[{"month":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Springer","title":"Interactive labeling of image segmentation hierarchies","author":[{"first_name":"Georg","last_name":"Zankl","full_name":"Zankl, Georg"},{"last_name":"Haxhimusa","first_name":"Yll","full_name":"Haxhimusa, Yll"},{"last_name":"Ion","id":"29F89302-F248-11E8-B48F-1D18A9856A87","first_name":"Adrian","full_name":"Ion, Adrian"}],"_id":"2971","abstract":[{"lang":"eng","text":"We study the task of interactive semantic labeling of a segmentation hierarchy. To this end we propose a framework interleaving two components: an automatic labeling step, based on a Conditional Random Field whose dependencies are defined by the inclusion tree of the segmentation hierarchy, and an interaction step that integrates incremental input from a human user. Evaluated on two distinct datasets, the proposed interactive approach efficiently integrates human interventions and illustrates the advantages of structured prediction in an interactive framework. "}],"date_updated":"2021-01-12T07:40:10Z","year":"2012","day":"01","quality_controlled":"1","volume":7476,"citation":{"chicago":"Zankl, Georg, Yll Haxhimusa, and Adrian Ion. “Interactive Labeling of Image Segmentation Hierarchies,” 7476:11–20. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_2.","apa":"Zankl, G., Haxhimusa, Y., & Ion, A. (2012). Interactive labeling of image segmentation hierarchies (Vol. 7476, pp. 11–20). Presented at the Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_2","ista":"Zankl G, Haxhimusa Y, Ion A. 2012. Interactive labeling of image segmentation hierarchies. Pattern Recognition vol. 7476, 11–20.","mla":"Zankl, Georg, et al. Interactive Labeling of Image Segmentation Hierarchies. Vol. 7476, Springer, 2012, pp. 11–20, doi:10.1007/978-3-642-32717-9_2.","short":"G. Zankl, Y. Haxhimusa, A. Ion, in:, Springer, 2012, pp. 11–20.","ieee":"G. Zankl, Y. Haxhimusa, and A. Ion, “Interactive labeling of image segmentation hierarchies,” presented at the Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 11–20.","ama":"Zankl G, Haxhimusa Y, Ion A. Interactive labeling of image segmentation hierarchies. In: Vol 7476. Springer; 2012:11-20. doi:10.1007/978-3-642-32717-9_2"},"intvolume":" 7476","scopus_import":1,"publist_id":"3737","type":"conference","oa_version":"None","date_published":"2012-01-01T00:00:00Z","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-32717-9_2","conference":{"start_date":"2012-08-28","name":"Pattern Recognition","end_date":"2012-08-31","location":"Graz, Austria"},"publication_status":"published","page":"11 - 20","date_created":"2018-12-11T12:00:37Z"},{"citation":{"ieee":"K. Chatterjee and L. Doyen, “Energy parity games,” Theoretical Computer Science, vol. 458. Elsevier, pp. 49–60, 2012.","ama":"Chatterjee K, Doyen L. Energy parity games. Theoretical Computer Science. 2012;458:49-60. doi:10.1016/j.tcs.2012.07.038","short":"K. Chatterjee, L. Doyen, Theoretical Computer Science 458 (2012) 49–60.","apa":"Chatterjee, K., & Doyen, L. (2012). Energy parity games. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2012.07.038","mla":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical Computer Science, vol. 458, Elsevier, 2012, pp. 49–60, doi:10.1016/j.tcs.2012.07.038.","ista":"Chatterjee K, Doyen L. 2012. Energy parity games. Theoretical Computer Science. 458, 49–60.","chicago":"Chatterjee, Krishnendu, and Laurent Doyen. “Energy Parity Games.” Theoretical Computer Science. Elsevier, 2012. https://doi.org/10.1016/j.tcs.2012.07.038."},"intvolume":" 458","file_date_updated":"2020-07-14T12:45:57Z","scopus_import":1,"ddc":["004"],"oa_version":"Published Version","date_published":"2012-11-02T00:00:00Z","publication_status":"published","doi":"10.1016/j.tcs.2012.07.038","month":"11","ec_funded":1,"status":"public","oa":1,"_id":"2972","date_updated":"2023-02-23T11:45:29Z","arxiv":1,"abstract":[{"text":"Energy parity games are infinite two-player turn-based games played on weighted graphs. The objective of the game combines a (qualitative) parity condition with the (quantitative) requirement that the sum of the weights (i.e., the level of energy in the game) must remain positive. Beside their own interest in the design and synthesis of resource-constrained omega-regular specifications, energy parity games provide one of the simplest model of games with combined qualitative and quantitative objectives. Our main results are as follows: (a) exponential memory is sufficient and may be necessary for winning strategies in energy parity games; (b) the problem of deciding the winner in energy parity games can be solved in NP ∩ coNP; and (c) we give an algorithm to solve energy parity by reduction to energy games. We also show that the problem of deciding the winner in energy parity games is logspace-equivalent to the problem of deciding the winner in mean-payoff parity games, which can thus be solved in NP ∩ coNP. As a consequence we also obtain a conceptually simple algorithm to solve mean-payoff parity games.","lang":"eng"}],"year":"2012","external_id":{"arxiv":["1001.5183"]},"volume":458,"quality_controlled":"1","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3851"}]},"publist_id":"3736","pubrep_id":"935","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"KrCh"}],"has_accepted_license":"1","date_created":"2018-12-11T12:00:37Z","page":"49 - 60","publication":"Theoretical Computer Science","publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Energy parity games","project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"}],"file":[{"file_size":351271,"content_type":"application/pdf","relation":"main_file","date_created":"2019-02-06T11:56:22Z","file_name":"2012_Elsevier_Chatterjee.pdf","date_updated":"2020-07-14T12:45:57Z","access_level":"open_access","file_id":"5935","checksum":"719e4a5af5a01ad3f2f7f7f05b3c2b09","creator":"kschuh"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"day":"02"},{"acknowledgement":"We are grateful to Petros Mol for helpful discussions on the reduction for the hardness of the xLPN problem.\r\n","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"day":"01","author":[{"full_name":"Jain, Abhishek","last_name":"Jain","first_name":"Abhishek"},{"first_name":"Stephan","orcid":"0000-0003-2835-9093","id":"329FCCF0-F248-11E8-B48F-1D18A9856A87","last_name":"Krenn","full_name":"Krenn, Stephan"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"full_name":"Tentes, Aris","last_name":"Tentes","first_name":"Aris"}],"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"file":[{"file_name":"IST-2016-721-v1+1_513.pdf","date_updated":"2020-07-14T12:45:58Z","date_created":"2018-12-12T10:14:00Z","file_id":"5048","creator":"system","checksum":"ab879537385efc4cb4203e7ef0fea17b","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":482570}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"Commitments and efficient zero knowledge proofs from learning parity with noise","alternative_title":["LNCS"],"has_accepted_license":"1","page":"663 - 680","date_created":"2018-12-11T12:00:38Z","type":"conference","department":[{"_id":"KrPi"}],"language":[{"iso":"eng"}],"pubrep_id":"721","publist_id":"3730","volume":7658,"editor":[{"full_name":"Wang, Xiaoyun","first_name":"Xiaoyun","last_name":"Wang"},{"last_name":"Sako","first_name":"Kazue","full_name":"Sako, Kazue"}],"abstract":[{"lang":"eng","text":"We construct a perfectly binding string commitment scheme whose security is based on the learning parity with noise (LPN) assumption, or equivalently, the hardness of decoding random linear codes. Our scheme not only allows for a simple and efficient zero-knowledge proof of knowledge for committed values (essentially a Σ-protocol), but also for such proofs showing any kind of relation amongst committed values, i.e. proving that messages m_0,...,m_u, are such that m_0=C(m_1,...,m_u) for any circuit C.\r\n\r\nTo get soundness which is exponentially small in a security parameter t, and when the zero-knowledge property relies on the LPN problem with secrets of length l, our 3 round protocol has communication complexity O(t|C|l log(l)) and computational complexity of O(t|C|l) bit operations. The hidden constants are small, and the computation consists mostly of computing inner products of bit-vectors."}],"date_updated":"2021-01-12T07:40:11Z","year":"2012","_id":"2974","status":"public","oa":1,"month":"12","ec_funded":1,"doi":"10.1007/978-3-642-34961-4_40","conference":{"end_date":"2012-12-06","location":"Beijing, China","start_date":"2012-12-02","name":"ASIACRYPT: Theory and Application of Cryptology and Information Security"},"publication_status":"published","oa_version":"Submitted Version","date_published":"2012-12-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:58Z","scopus_import":1,"ddc":["004","005"],"citation":{"apa":"Jain, A., Krenn, S., Pietrzak, K. Z., & Tentes, A. (2012). Commitments and efficient zero knowledge proofs from learning parity with noise. In X. Wang & K. Sako (Eds.) (Vol. 7658, pp. 663–680). Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China: Springer. https://doi.org/10.1007/978-3-642-34961-4_40","ista":"Jain A, Krenn S, Pietrzak KZ, Tentes A. 2012. Commitments and efficient zero knowledge proofs from learning parity with noise. ASIACRYPT: Theory and Application of Cryptology and Information Security, LNCS, vol. 7658, 663–680.","mla":"Jain, Abhishek, et al. Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise. Edited by Xiaoyun Wang and Kazue Sako, vol. 7658, Springer, 2012, pp. 663–80, doi:10.1007/978-3-642-34961-4_40.","chicago":"Jain, Abhishek, Stephan Krenn, Krzysztof Z Pietrzak, and Aris Tentes. “Commitments and Efficient Zero Knowledge Proofs from Learning Parity with Noise.” edited by Xiaoyun Wang and Kazue Sako, 7658:663–80. Springer, 2012. https://doi.org/10.1007/978-3-642-34961-4_40.","ama":"Jain A, Krenn S, Pietrzak KZ, Tentes A. Commitments and efficient zero knowledge proofs from learning parity with noise. In: Wang X, Sako K, eds. Vol 7658. Springer; 2012:663-680. doi:10.1007/978-3-642-34961-4_40","ieee":"A. Jain, S. Krenn, K. Z. Pietrzak, and A. Tentes, “Commitments and efficient zero knowledge proofs from learning parity with noise,” presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Beijing, China, 2012, vol. 7658, pp. 663–680.","short":"A. Jain, S. Krenn, K.Z. Pietrzak, A. Tentes, in:, X. Wang, K. Sako (Eds.), Springer, 2012, pp. 663–680."},"intvolume":" 7658"},{"title":"Deconstructing approximate offsets","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","day":"01","acknowledgement":"We thank Eyal Flato (Plataine Ltd.) for raising the offset-deconstruction problem in connection with wood cutting. We also thank Tim Bretl (UIUC) for suggesting the digital-pen offset-deconstruction problem. This work has been supported in part by the Israel Science Foundation (grant no. 1102/11), by the German–Israeli Foundation (grant no. 969/07), by the Hermann Minkowski–Minerva Center for Geometry at Tel Aviv University, and by the EU Project under Contract No. 255827 (CGL—Computational Geometry Learning).\r\n","author":[{"full_name":"Berberich, Eric","first_name":"Eric","last_name":"Berberich"},{"last_name":"Halperin","first_name":"Dan","full_name":"Halperin, Dan"},{"orcid":"0000-0002-8030-9299","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","full_name":"Kerber, Michael"},{"last_name":"Pogalnikova","first_name":"Roza","full_name":"Pogalnikova, Roza"}],"publist_id":"3584","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"3329"}]},"volume":48,"quality_controlled":"1","external_id":{"arxiv":["1109.2158"]},"publication":"Discrete & Computational Geometry","page":"964 - 989","date_created":"2018-12-11T12:01:28Z","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"type":"journal_article","oa":1,"status":"public","month":"12","year":"2012","arxiv":1,"issue":"4","abstract":[{"lang":"eng","text":"We consider the offset-deconstruction problem: Given a polygonal shape Q with n vertices, can it be expressed, up to a tolerance ε in Hausdorff distance, as the Minkowski sum of another polygonal shape P with a disk of fixed radius? If it does, we also seek a preferably simple-looking solution P; then, P's offset constitutes an accurate, vertex-reduced, and smoothened approximation of Q. We give an O(nlogn)-time exact decision algorithm that handles any polygonal shape, assuming the real-RAM model of computation. A variant of the algorithm, which we have implemented using the cgal library, is based on rational arithmetic and answers the same deconstruction problem up to an uncertainty parameter δ its running time additionally depends on δ. If the input shape is found to be approximable, this algorithm also computes an approximate solution for the problem. It also allows us to solve parameter-optimization problems induced by the offset-deconstruction problem. For convex shapes, the complexity of the exact decision algorithm drops to O(n), which is also the time required to compute a solution P with at most one more vertex than a vertex-minimal one."}],"date_updated":"2023-02-23T11:22:30Z","_id":"3115","main_file_link":[{"url":"http://arxiv.org/abs/1109.2158","open_access":"1"}],"scopus_import":1,"intvolume":" 48","citation":{"ieee":"E. Berberich, D. Halperin, M. Kerber, and R. Pogalnikova, “Deconstructing approximate offsets,” Discrete & Computational Geometry, vol. 48, no. 4. Springer, pp. 964–989, 2012.","ama":"Berberich E, Halperin D, Kerber M, Pogalnikova R. Deconstructing approximate offsets. Discrete & Computational Geometry. 2012;48(4):964-989. doi:10.1007/s00454-012-9441-5","short":"E. Berberich, D. Halperin, M. Kerber, R. Pogalnikova, Discrete & Computational Geometry 48 (2012) 964–989.","chicago":"Berberich, Eric, Dan Halperin, Michael Kerber, and Roza Pogalnikova. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry. Springer, 2012. https://doi.org/10.1007/s00454-012-9441-5.","apa":"Berberich, E., Halperin, D., Kerber, M., & Pogalnikova, R. (2012). Deconstructing approximate offsets. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-012-9441-5","mla":"Berberich, Eric, et al. “Deconstructing Approximate Offsets.” Discrete & Computational Geometry, vol. 48, no. 4, Springer, 2012, pp. 964–89, doi:10.1007/s00454-012-9441-5.","ista":"Berberich E, Halperin D, Kerber M, Pogalnikova R. 2012. Deconstructing approximate offsets. Discrete & Computational Geometry. 48(4), 964–989."},"doi":"10.1007/s00454-012-9441-5","publication_status":"published","date_published":"2012-12-01T00:00:00Z","oa_version":"Preprint"},{"month":"10","publisher":"Elsevier","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Minimizing a sum of submodular functions","oa":1,"author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"}],"_id":"3117","date_updated":"2021-01-12T07:41:11Z","abstract":[{"text":"We consider the problem of minimizing a function represented as a sum of submodular terms. We assume each term allows an efficient computation of exchange capacities. This holds, for example, for terms depending on a small number of variables, or for certain cardinality-dependent terms. A naive application of submodular minimization algorithms would not exploit the existence of specialized exchange capacity subroutines for individual terms. To overcome this, we cast the problem as a submodular flow (SF) problem in an auxiliary graph in such a way that applying most existing SF algorithms would rely only on these subroutines. We then explore in more detail Iwata's capacity scaling approach for submodular flows (Iwata 1997 [19]). In particular, we show how to improve its complexity in the case when the function contains cardinality-dependent terms.","lang":"eng"}],"issue":"15","day":"01","year":"2012","volume":160,"citation":{"ama":"Kolmogorov V. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 2012;160(15):2246-2258. doi:10.1016/j.dam.2012.05.025","ieee":"V. Kolmogorov, “Minimizing a sum of submodular functions,” Discrete Applied Mathematics, vol. 160, no. 15. Elsevier, pp. 2246–2258, 2012.","short":"V. Kolmogorov, Discrete Applied Mathematics 160 (2012) 2246–2258.","chicago":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics. Elsevier, 2012. https://doi.org/10.1016/j.dam.2012.05.025.","mla":"Kolmogorov, Vladimir. “Minimizing a Sum of Submodular Functions.” Discrete Applied Mathematics, vol. 160, no. 15, Elsevier, 2012, pp. 2246–58, doi:10.1016/j.dam.2012.05.025.","apa":"Kolmogorov, V. (2012). Minimizing a sum of submodular functions. Discrete Applied Mathematics. Elsevier. https://doi.org/10.1016/j.dam.2012.05.025","ista":"Kolmogorov V. 2012. Minimizing a sum of submodular functions. Discrete Applied Mathematics. 160(15), 2246–2258."},"intvolume":" 160","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1006.1990"}],"publist_id":"3582","scopus_import":1,"oa_version":"Preprint","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"VlKo"}],"date_published":"2012-10-01T00:00:00Z","publication_status":"published","doi":"10.1016/j.dam.2012.05.025","date_created":"2018-12-11T12:01:29Z","page":"2246 - 2258","publication":"Discrete Applied Mathematics"},{"publication_status":"published","doi":"10.1145/2185520.2185549","oa_version":"Submitted Version","date_published":"2012-07-01T00:00:00Z","scopus_import":"1","file_date_updated":"2020-07-14T12:46:00Z","ddc":["000"],"citation":{"short":"M. Bojsen-Hansen, H. Li, C. Wojtan, ACM Transactions on Graphics 31 (2012).","ieee":"M. Bojsen-Hansen, H. Li, and C. Wojtan, “Tracking surfaces with evolving topology,” ACM Transactions on Graphics, vol. 31, no. 4. ACM, 2012.","ama":"Bojsen-Hansen M, Li H, Wojtan C. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 2012;31(4). doi:10.1145/2185520.2185549","ista":"Bojsen-Hansen M, Li H, Wojtan C. 2012. Tracking surfaces with evolving topology. ACM Transactions on Graphics. 31(4), 53.","mla":"Bojsen-Hansen, Morten, et al. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics, vol. 31, no. 4, 53, ACM, 2012, doi:10.1145/2185520.2185549.","apa":"Bojsen-Hansen, M., Li, H., & Wojtan, C. (2012). Tracking surfaces with evolving topology. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2185520.2185549","chicago":"Bojsen-Hansen, Morten, Hao Li, and Chris Wojtan. “Tracking Surfaces with Evolving Topology.” ACM Transactions on Graphics. ACM, 2012. https://doi.org/10.1145/2185520.2185549."