[{"_id":"3183","status":"public","conference":{"name":"CVPR: Computer Vision and Pattern Recognition"},"type":"conference","extern":1,"citation":{"chicago":"Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.91.","ista":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol. 2, 407–414.","mla":"Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video. Vol. 2, IEEE, 2005, pp. 407–14, doi:10.1109/CVPR.2005.91.","apa":"Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005). Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.91","ama":"Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:10.1109/CVPR.2005.91","ieee":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 2, pp. 407–414.","short":"V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 407–414."},"date_updated":"2021-01-12T07:41:38Z","title":"Bi-layer segmentation of binocular stereo video","publist_id":"3502","author":[{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Criminisi","full_name":"Criminisi, Antonio","first_name":"Antonio"},{"last_name":"Blake","full_name":"Blake, Andrew","first_name":"Andrew"},{"last_name":"Cross","full_name":"Cross, Geoffrey","first_name":"Geoffrey"},{"first_name":"Carsten","full_name":"Rother, Carsten","last_name":"Rother"}],"abstract":[{"lang":"eng","text":"This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, 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 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour 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 marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour 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 perfomance, substantially better than stereo or colour/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."}],"intvolume":" 2","month":"07","main_file_link":[{"open_access":"0","url":"http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf"}],"publisher":"IEEE","quality_controlled":0,"day":"25","publication_status":"published","year":"2005","date_created":"2018-12-11T12:01:52Z","date_published":"2005-07-25T00:00:00Z","doi":"10.1109/CVPR.2005.91","volume":2,"page":"407 - 414"},{"publication_status":"published","year":"2005","day":"05","page":"564 - 571","date_created":"2018-12-11T12:01:52Z","date_published":"2005-12-05T00:00:00Z","volume":1,"doi":"10.1109/ICCV.2005.252","abstract":[{"text":"In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such "submodular" metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the "shrinking" problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints.","lang":"eng"}],"quality_controlled":0,"publisher":"IEEE","intvolume":" 1","month":"12","date_updated":"2021-01-12T07:41:38Z","citation":{"ista":"Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts or global optimization of length area and flux. ICCV: International Conference on Computer Vision vol. 1, 564–571.","chicago":"Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005. https://doi.org/10.1109/ICCV.2005.252.","short":"V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571.","ieee":"V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts or global optimization of length area and flux,” presented at the ICCV: International Conference on Computer Vision, 2005, vol. 1, pp. 564–571.","apa":"Kolmogorov, V., & Boykov, Y. (2005). What metrics can be approximated by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571). Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2005.252","ama":"Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:10.1109/ICCV.2005.252","mla":"Kolmogorov, Vladimir, and Yuri Boykov. What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux. Vol. 1, IEEE, 2005, pp. 564–71, doi:10.1109/ICCV.2005.252."},"extern":1,"publist_id":"3501","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Vladimir Kolmogorov","last_name":"Kolmogorov"},{"last_name":"Boykov","full_name":"Boykov, Yuri","first_name":"Yuri"}],"title":"What metrics can be approximated by geo cuts or global optimization of length area and flux","_id":"3182","conference":{"name":"ICCV: International Conference on Computer Vision"},"type":"conference","status":"public"},{"page":"316 - 323","date_published":"2005-07-01T00:00:00Z","date_created":"2018-12-11T12:01:51Z","publication_status":"published","year":"2005","day":"01","quality_controlled":0,"publisher":"AUAI Press","main_file_link":[{"url":"http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf","open_access":"0"}],"month":"07","abstract":[{"text":"Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method.","lang":"eng"}],"publist_id":"3500","author":[{"last_name":"Kolmogorov","full_name":"Vladimir Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"first_name":"Martin","full_name":"Wainwright, Martin J","last_name":"Wainwright"}],"title":"On the optimality of tree reweighted max product message passing","date_updated":"2021-01-12T07:41:38Z","citation":{"mla":"Kolmogorov, Vladimir, and Martin Wainwright. On the Optimality of Tree Reweighted Max Product Message Passing. AUAI Press, 2005, pp. 316–23.","ama":"Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product message passing. In: AUAI Press; 2005:316-323.","apa":"Kolmogorov, V., & Wainwright, M. (2005). On the optimality of tree reweighted max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press.","ieee":"V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 316–323.","short":"V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323.","chicago":"Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005.","ista":"Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323."},"extern":1,"type":"conference","conference":{"name":"UAI: Uncertainty in Artificial Intelligence"},"status":"public","_id":"3181"},{"publisher":"Wiley-Blackwell","quality_controlled":0,"month":"05","intvolume":" 218","abstract":[{"lang":"eng","text":"Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/."}],"page":"125 - 132","issue":"2","volume":218,"doi":"10.1111/j.1365-2818.2005.01478.x","date_published":"2005-05-01T00:00:00Z","date_created":"2018-12-11T12:03:13Z","year":"2005","publication_status":"published","day":"01","publication":"Journal of Microscopy","type":"journal_article","status":"public","_id":"3417","author":[{"full_name":"Kuhn, Michael","last_name":"Kuhn","first_name":"Michael"},{"full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hubain, Maurice","last_name":"Hubain","first_name":"Maurice"},{"full_name":"Mueller, Daniel J","last_name":"Mueller","first_name":"Daniel"}],"publist_id":"2984","title":"Automated alignment and pattern recognition of single-molecule force spectroscopy data","date_updated":"2021-01-12T07:43:20Z","citation":{"mla":"Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” Journal of Microscopy, vol. 218, no. 2, Wiley-Blackwell, 2005, pp. 125–32, doi:10.1111/j.1365-2818.2005.01478.x.","ama":"Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 2005;218(2):125-132. doi:10.1111/j.1365-2818.2005.01478.x","apa":"Kuhn, M., Janovjak, H. L., Hubain, M., & Mueller, D. (2005). Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2818.2005.01478.x","short":"M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218 (2005) 125–132.","ieee":"M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and pattern recognition of single-molecule force spectroscopy data,” Journal of Microscopy, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005.","chicago":"Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” Journal of Microscopy. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1365-2818.2005.01478.x.","ista":"Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 218(2), 125–132."},"extern":1},{"page":"37 - 39","doi":"10.1529/biophysj.105.059774","issue":"5","date_published":"2005-05-01T00:00:00Z","volume":88,"date_created":"2018-12-11T12:03:13Z","publication_status":"published","year":"2005","day":"01","publication":"Biophysical Journal","quality_controlled":0,"publisher":"Biophysical Society","oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/","open_access":"1"}],"month":"05","intvolume":" 88","abstract":[{"lang":"eng","text":"In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins."}],"author":[{"full_name":"Harald Janovjak","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tanuj","last_name":"Sapra","full_name":"Sapra, Tanuj K"},{"first_name":"Daniel","full_name":"Mueller, Daniel J","last_name":"Mueller"}],"publist_id":"2985","title":"Complex stability of single proteins explored by forced unfolding experiments","date_updated":"2021-01-12T07:43:19Z","citation":{"mla":"Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal, vol. 88, no. 5, Biophysical Society, 2005, pp. 37–39, doi:10.1529/biophysj.105.059774.","apa":"Janovjak, H. L., Sapra, T., & Mueller, D. (2005). Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.059774","ama":"Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 2005;88(5):37-39. doi:10.1529/biophysj.105.059774","ieee":"H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins explored by forced unfolding experiments,” Biophysical Journal, vol. 88, no. 5. Biophysical Society, pp. 37–39, 2005.","short":"H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.","chicago":"Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.105.059774.","ista":"Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39."},"extern":1,"type":"journal_article","status":"public","_id":"3416"}]