"publication":"Current Opinion in Genetics & Development","page":"618 - 623","quality_controlled":0},{"extern":1,"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 retina, and show that pairwise interactions account for observed higher-order correlations. By first finding a representative ensemble for observed networks we can 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.","lang":"eng"}],"publist_id":"2969","type":"preprint","date_created":"2018-12-11T12:03:18Z","date_updated":"2021-01-12T07:43:25Z","author":[{"first_name":"Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Gasper Tkacik"},{"full_name":"Schneidman, E.","last_name":"Schneidman","first_name":"E."},{"last_name":"Berry","first_name":"M.","full_name":"Berry, M. J."},{"full_name":"Bialek, William S","first_name":"William","last_name":"Bialek"}],"title":"Ising models for networks of real neurons","publication_status":"published","status":"public","publisher":"ArXiv","_id":"3431","year":"2006","day":"22","month":"11","date_published":"2006-11-22T00:00:00Z","quality_controlled":0,"page":"1 - 4","publication":"ArXiv","oa":1,"citation":{"mla":"Tkačik, Gašper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4.","short":"G. Tkačik, E. Schneidman, M. Berry, W. Bialek, ArXiv (2006) 1–4.","chicago":"Tkačik, Gašper, E. Schneidman, M. Berry, and William Bialek. “Ising Models for Networks of Real Neurons.” ArXiv. ArXiv, 2006.","ama":"Tkačik G, Schneidman E, Berry M, Bialek W. Ising models for networks of real neurons. ArXiv. 2006:1-4.","ista":"Tkačik G, Schneidman E, Berry M, Bialek W. 2006. Ising models for networks of real neurons. ArXiv, 1–4, .","apa":"Tkačik, G., Schneidman, E., Berry, M., & Bialek, W. (2006). Ising models for networks of real neurons. ArXiv. ArXiv.","ieee":"G. Tkačik, E. Schneidman, M. Berry, and W. Bialek, “Ising models for networks of real neurons,” ArXiv. ArXiv, pp. 1–4, 2006."},"main_file_link":[{"url":"http://arxiv.org/abs/q-bio/0611072","open_access":"1"}]},{"doi":"10.1109/CSFW.2006.14","date_published":"2006-07-31T00:00:00Z","conference":{"name":"CSF: Computer Security Foundations"},"citation":{"ieee":"K. Chatterjee, R. Jagadeesan, and C. Pitcher, “Games for controls,” presented at the CSF: Computer Security Foundations, 2006, pp. 70–82.","apa":"Chatterjee, K., Jagadeesan, R., & Pitcher, C. (2006). Games for controls (pp. 70–82). Presented at the CSF: Computer Security Foundations, IEEE. https://doi.org/10.1109/CSFW.2006.14","ista":"Chatterjee K, Jagadeesan R, Pitcher C. 2006. Games for controls. CSF: Computer Security Foundations, 70–82.","ama":"Chatterjee K, Jagadeesan R, Pitcher C. Games for controls. In: IEEE; 2006:70-82. doi:10.1109/CSFW.2006.14","chicago":"Chatterjee, Krishnendu, Rhada Jagadeesan, and Corin Pitcher. “Games for Controls,” 70–82. IEEE, 2006. https://doi.org/10.1109/CSFW.2006.14.","short":"K. Chatterjee, R. Jagadeesan, C. Pitcher, in:, IEEE, 2006, pp. 70–82.","mla":"Chatterjee, Krishnendu, et al. Games for Controls. IEEE, 2006, pp. 70–82, doi:10.1109/CSFW.2006.14."},"page":"70 - 82","quality_controlled":0,"month":"07","day":"31","author":[{"full_name":"Krishnendu Chatterjee","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jagadeesan, Rhada","first_name":"Rhada","last_name":"Jagadeesan"},{"first_name":"Corin","last_name":"Pitcher","full_name":"Pitcher, Corin"}],"date_created":"2018-12-11T12:03:23Z","date_updated":"2021-01-12T07:43:32Z","year":"2006","_id":"3449","publisher":"IEEE","status":"public","publication_status":"published","title":"Games for controls","publist_id":"2938","abstract":[{"lang":"eng","text":"We argue that games are expressive enough to encompass (history-based) access control, (resource) usage control (e.g., dynamic adaptive access control of reputation systems), accountability based controls (e.g., insurance), controls derived from rationality assumptions on participants (e.g., network mechanisms), and their composition. Building on the extensive research into games, we demonstrate that this expressive power coexists with a formal analysis framework comparable to that available for access control."}],"extern":1,"type":"conference"}]