},"intvolume":" 31","date_updated":"2022-05-24T08:21:11Z","abstract":[{"text":"We present a method for recovering a temporally coherent, deforming triangle mesh with arbitrarily changing topology from an incoherent sequence of static closed surfaces. We solve this problem using the surface geometry alone, without any prior information like surface templates or velocity fields. Our system combines a proven strategy for triangle mesh improvement, a robust multi-resolution non-rigid registration routine, and a reliable technique for changing surface mesh topology. We also introduce a novel topological constraint enforcement algorithm to ensure that the output and input always have similar topology. We apply our technique to a series of diverse input data from video reconstructions, physics simulations, and artistic morphs. The structured output of our algorithm allows us to efficiently track information like colors and displacement maps, recover velocity information, and solve PDEs on the mesh as a post process.","lang":"eng"}],"issue":"4","year":"2012","article_number":"53","_id":"3118","status":"public","oa":1,"month":"07","has_accepted_license":"1","date_created":"2018-12-11T12:01:29Z","publication":"ACM Transactions on Graphics","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"publist_id":"3581","pubrep_id":"602","article_processing_charge":"No","article_type":"original","quality_controlled":"1","volume":31,"acknowledgement":"This work is supported by the SNF fellowship PBEZP2-134464.\r\nWe would like to thank Xiaochen Hu for implementing mesh con- version tools, Duygu Ceylan for helping with the rendering, and Art Tevs for the human performance data comparison. We also thank Nils Thuerey and Christopher Batty for helpful discussions. ","day":"01","author":[{"first_name":"Morten","orcid":"0000-0002-4417-3224","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","last_name":"Bojsen-Hansen","full_name":"Bojsen-Hansen, Morten"},{"full_name":"Li, Hao","last_name":"Li","first_name":"Hao"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"file":[{"creator":"system","checksum":"1e219c5bf4e5552c1290c62eefa5cd60","file_id":"5359","access_level":"open_access","file_name":"IST-2016-602-v1+1_topoReg.pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:18:37Z","relation":"main_file","content_type":"application/pdf","file_size":44538518}],"publisher":"ACM","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Tracking surfaces with evolving topology","alternative_title":["SIGGRAPH"]},{"file_date_updated":"2020-07-14T12:46:00Z","scopus_import":1,"ddc":["000"],"citation":{"ieee":"K. Raveendran, N. Thuerey, C. Wojtan, and G. Turk, “Controlling liquids using meshes,” in Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, Aire-la-Ville, Switzerland, 2012, pp. 255–264.","ama":"Raveendran K, Thuerey N, Wojtan C, Turk G. Controlling liquids using meshes. In: Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. ACM; 2012:255-264.","short":"K. Raveendran, N. Thuerey, C. Wojtan, G. Turk, in:, Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–264.","chicago":"Raveendran, Karthik, Nils Thuerey, Chris Wojtan, and Greg Turk. “Controlling Liquids Using Meshes.” In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, 255–64. ACM, 2012.","apa":"Raveendran, K., Thuerey, N., Wojtan, C., & Turk, G. (2012). Controlling liquids using meshes. In Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation (pp. 255–264). Aire-la-Ville, Switzerland: ACM.","mla":"Raveendran, Karthik, et al. “Controlling Liquids Using Meshes.” Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation, ACM, 2012, pp. 255–64.","ista":"Raveendran K, Thuerey N, Wojtan C, Turk G. 2012. Controlling liquids using meshes. Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 255–264."},"conference":{"location":"Aire-la-Ville, Switzerland","end_date":"2012-07-31","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2012-07-29"},"publication_status":"published","oa_version":"Submitted Version","date_published":"2012-07-29T00:00:00Z","status":"public","oa":1,"month":"07","abstract":[{"text":"We present an approach for artist-directed animation of liquids using multiple levels of control over the simulation, ranging from the overall tracking of desired shapes to highly detailed secondary effects such as dripping streams, separating sheets of fluid, surface waves and ripples. The first portion of our technique is a volume preserving morph that allows the animator to produce a plausible fluid-like motion from a sparse set of control meshes. By rasterizing the resulting control meshes onto the simulation grid, the mesh velocities act as boundary conditions during the projection step of the fluid simulation. We can then blend this motion together with uncontrolled fluid velocities to achieve a more relaxed control over the fluid that captures natural inertial effects. Our method can produce highly detailed liquid surfaces with control over sub-grid details by using a mesh-based surface tracker on top of a coarse grid-based fluid simulation. We can create ripples and waves on the fluid surface attracting the surface mesh to the control mesh with spring-like forces and also by running a wave simulation over the surface mesh. Our video results demonstrate how our control scheme can be used to create animated characters and shapes that are made of water.\r\n","lang":"eng"}],"date_updated":"2023-02-23T11:13:07Z","year":"2012","_id":"3119","pubrep_id":"600","publist_id":"3580","quality_controlled":"1","related_material":{"link":[{"url":"http://dl.acm.org/citation.cfm?id=2422393","relation":"table_of_contents"}]},"has_accepted_license":"1","publication":"Proceedings of the ACM SIGGRAPH/Eurographics Symposium on Computer Animation","page":"255 - 264","date_created":"2018-12-11T12:01:30Z","type":"conference","department":[{"_id":"ChWo"}],"language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"ACM","title":"Controlling liquids using meshes","acknowledgement":"This work was partially funded by NSF grants CCF-0811485 and IIS-1130934. We would like to thank Scanline VFX for additional funding. We would like to thank Jie Tan as well as our anonymous reviewers for their useful suggestions and feedback.","day":"29","author":[{"full_name":"Raveendran, Karthik","last_name":"Raveendran","first_name":"Karthik"},{"last_name":"Thuerey","first_name":"Nils","full_name":"Thuerey, Nils"},{"full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Turk, Greg","last_name":"Turk","first_name":"Greg"}],"file":[{"relation":"main_file","content_type":"application/pdf","file_size":4939370,"file_name":"IST-2016-600-v1+1_ControllingLiquids_Preprint.pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2018-12-12T10:11:23Z","creator":"system","checksum":"babda64c24cf90a4d05ae86d712bed08","file_id":"4877","access_level":"open_access"}]},{"volume":148,"quality_controlled":"1","publist_id":"3579","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"page":"1171 - 1194","date_created":"2018-12-11T12:01:30Z","publication":"Compositio Mathematica","publisher":"Cambridge University Press","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Fano 3 folds in codimension 4 Tom and Jerry Part I","author":[{"last_name":"Brown","first_name":"Gavin","full_name":"Brown, Gavin"},{"full_name":"Kerber, Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","last_name":"Kerber","first_name":"Michael","orcid":"0000-0002-8030-9299"},{"last_name":"Reid","first_name":"Miles","full_name":"Reid, Miles"}],"acknowledgement":"This research is supported by the Korean Government WCU Grant R33-2008-000-10101-0.","day":"01","citation":{"short":"G. Brown, M. Kerber, M. Reid, Compositio Mathematica 148 (2012) 1171–1194.","ieee":"G. Brown, M. Kerber, and M. Reid, “Fano 3 folds in codimension 4 Tom and Jerry Part I,” Compositio Mathematica, vol. 148, no. 4. Cambridge University Press, pp. 1171–1194, 2012.","ama":"Brown G, Kerber M, Reid M. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 2012;148(4):1171-1194. doi:10.1112/S0010437X11007226","apa":"Brown, G., Kerber, M., & Reid, M. (2012). Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. Cambridge University Press. https://doi.org/10.1112/S0010437X11007226","ista":"Brown G, Kerber M, Reid M. 2012. Fano 3 folds in codimension 4 Tom and Jerry Part I. Compositio Mathematica. 148(4), 1171–1194.","mla":"Brown, Gavin, et al. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica, vol. 148, no. 4, Cambridge University Press, 2012, pp. 1171–94, doi:10.1112/S0010437X11007226.","chicago":"Brown, Gavin, Michael Kerber, and Miles Reid. “Fano 3 Folds in Codimension 4 Tom and Jerry Part I.” Compositio Mathematica. Cambridge University Press, 2012. https://doi.org/10.1112/S0010437X11007226."},"intvolume":" 148","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1009.4313","open_access":"1"}],"oa_version":"Preprint","date_published":"2012-07-01T00:00:00Z","publication_status":"published","doi":"10.1112/S0010437X11007226","month":"07","status":"public","oa":1,"_id":"3120","date_updated":"2021-01-12T07:41:12Z","issue":"4","abstract":[{"text":"We introduce a strategy based on Kustin-Miller unprojection that allows us to construct many hundreds of Gorenstein codimension 4 ideals with 9 × 16 resolutions (that is, nine equations and sixteen first syzygies). Our two basic games are called Tom and Jerry; the main application is the biregular construction of most of the anticanonically polarised Mori Fano 3-folds of Altinok's thesis. There are 115 cases whose numerical data (in effect, the Hilbert series) allow a Type I projection. In every case, at least one Tom and one Jerry construction works, providing at least two deformation families of quasismooth Fano 3-folds having the same numerics but different topology. © 2012 Copyright Foundation Compositio Mathematica.","lang":"eng"}],"year":"2012"},{"citation":{"chicago":"Williams, Courtney, Wenyan Chen, Chia Lee, Daniel Yaeger, Nicholas Vyleta, and Stephen Smith. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3162.","apa":"Williams, C., Chen, W., Lee, C., Yaeger, D., Vyleta, N., & Smith, S. (2012). Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3162","mla":"Williams, Courtney, et al. “Coactivation of Multiple Tightly Coupled Calcium Channels Triggers Spontaneous Release of GABA.” Nature Neuroscience, vol. 15, no. 9, Nature Publishing Group, 2012, pp. 1195–97, doi:10.1038/nn.3162.","ista":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. 2012. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 15(9), 1195–1197.","ama":"Williams C, Chen W, Lee C, Yaeger D, Vyleta N, Smith S. Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA. Nature Neuroscience. 2012;15(9):1195-1197. doi:10.1038/nn.3162","ieee":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, and S. Smith, “Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA,” Nature Neuroscience, vol. 15, no. 9. Nature Publishing Group, pp. 1195–1197, 2012.","short":"C. Williams, W. Chen, C. Lee, D. Yaeger, N. Vyleta, S. Smith, Nature Neuroscience 15 (2012) 1195–1197."},"intvolume":" 15","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431448/"}],"scopus_import":1,"oa_version":"Submitted Version","date_published":"2012-09-01T00:00:00Z","publication_status":"published","doi":"10.1038/nn.3162","month":"09","status":"public","oa":1,"_id":"3121","date_updated":"2021-01-12T07:41:12Z","abstract":[{"lang":"eng","text":"Voltage-activated Ca(2+) channels (VACCs) mediate Ca(2+) influx to trigger action potential-evoked neurotransmitter release, but the mechanism by which Ca(2+) regulates spontaneous transmission is unclear. We found that VACCs are the major physiological triggers for spontaneous release at mouse neocortical inhibitory synapses. Moreover, despite the absence of a synchronizing action potential, we found that spontaneous fusion of a GABA-containing vesicle required the activation of multiple tightly coupled VACCs of variable type."}],"issue":"9","year":"2012","external_id":{"pmid":["22842148"]},"quality_controlled":"1","volume":15,"publist_id":"3578","type":"journal_article","language":[{"iso":"eng"}],"department":[{"_id":"PeJo"}],"date_created":"2018-12-11T12:01:30Z","page":"1195 - 1197","publication":"Nature Neuroscience","publisher":"Nature Publishing Group","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Coactivation of multiple tightly coupled calcium channels triggers spontaneous release of GABA","author":[{"full_name":"Williams, Courtney","first_name":"Courtney","last_name":"Williams"},{"full_name":"Chen, Wenyan","first_name":"Wenyan","last_name":"Chen"},{"full_name":"Lee, Chia","last_name":"Lee","first_name":"Chia"},{"full_name":"Yaeger, Daniel","first_name":"Daniel","last_name":"Yaeger"},{"id":"36C4978E-F248-11E8-B48F-1D18A9856A87","last_name":"Vyleta","first_name":"Nicholas","full_name":"Vyleta, Nicholas"},{"full_name":"Smith, Stephen","first_name":"Stephen","last_name":"Smith"}],"acknowledgement":"The work was supported by the US National Institutes of Health (DA027110 and GM097433) and OCTRI. C.W. and N.P.V. were supported by a grant from the National Heart, Lung, and Blood Institute (T32HL033808).\r\nWe thank M. Andresen and K. Khodakhah for helpful comments. ","pmid":1,"day":"01"},{"_id":"3122","author":[{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","last_name":"Field","first_name":"David","orcid":"0000-0002-4014-8478","full_name":"Field, David"},{"full_name":"Barrett, Spencer","first_name":"Spencer","last_name":"Barrett"}],"day":"01","year":"2012","date_updated":"2021-01-12T07:41:13Z","issue":"15","abstract":[{"text":"Since Darwin's pioneering research on plant reproductive biology (e.g. Darwin 1877), understanding the mechanisms maintaining the diverse sexual strategies of plants has remained an important challenge for evolutionary biologists. In some species, populations are sexually polymorphic and contain two or more mating morphs (sex phenotypes). Differences in morphology or phenology among the morphs influence patterns of non-random mating. In these populations, negative frequency-dependent selection arising from disassortative (intermorph) mating is usually required for the evolutionary maintenance of sexual polymorphism, but few studies have demonstrated the required patterns of non-random mating. In the current issue of Molecular Ecology, Shang (2012) make an important contribution to our understanding of how disassortative mating influences sex phenotype ratios in Acer pictum subsp. mono (painted maple), a heterodichogamous, deciduous tree of eastern China. They monitored sex expression in 97 adults and used paternity analysis of open-pollinated seed to examine disassortative mating among three sex phenotypes. Using a deterministic 'pollen transfer' model, Shang et al. present convincing evidence that differences in the degree of disassortative mating in progeny arrays of the sex phenotypes can explain their uneven frequencies in the adult population. This study provides a useful example of how the deployment of genetic markers, demographic monitoring and modelling can be integrated to investigate the maintenance of sexual diversity in plants. ","lang":"eng"}],"month":"08","title":"Disassortative mating and the maintenance of sexual polymorphism in painted maple","publisher":"Wiley-Blackwell","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_published":"2012-08-01T00:00:00Z","type":"journal_article","oa_version":"None","date_created":"2018-12-11T12:01:31Z","page":"3640 - 3643","publication":"Molecular Ecology","publication_status":"published","doi":"10.1111/j.1365-294X.2012.05643.x","intvolume":" 21","quality_controlled":"1","volume":21,"citation":{"chicago":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology. Wiley-Blackwell, 2012. https://doi.org/10.1111/j.1365-294X.2012.05643.x.","ista":"Field D, Barrett S. 2012. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 21(15), 3640–3643.","mla":"Field, David, and Spencer Barrett. “Disassortative Mating and the Maintenance of Sexual Polymorphism in Painted Maple.” Molecular Ecology, vol. 21, no. 15, Wiley-Blackwell, 2012, pp. 3640–43, doi:10.1111/j.1365-294X.2012.05643.x.","apa":"Field, D., & Barrett, S. (2012). Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. Wiley-Blackwell. https://doi.org/10.1111/j.1365-294X.2012.05643.x","short":"D. Field, S. Barrett, Molecular Ecology 21 (2012) 3640–3643.","ieee":"D. Field and S. Barrett, “Disassortative mating and the maintenance of sexual polymorphism in painted maple,” Molecular Ecology, vol. 21, no. 15. Wiley-Blackwell, pp. 3640–3643, 2012.","ama":"Field D, Barrett S. Disassortative mating and the maintenance of sexual polymorphism in painted maple. Molecular Ecology. 2012;21(15):3640-3643. doi:10.1111/j.1365-294X.2012.05643.x"},"publist_id":"3577","scopus_import":1},{"publication_identifier":{"eissn":["1467-8659"],"issn":["0167-7055"]},"oa":1,"status":"public","month":"05","year":"2012","date_updated":"2023-10-16T09:54:40Z","issue":"2","abstract":[{"lang":"eng","text":"We introduce the idea of using an explicit triangle mesh to track the air/fluid interface in a smoothed particle hydrodynamics (SPH) simulator. Once an initial surface mesh is created, this mesh is carried forward in time using nearby particle velocities to advect the mesh vertices. The mesh connectivity remains mostly unchanged across time-steps; it is only modified locally for topology change events or for the improvement of triangle quality. In order to ensure that the surface mesh does not diverge from the underlying particle simulation, we periodically project the mesh surface onto an implicit surface defined by the physics simulation. The mesh surface gives us several advantages over previous SPH surface tracking techniques. We demonstrate a new method for surface tension calculations that clearly outperforms the state of the art in SPH surface tension for computer graphics. We also demonstrate a method for tracking detailed surface information (like colors) that is less susceptible to numerical diffusion than competing techniques. Finally, our temporally-coherent surface mesh allows us to simulate high-resolution surface wave dynamics without being limited by the particle resolution of the SPH simulation."}],"_id":"3123","ddc":["000"],"file_date_updated":"2020-07-14T12:46:00Z","scopus_import":"1","intvolume":" 31","citation":{"chicago":"Yu, Jihun, Chris Wojtan, Greg Turk, and Chee Yap. “Explicit Mesh Surfaces for Particle Based Fluids.” In Computer Graphics Forum, 31:815–24. Wiley, 2012. https://doi.org/10.1111/j.1467-8659.2012.03062.x.","ista":"Yu J, Wojtan C, Turk G, Yap C. 2012. Explicit mesh surfaces for particle based fluids. Computer Graphics Forum. EUROGRAPHICS: Conference on European Association for Computer Graphics, Eurographics, vol. 31, 815–824.","apa":"Yu, J., Wojtan, C., Turk, G., & Yap, C. (2012). Explicit mesh surfaces for particle based fluids. In Computer Graphics Forum (Vol. 31, pp. 815–824). Cagliari, Sardinia, Italy: Wiley. https://doi.org/10.1111/j.1467-8659.2012.03062.x","mla":"Yu, Jihun, et al. “Explicit Mesh Surfaces for Particle Based Fluids.” Computer Graphics Forum, vol. 31, no. 2, Wiley, 2012, pp. 815–24, doi:10.1111/j.1467-8659.2012.03062.x.","short":"J. Yu, C. Wojtan, G. Turk, C. Yap, in:, Computer Graphics Forum, Wiley, 2012, pp. 815–824.","ama":"Yu J, Wojtan C, Turk G, Yap C. Explicit mesh surfaces for particle based fluids. In: Computer Graphics Forum. Vol 31. Wiley; 2012:815-824. doi:10.1111/j.1467-8659.2012.03062.x","ieee":"J. Yu, C. Wojtan, G. Turk, and C. Yap, “Explicit mesh surfaces for particle based fluids,” in Computer Graphics Forum, Cagliari, Sardinia, Italy, 2012, vol. 31, no. 2, pp. 815–824."},"conference":{"location":"Cagliari, Sardinia, Italy","end_date":"2012-05-18","name":"EUROGRAPHICS: Conference on European Association for Computer Graphics","start_date":"2012-05-13"},"publication_status":"published","doi":"10.1111/j.1467-8659.2012.03062.x","date_published":"2012-05-01T00:00:00Z","oa_version":"Submitted Version","title":"Explicit mesh surfaces for particle based fluids","publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Eurographics"],"day":"01","acknowledgement":"This work was funded by NSF grant IIS-1017014 and CCF- 0917093.","file":[{"file_size":5740527,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"system","checksum":"acb325dd1e31859bedd30e013f61d0b9","file_id":"5092","date_created":"2018-12-12T10:14:39Z","file_name":"IST-2016-601-v1+1_meshSPH.pdf","date_updated":"2020-07-14T12:46:00Z"}],"author":[{"full_name":"Yu, Jihun","first_name":"Jihun","last_name":"Yu"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"},{"first_name":"Chee","last_name":"Yap","full_name":"Yap, Chee"}],"publist_id":"3576","article_processing_charge":"No","pubrep_id":"601","volume":31,"quality_controlled":"1","page":"815 - 824","date_created":"2018-12-11T12:01:31Z","publication":"Computer Graphics Forum","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"ChWo"}],"type":"conference"},{"citation":{"ieee":"F. Korc, V. Kolmogorov, and C. Lampert, “Approximating marginals using discrete energy minimization,” presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland, 2012.","ama":"Korc F, Kolmogorov V, Lampert C. Approximating marginals using discrete energy minimization. In: ICML; 2012.","short":"F. Korc, V. Kolmogorov, C. Lampert, in:, ICML, 2012.","mla":"Korc, Filip, et al. Approximating Marginals Using Discrete Energy Minimization. ICML, 2012.","apa":"Korc, F., Kolmogorov, V., & Lampert, C. (2012). Approximating marginals using discrete energy minimization. Presented at the ICML: International Conference on Machine Learning, Edinburgh, Scotland: ICML.","ista":"Korc F, Kolmogorov V, Lampert C. 2012. Approximating marginals using discrete energy minimization. ICML: International Conference on Machine Learning, Inferning 2012, .","chicago":"Korc, Filip, Vladimir Kolmogorov, and Christoph Lampert. “Approximating Marginals Using Discrete Energy Minimization.” ICML, 2012."},"quality_controlled":"1","related_material":{"record":[{"relation":"later_version","status":"public","id":"5396"}]},"file_date_updated":"2020-07-14T12:46:00Z","publist_id":"3575","pubrep_id":"565","ddc":["000"],"oa_version":"Submitted Version","type":"conference","language":[{"iso":"eng"}],"department":[{"_id":"ChLa"},{"_id":"VlKo"}],"date_published":"2012-06-30T00:00:00Z","has_accepted_license":"1","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2012-06-26","location":"Edinburgh, Scotland","end_date":"2012-07-01"},"publication_status":"published","date_created":"2018-12-11T12:01:31Z","month":"06","alternative_title":["Inferning 2012"],"publisher":"ICML","status":"public","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Approximating marginals using discrete energy minimization","oa":1,"author":[{"full_name":"Korc, Filip","id":"476A2FD6-F248-11E8-B48F-1D18A9856A87","last_name":"Korc","first_name":"Filip"},{"full_name":"Kolmogorov, Vladimir","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"}],"file":[{"date_created":"2018-12-12T10:11:34Z","file_name":"IST-2016-565-v1+1_DM-inferning2012.pdf","date_updated":"2020-07-14T12:46:00Z","access_level":"open_access","file_id":"4889","creator":"system","checksum":"3d0d4246548c736857302aadb2ff5d15","file_size":305836,"content_type":"application/pdf","relation":"main_file"}],"_id":"3124","date_updated":"2023-02-23T12:24:24Z","abstract":[{"lang":"eng","text":"We consider the problem of inference in a graphical model with binary variables. While in theory it is arguably preferable to compute marginal probabilities, in practice researchers often use MAP inference due to the availability of efficient discrete optimization algorithms. We bridge the gap between the two approaches by introducing the Discrete Marginals technique in which approximate marginals are obtained by minimizing an objective function with unary and pairwise terms over a discretized domain. This allows the use of techniques originally developed for MAP-MRF inference and learning. We explore two ways to set up the objective function - by discretizing the Bethe free energy and by learning it from training data. Experimental results show that for certain types of graphs a learned function can outperform the Bethe approximation. We also establish a link between the Bethe free energy and submodular functions.\r\n"}],"day":"30","year":"2012"},{"_id":"3125","year":"2012","issue":"PART 5","abstract":[{"lang":"eng","text":"We propose a new learning method to infer a mid-level feature representation that combines the advantage of semantic attribute representations with the higher expressive power of non-semantic features. The idea lies in augmenting an existing attribute-based representation with additional dimensions for which an autoencoder model is coupled with a large-margin principle. This construction allows a smooth transition between the zero-shot regime with no training example, the unsupervised regime with training examples but without class labels, and the supervised regime with training examples and with class labels. The resulting optimization problem can be solved efficiently, because several of the necessity steps have closed-form solutions. Through extensive experiments we show that the augmented representation achieves better results in terms of object categorization accuracy than the semantic representation alone."}],"date_updated":"2023-02-23T11:13:25Z","month":"10","oa":1,"status":"public","date_published":"2012-10-01T00:00:00Z","oa_version":"Submitted Version","doi":"10.1007/978-3-642-33715-4_18","conference":{"end_date":"2012-10-13","location":"Florence, Italy","start_date":"2012-10-07","name":"ECCV: European Conference on Computer Vision"},"publication_status":"published","intvolume":" 7576","citation":{"apa":"Sharmanska, V., Quadrianto, N., & Lampert, C. (2012). Augmented attribute representations (Vol. 7576, pp. 242–255). Presented at the ECCV: European Conference on Computer Vision, Florence, Italy: Springer. https://doi.org/10.1007/978-3-642-33715-4_18","mla":"Sharmanska, Viktoriia, et al. Augmented Attribute Representations. Vol. 7576, no. PART 5, Springer, 2012, pp. 242–55, doi:10.1007/978-3-642-33715-4_18.","ista":"Sharmanska V, Quadrianto N, Lampert C. 2012. Augmented attribute representations. ECCV: European Conference on Computer Vision, LNCS, vol. 7576, 242–255.","chicago":"Sharmanska, Viktoriia, Novi Quadrianto, and Christoph Lampert. “Augmented Attribute Representations,” 7576:242–55. Springer, 2012. https://doi.org/10.1007/978-3-642-33715-4_18.","short":"V. Sharmanska, N. Quadrianto, C. Lampert, in:, Springer, 2012, pp. 242–255.","ama":"Sharmanska V, Quadrianto N, Lampert C. Augmented attribute representations. In: Vol 7576. Springer; 2012:242-255. doi:10.1007/978-3-642-33715-4_18","ieee":"V. Sharmanska, N. Quadrianto, and C. Lampert, “Augmented attribute representations,” presented at the ECCV: European Conference on Computer Vision, Florence, Italy, 2012, vol. 7576, no. PART 5, pp. 242–255."},"ddc":["000"],"file_date_updated":"2020-07-14T12:46:00Z","scopus_import":1,"file":[{"content_type":"application/pdf","relation":"main_file","file_size":6073897,"file_id":"7861","checksum":"bccdbe0663780d25a1e0524002b2d896","creator":"dernst","access_level":"open_access","file_name":"2012_ECCV_Sharmanska.pdf","date_updated":"2020-07-14T12:46:00Z","date_created":"2020-05-15T12:29:04Z"}],"author":[{"full_name":"Sharmanska, Viktoriia","last_name":"Sharmanska","id":"2EA6D09E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0192-9308","first_name":"Viktoriia"},{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"day":"01","alternative_title":["LNCS"],"title":"Augmented attribute representations","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"type":"conference","date_created":"2018-12-11T12:01:32Z","page":"242 - 255","has_accepted_license":"1","quality_controlled":"1","volume":7576,"article_processing_charge":"No","publist_id":"3574"},{"author":[{"full_name":"Müller, Andreas","first_name":"Andreas","last_name":"Müller"},{"first_name":"Sebastian","last_name":"Nowozin","full_name":"Nowozin, Sebastian"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"}],"_id":"3126","abstract":[{"text":"In this work we propose a new information-theoretic clustering algorithm that infers cluster memberships by direct optimization of a non-parametric mutual information estimate between data distribution and cluster assignment. Although the optimization objective has a solid theoretical foundation it is hard to optimize. We propose an approximate optimization formulation that leads to an efficient algorithm with low runtime complexity. The algorithm has a single free parameter, the number of clusters to find. We demonstrate superior performance on several synthetic and real datasets.\r\n","lang":"eng"}],"date_updated":"2021-01-12T07:41:14Z","year":"2012","day":"14","alternative_title":["LNCS"],"month":"08","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Springer","title":"Information theoretic clustering using minimal spanning trees","oa_version":"None","type":"conference","date_published":"2012-08-14T00:00:00Z","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"doi":"10.1007/978-3-642-32717-9_21","conference":{"start_date":"2012-08-28","name":"DAGM: German Association For Pattern Recognition","end_date":"2012-08-31","location":"Graz, Austria"},"publication_status":"published","date_created":"2018-12-11T12:01:32Z","page":"205 - 215","quality_controlled":"1","intvolume":" 7476","citation":{"mla":"Müller, Andreas, et al. Information Theoretic Clustering Using Minimal Spanning Trees. Vol. 7476, Springer, 2012, pp. 205–15, doi:10.1007/978-3-642-32717-9_21.","apa":"Müller, A., Nowozin, S., & Lampert, C. (2012). Information theoretic clustering using minimal spanning trees (Vol. 7476, pp. 205–215). Presented at the DAGM: German Association For Pattern Recognition, Graz, Austria: Springer. https://doi.org/10.1007/978-3-642-32717-9_21","ista":"Müller A, Nowozin S, Lampert C. 2012. Information theoretic clustering using minimal spanning trees. DAGM: German Association For Pattern Recognition, LNCS, vol. 7476, 205–215.","chicago":"Müller, Andreas, Sebastian Nowozin, and Christoph Lampert. “Information Theoretic Clustering Using Minimal Spanning Trees,” 7476:205–15. Springer, 2012. https://doi.org/10.1007/978-3-642-32717-9_21.","short":"A. Müller, S. Nowozin, C. Lampert, in:, Springer, 2012, pp. 205–215.","ieee":"A. Müller, S. Nowozin, and C. Lampert, “Information theoretic clustering using minimal spanning trees,” presented at the DAGM: German Association For Pattern Recognition, Graz, Austria, 2012, vol. 7476, pp. 205–215.","ama":"Müller A, Nowozin S, Lampert C. Information theoretic clustering using minimal spanning trees. In: Vol 7476. Springer; 2012:205-215. doi:10.1007/978-3-642-32717-9_21"},"volume":7476,"scopus_import":1,"publist_id":"3573"},{"oa":1,"title":"The most persistent soft-clique in a set of sampled graphs","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"ML Research Press","month":"06","year":"2012","day":"01","abstract":[{"text":"When searching for characteristic subpatterns in potentially noisy graph data, it appears self-evident that having multiple observations would be better than having just one. However, it turns out that the inconsistencies introduced when different graph instances have different edge sets pose a serious challenge. In this work we address this challenge for the problem of finding maximum weighted cliques.\r\n We introduce the concept of most persistent soft-clique. This is subset of vertices, that 1) is almost fully or at least densely connected, 2) occurs in all or almost all graph instances, and 3) has the maximum weight. We present a measure of clique-ness, that essentially counts the number of edge missing to make a subset of vertices into a clique. With this measure, we show that the problem of finding the most persistent soft-clique problem can be cast either as: a) a max-min two person game optimization problem, or b) a min-min soft margin optimization problem. Both formulations lead to the same solution when using a partial Lagrangian method to solve the optimization problems. By experiments on synthetic data and on real social network data, we show that the proposed method is able to reliably find soft cliques in graph data, even if that is distorted by random noise or unreliable observations.","lang":"eng"}],"date_updated":"2023-10-17T11:55:06Z","_id":"3127","author":[{"full_name":"Quadrianto, Novi","first_name":"Novi","last_name":"Quadrianto"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert"},{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"}],"article_processing_charge":"No","publist_id":"3572","main_file_link":[{"url":"http://arxiv.org/abs/1206.4652","open_access":"1"}],"scopus_import":"1","citation":{"short":"N. Quadrianto, C. Lampert, C. Chen, in:, Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–218.","ieee":"N. Quadrianto, C. Lampert, and C. Chen, “The most persistent soft-clique in a set of sampled graphs,” in Proceedings of the 29th International Conference on Machine Learning, Edinburgh, United Kingdom, 2012, pp. 211–218.","ama":"Quadrianto N, Lampert C, Chen C. The most persistent soft-clique in a set of sampled graphs. In: Proceedings of the 29th International Conference on Machine Learning. ML Research Press; 2012:211-218.","chicago":"Quadrianto, Novi, Christoph Lampert, and Chao Chen. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” In Proceedings of the 29th International Conference on Machine Learning, 211–18. ML Research Press, 2012.","mla":"Quadrianto, Novi, et al. “The Most Persistent Soft-Clique in a Set of Sampled Graphs.” Proceedings of the 29th International Conference on Machine Learning, ML Research Press, 2012, pp. 211–18.","apa":"Quadrianto, N., Lampert, C., & Chen, C. (2012). The most persistent soft-clique in a set of sampled graphs. In Proceedings of the 29th International Conference on Machine Learning (pp. 211–218). Edinburgh, United Kingdom: ML Research Press.","ista":"Quadrianto N, Lampert C, Chen C. 2012. The most persistent soft-clique in a set of sampled graphs. Proceedings of the 29th International Conference on Machine Learning. ICML: International Conference on Machine Learning, 211–218."},"quality_controlled":"1","publication":"Proceedings of the 29th International Conference on Machine Learning","page":"211-218","date_created":"2018-12-11T12:01:33Z","publication_status":"published","conference":{"location":"Edinburgh, United Kingdom","end_date":"2012-07-01","name":"ICML: International Conference on Machine Learning","start_date":"2012-06-26"},"department":[{"_id":"ChLa"},{"_id":"HeEd"}],"date_published":"2012-06-01T00:00:00Z","language":[{"iso":"eng"}],"oa_version":"Preprint","type":"conference"},{"_id":"3128","abstract":[{"text":"We consider two-player zero-sum stochastic games on graphs with ω-regular winning conditions specified as parity objectives. These games have applications in the design and control of reactive systems. We survey the complexity results for the problem of deciding the winner in such games, and in classes of interest obtained as special cases, based on the information and the power of randomization available to the players, on the class of objectives and on the winning mode. On the basis of information, these games can be classified as follows: (a) partial-observation (both players have partial view of the game); (b) one-sided partial-observation (one player has partial-observation and the other player has complete-observation); and (c) complete-observation (both players have complete view of the game). The one-sided partial-observation games have two important subclasses: the one-player games, known as partial-observation Markov decision processes (POMDPs), and the blind one-player games, known as probabilistic automata. On the basis of randomization, (a) the players may not be allowed to use randomization (pure strategies), or (b) they may choose a probability distribution over actions but the actual random choice is external and not visible to the player (actions invisible), or (c) they may use full randomization. Finally, various classes of games are obtained by restricting the parity objective to a reachability, safety, Büchi, or coBüchi condition. We also consider several winning modes, such as sure-winning (i.e., all outcomes of a strategy have to satisfy the winning condition), almost-sure winning (i.e., winning with probability 1), limit-sure winning (i.e., winning with probability arbitrarily close to 1), and value-threshold winning (i.e., winning with probability at least ν, where ν is a given rational). ","lang":"eng"}],"issue":"2","date_updated":"2021-01-12T07:41:15Z","year":"2012","month":"10","ec_funded":1,"status":"public","oa":1,"oa_version":"Submitted Version","date_published":"2012-10-01T00:00:00Z","doi":"10.1007/s10703-012-0164-2","publication_status":"published","citation":{"short":"K. Chatterjee, L. Doyen, T.A. Henzinger, Formal Methods in System Design 43 (2012) 268–284.","ama":"Chatterjee K, Doyen L, Henzinger TA. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 2012;43(2):268-284. doi:10.1007/s10703-012-0164-2","ieee":"K. Chatterjee, L. Doyen, and T. A. Henzinger, “A survey of partial-observation stochastic parity games,” Formal Methods in System Design, vol. 43, no. 2. Springer, pp. 268–284, 2012.","chicago":"Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design. Springer, 2012. https://doi.org/10.1007/s10703-012-0164-2.","ista":"Chatterjee K, Doyen L, Henzinger TA. 2012. A survey of partial-observation stochastic parity games. Formal Methods in System Design. 43(2), 268–284.","mla":"Chatterjee, Krishnendu, et al. “A Survey of Partial-Observation Stochastic Parity Games.” Formal Methods in System Design, vol. 43, no. 2, Springer, 2012, pp. 268–84, doi:10.1007/s10703-012-0164-2.","apa":"Chatterjee, K., Doyen, L., & Henzinger, T. A. (2012). A survey of partial-observation stochastic parity games. Formal Methods in System Design. Springer. https://doi.org/10.1007/s10703-012-0164-2"},"intvolume":" 43","scopus_import":1,"file_date_updated":"2020-07-14T12:46:00Z","ddc":["005"],"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","last_name":"Doyen","first_name":"Laurent"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","first_name":"Thomas A"}],"project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"file":[{"date_created":"2018-12-12T10:11:27Z","date_updated":"2020-07-14T12:46:00Z","file_name":"IST-2014-303-v1+1_Survey_Partial-Observation_Stochastic_Parity_Games.pdf","access_level":"open_access","checksum":"dd3d590f383bb2ac6cfda1489ac1c42a","creator":"system","file_id":"4882","file_size":163983,"content_type":"application/pdf","relation":"main_file"}],"acknowledgement":"The research was supported by Austrian Science Fund (FWF) Grant No. P 23499-N23 on Modern Graph Algorithmic Techniques in Formal Verification, FWF NFN Grant No. S11407-N23(RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, ERC Advanced grant QUAREM, and FWF Grant No. S11403-N23 (RiSE).","day":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","title":"A survey of partial-observation stochastic parity games","type":"journal_article","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","publication":"Formal Methods in System Design","date_created":"2018-12-11T12:01:33Z","page":"268 - 284","quality_controlled":"1","volume":43,"pubrep_id":"303","publist_id":"3570"},{"page":"189 - 200","date_created":"2018-12-11T12:01:33Z","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"type":"conference","publist_id":"3569","external_id":{"arxiv":["1107.3793"]},"volume":7357,"quality_controlled":"1","day":"19","author":[{"full_name":"Busaryev, Oleksiy","first_name":"Oleksiy","last_name":"Busaryev"},{"full_name":"Cabello, Sergio","last_name":"Cabello","first_name":"Sergio"},{"full_name":"Chen, Chao","first_name":"Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dey, Tamal","first_name":"Tamal","last_name":"Dey"},{"last_name":"Wang","first_name":"Yusu","full_name":"Wang, Yusu"}],"title":"Annotating simplices with a homology basis and its applications","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LNCS"],"publication_status":"published","conference":{"location":"Helsinki, Finland","end_date":"2012-07-06","name":"SWAT: Symposium and Workshops on Algorithm Theory","start_date":"2012-07-04"},"doi":"10.1007/978-3-642-31155-0_17","date_published":"2012-06-19T00:00:00Z","oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"http://arxiv.org/abs/1107.3793","open_access":"1"}],"intvolume":" 7357","citation":{"apa":"Busaryev, O., Cabello, S., Chen, C., Dey, T., & Wang, Y. (2012). Annotating simplices with a homology basis and its applications (Vol. 7357, pp. 189–200). Presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland: Springer. https://doi.org/10.1007/978-3-642-31155-0_17","mla":"Busaryev, Oleksiy, et al. Annotating Simplices with a Homology Basis and Its Applications. Vol. 7357, Springer, 2012, pp. 189–200, doi:10.1007/978-3-642-31155-0_17.","ista":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. 2012. Annotating simplices with a homology basis and its applications. SWAT: Symposium and Workshops on Algorithm Theory, LNCS, vol. 7357, 189–200.","chicago":"Busaryev, Oleksiy, Sergio Cabello, Chao Chen, Tamal Dey, and Yusu Wang. “Annotating Simplices with a Homology Basis and Its Applications,” 7357:189–200. Springer, 2012. https://doi.org/10.1007/978-3-642-31155-0_17.","short":"O. Busaryev, S. Cabello, C. Chen, T. Dey, Y. Wang, in:, Springer, 2012, pp. 189–200.","ieee":"O. Busaryev, S. Cabello, C. Chen, T. Dey, and Y. Wang, “Annotating simplices with a homology basis and its applications,” presented at the SWAT: Symposium and Workshops on Algorithm Theory, Helsinki, Finland, 2012, vol. 7357, pp. 189–200.","ama":"Busaryev O, Cabello S, Chen C, Dey T, Wang Y. Annotating simplices with a homology basis and its applications. In: Vol 7357. Springer; 2012:189-200. doi:10.1007/978-3-642-31155-0_17"},"year":"2012","date_updated":"2021-01-12T07:41:15Z","arxiv":1,"abstract":[{"lang":"eng","text":"Let K be a simplicial complex and g the rank of its p-th homology group Hp(K) defined with ℤ2 coefficients. We show that we can compute a basis H of Hp(K) and annotate each p-simplex of K with a binary vector of length g with the following property: the annotations, summed over all p-simplices in any p-cycle z, provide the coordinate vector of the homology class [z] in the basis H. The basis and the annotations for all simplices can be computed in O(n ω ) time, where n is the size of K and ω < 2.376 is a quantity so that two n×n matrices can be multiplied in O(n ω ) time. The precomputed annotations permit answering queries about the independence or the triviality of p-cycles efficiently.\r\n\r\nUsing annotations of edges in 2-complexes, we derive better algorithms for computing optimal basis and optimal homologous cycles in 1 - dimensional homology. Specifically, for computing an optimal basis of H1(K) , we improve the previously known time complexity from O(n 4) to O(n ω + n 2 g ω − 1). Here n denotes the size of the 2-skeleton of K and g the rank of H1(K) . Computing an optimal cycle homologous to a given 1-cycle is NP-hard even for surfaces and an algorithm taking 2 O(g) nlogn time is known for surfaces. We extend this algorithm to work with arbitrary 2-complexes in O(n ω ) + 2 O(g) n 2logn time using annotations.\r\n"}],"_id":"3129","oa":1,"status":"public","month":"06"},{"file":[{"file_size":2674138,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"f8506fb579eda6fc5613ba9bf421b86a","file_id":"4973","creator":"system","date_created":"2018-12-12T10:12:52Z","file_name":"IST-2015-386-v1+1_journal.pgen.1002803.pdf","date_updated":"2020-07-14T12:46:01Z"}],"author":[{"last_name":"Bergmiller","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5396-4346","first_name":"Tobias","full_name":"Bergmiller, Tobias"},{"full_name":"Ackermann, Martin","first_name":"Martin","last_name":"Ackermann"},{"full_name":"Silander, Olin","first_name":"Olin","last_name":"Silander"}],"day":"28","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"We thank Alex Boehm for discussions and comments.","title":"Patterns of evolutionary conservation of essential genes correlate with their compensability","publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"department":[{"_id":"CaGu"}],"type":"journal_article","date_created":"2018-12-11T12:01:34Z","publication":"PLoS Genetics","has_accepted_license":"1","volume":8,"quality_controlled":"1","publist_id":"3567","pubrep_id":"386","_id":"3130","article_number":"e1002803","year":"2012","date_updated":"2021-01-12T07:41:16Z","issue":"6","abstract":[{"text":"Essential genes code for fundamental cellular functions required for the viability of an organism. For this reason, essential genes are often highly conserved across organisms. However, this is not always the case: orthologues of genes that are essential in one organism are sometimes not essential in other organisms or are absent from their genomes. This suggests that, in the course of evolution, essential genes can be rendered nonessential. How can a gene become non-essential? Here we used genetic manipulation to deplete the products of 26 different essential genes in Escherichia coli. This depletion results in a lethal phenotype, which could often be rescued by the overexpression of a non-homologous, non-essential gene, most likely through replacement of the essential function. We also show that, in a smaller number of cases, the essential genes can be fully deleted from the genome, suggesting that complete functional replacement is possible. Finally, we show that essential genes whose function can be replaced in the laboratory are more likely to be non-essential or not present in other taxa. These results are consistent with the notion that patterns of evolutionary conservation of essential genes are influenced by their compensability-that is, by how easily they can be functionally replaced, for example through increased expression of other genes.","lang":"eng"}],"month":"06","oa":1,"status":"public","date_published":"2012-06-28T00:00:00Z","oa_version":"Published Version","publication_status":"published","doi":"10.1371/journal.pgen.1002803","citation":{"short":"T. Bergmiller, M. Ackermann, O. Silander, PLoS Genetics 8 (2012).","ama":"Bergmiller T, Ackermann M, Silander O. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002803","ieee":"T. Bergmiller, M. Ackermann, and O. Silander, “Patterns of evolutionary conservation of essential genes correlate with their compensability,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","ista":"Bergmiller T, Ackermann M, Silander O. 2012. Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. 8(6), e1002803.","apa":"Bergmiller, T., Ackermann, M., & Silander, O. (2012). Patterns of evolutionary conservation of essential genes correlate with their compensability. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002803","mla":"Bergmiller, Tobias, et al. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics, vol. 8, no. 6, e1002803, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002803.","chicago":"Bergmiller, Tobias, Martin Ackermann, and Olin Silander. “Patterns of Evolutionary Conservation of Essential Genes Correlate with Their Compensability.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002803."},"intvolume":" 8","ddc":["576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:46:01Z"},{"publist_id":"3566","pubrep_id":"114","volume":8,"quality_controlled":"1","date_created":"2018-12-11T12:01:34Z","publication":"PLoS Genetics","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"type":"journal_article","title":"Limits to the rate of adaptive substitution in sexual populations","publisher":"Public Library of Science","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","day":"07","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"The work was funded by ERC grant 250152.\r\nWe thank B. Charlesworth, O. Hallatschek, W. G. Hill, R. A. Neher, S. P. Otto, and the anonymous reviewers for their helpful suggestions.","file":[{"relation":"main_file","content_type":"application/pdf","file_size":1284801,"file_name":"IST-2013-114-v1+1_WeissmanBarton2012.pdf","date_updated":"2020-07-14T12:46:01Z","date_created":"2018-12-12T10:08:00Z","creator":"system","checksum":"729a4becda7d786c4c3db8f9a1f77953","file_id":"4659","access_level":"open_access"}],"project":[{"grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation"}],"author":[{"full_name":"Weissman, Daniel","id":"2D0CE020-F248-11E8-B48F-1D18A9856A87","last_name":"Weissman","first_name":"Daniel"},{"last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H"}],"ddc":["570","576"],"scopus_import":1,"file_date_updated":"2020-07-14T12:46:01Z","intvolume":" 8","citation":{"short":"D. Weissman, N.H. Barton, PLoS Genetics 8 (2012).","ieee":"D. Weissman and N. H. Barton, “Limits to the rate of adaptive substitution in sexual populations,” PLoS Genetics, vol. 8, no. 6. Public Library of Science, 2012.","ama":"Weissman D, Barton NH. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 2012;8(6). doi:10.1371/journal.pgen.1002740","ista":"Weissman D, Barton NH. 2012. Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. 8(6), e1002740.","apa":"Weissman, D., & Barton, N. H. (2012). Limits to the rate of adaptive substitution in sexual populations. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1002740","mla":"Weissman, Daniel, and Nicholas H. Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics, vol. 8, no. 6, e1002740, Public Library of Science, 2012, doi:10.1371/journal.pgen.1002740.","chicago":"Weissman, Daniel, and Nicholas H Barton. “Limits to the Rate of Adaptive Substitution in Sexual Populations.” PLoS Genetics. Public Library of Science, 2012. https://doi.org/10.1371/journal.pgen.1002740."},"publication_status":"published","doi":"10.1371/journal.pgen.1002740","date_published":"2012-06-07T00:00:00Z","oa_version":"Published Version","oa":1,"status":"public","ec_funded":1,"month":"06","year":"2012","date_updated":"2021-01-12T07:41:17Z","issue":"6","abstract":[{"lang":"eng","text":"In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, Λ, that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is Λ 0=2NU〈s〉 is the population size, U is the rate of beneficial mutations per genome, and 〈s〉 is their mean selective advantage. Heritable variance ν in log fitness due to unlinked loci reduces Λ by e -4ν under polygamy and e -8ν under monogamy. With a linear genetic map of length R Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on s, N, U, and R only through the baseline density: Λ/R=F(Λ 0/R). Under the approximation that the interference due to different sweeps adds up, we show that Λ/R~(Λ 0/R)/(1+2Λ 0/R), implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for Λ 0/R 1; for higher Λ 0/R, the rate of adaptation grows above R/2, but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection."}],"_id":"3131","article_number":"e1002740"},{"_id":"3132","author":[{"full_name":"Konrad, Matthias","first_name":"Matthias","last_name":"Konrad","id":"46528076-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pamminger","first_name":"Tobias","full_name":"Pamminger, Tobias"},{"full_name":"Foitzik, Susanne","first_name":"Susanne","last_name":"Foitzik"}],"year":"2012","day":"01","acknowledgement":"We like to thank the editor and three anonymous reviewers for their time and constructive criticism and Inon Scharf, Volker Witte and Andreas Modlmeier for helpful comments on earlier versions of the manuscript. The first and second authors appear in alphabetical order and contributed equally to this paper.","issue":"8","abstract":[{"lang":"eng","text":"Reproductive division of labour is a characteristic trait of social insects. The dominant reproductive individual, often the queen, uses chemical communication and/or behaviour to maintain her social status. Queens of many social insects communicate their fertility status via cuticle-bound substances. As these substances usually possess a low volatility, their range in queen–worker communication is potentially limited. Here, we investigate the range and impact of behavioural and chemical queen signals on workers of the ant Temnothorax longispinosus. We compared the behaviour and ovary development of workers subjected to three different treatments: workers with direct chemical and physical contact to the queen, those solely under the influence of volatile queen substances and those entirely separated from the queen. In addition to short-ranged queen signals preventing ovary development in workers, we discovered a novel secondary pathway influencing worker behaviour. Workers with no physical contact to the queen, but exposed to volatile substances, started to develop their ovaries, but did not change their behaviour compared to workers in direct contact to the queen. In contrast, workers in queen-separated groups showed both increased ovary development and aggressive dominance interactions. We conclude that T. longispinosus queens influence worker ovary development and behaviour via two independent signals, both ensuring social harmony within the colony."}],"date_updated":"2021-01-12T07:41:17Z","month":"08","title":"Two pathways ensuring social harmony","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","publisher":"Springer","date_published":"2012-08-01T00:00:00Z","department":[{"_id":"SyCr"}],"language":[{"iso":"eng"}],"oa_version":"None","type":"journal_article","publication":"Naturwissenschaften","page":"627 - 636","date_created":"2018-12-11T12:01:34Z","doi":"10.1007/s00114-012-0943-z","publication_status":"published","volume":99,"quality_controlled":"1","intvolume":" 99","citation":{"short":"M. Konrad, T. Pamminger, S. Foitzik, Naturwissenschaften 99 (2012) 627–636.","ama":"Konrad M, Pamminger T, Foitzik S. Two pathways ensuring social harmony. Naturwissenschaften. 2012;99(8):627-636. doi:10.1007/s00114-012-0943-z","ieee":"M. Konrad, T. Pamminger, and S. Foitzik, “Two pathways ensuring social harmony,” Naturwissenschaften, vol. 99, no. 8. Springer, pp. 627–636, 2012.","chicago":"Konrad, Matthias, Tobias Pamminger, and Susanne Foitzik. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften. Springer, 2012. https://doi.org/10.1007/s00114-012-0943-z.","ista":"Konrad M, Pamminger T, Foitzik S. 2012. Two pathways ensuring social harmony. Naturwissenschaften. 99(8), 627–636.","mla":"Konrad, Matthias, et al. “Two Pathways Ensuring Social Harmony.” Naturwissenschaften, vol. 99, no. 8, Springer, 2012, pp. 627–36, doi:10.1007/s00114-012-0943-z.","apa":"Konrad, M., Pamminger, T., & Foitzik, S. (2012). Two pathways ensuring social harmony. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-012-0943-z"},"publist_id":"3565","scopus_import":1}]