[{"doi":"10.1007/978-3-319-96145-3_25","abstract":[{"lang":"eng","text":"Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools."}],"_id":"140","title":"Space-time interpolants","author":[{"full_name":"Frehse, Goran","last_name":"Frehse","first_name":"Goran"},{"orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco","full_name":"Giacobbe, Mirco","last_name":"Giacobbe"},{"orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A"}],"status":"public","publication_status":"published","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"issn":["03029743"]},"oa_version":"Published Version","conference":{"end_date":"2018-07-17","start_date":"2018-07-14","location":"Oxford, United Kingdom","name":"CAV: Computer Aided Verification"},"ddc":["005"],"month":"07","file_date_updated":"2020-07-14T12:44:50Z","citation":{"short":"G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486.","ama":"Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>","ista":"Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.","apa":"Frehse, G., Giacobbe, M., &#38; Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>","ieee":"G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.","mla":"Frehse, Goran, et al. <i>Space-Time Interpolants</i>. Vol. 10981, Springer, 2018, pp. 468–86, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">10.1007/978-3-319-96145-3_25</a>.","chicago":"Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_25\">https://doi.org/10.1007/978-3-319-96145-3_25</a>."},"pubrep_id":"1010","day":"18","article_processing_charge":"No","volume":10981,"has_accepted_license":"1","file":[{"date_updated":"2020-07-14T12:44:50Z","access_level":"open_access","content_type":"application/pdf","checksum":"6dca832f575d6b3f0ea9dff56f579142","file_name":"IST-2018-1010-v1+1_space-time_interpolants.pdf","relation":"main_file","creator":"system","file_size":563710,"file_id":"5310","date_created":"2018-12-12T10:17:53Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"alternative_title":["LNCS"],"year":"2018","oa":1,"page":"468 - 486","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6894"}]},"date_updated":"2023-09-19T09:30:43Z","date_created":"2018-12-11T11:44:50Z","scopus_import":"1","date_published":"2018-07-18T00:00:00Z","external_id":{"isi":["000491481600025"]},"publist_id":"7783","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"ToHe"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"isi":1,"publisher":"Springer","intvolume":"     10981"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-07-01T00:00:00Z","extern":"1","scopus_import":"1","date_created":"2023-08-10T06:34:48Z","intvolume":"         8","main_file_link":[{"url":"https://doi.org/10.1103/PhysRevX.8.031060","open_access":"1"}],"publisher":"American Physical Society","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"oa":1,"year":"2018","keyword":["General Physics and Astronomy"],"publication":"Physical Review X","date_updated":"2023-08-22T07:42:07Z","article_type":"original","article_number":"031060","day":"01","citation":{"mla":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” <i>Physical Review X</i>, vol. 8, no. 3, 031060, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/physrevx.8.031060\">10.1103/physrevx.8.031060</a>.","chicago":"Baykusheva, Denitsa Rangelova, and Hans Jakob Wörner. “Chiral Discrimination through Bielliptical High-Harmonic Spectroscopy.” <i>Physical Review X</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/physrevx.8.031060\">https://doi.org/10.1103/physrevx.8.031060</a>.","short":"D.R. Baykusheva, H.J. Wörner, Physical Review X 8 (2018).","ama":"Baykusheva DR, Wörner HJ. Chiral discrimination through bielliptical high-harmonic spectroscopy. <i>Physical Review X</i>. 2018;8(3). doi:<a href=\"https://doi.org/10.1103/physrevx.8.031060\">10.1103/physrevx.8.031060</a>","ista":"Baykusheva DR, Wörner HJ. 2018. Chiral discrimination through bielliptical high-harmonic spectroscopy. Physical Review X. 8(3), 031060.","ieee":"D. R. Baykusheva and H. J. Wörner, “Chiral discrimination through bielliptical high-harmonic spectroscopy,” <i>Physical Review X</i>, vol. 8, no. 3. American Physical Society, 2018.","apa":"Baykusheva, D. R., &#38; Wörner, H. J. (2018). Chiral discrimination through bielliptical high-harmonic spectroscopy. <i>Physical Review X</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevx.8.031060\">https://doi.org/10.1103/physrevx.8.031060</a>"},"month":"07","oa_version":"Published Version","article_processing_charge":"No","volume":8,"author":[{"last_name":"Baykusheva","full_name":"Baykusheva, Denitsa Rangelova","first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530"},{"first_name":"Hans Jakob","full_name":"Wörner, Hans Jakob","last_name":"Wörner"}],"title":"Chiral discrimination through bielliptical high-harmonic spectroscopy","_id":"14003","issue":"3","abstract":[{"lang":"eng","text":"Molecular chirality plays an essential role in most biochemical processes. The observation and quantification of chirality-sensitive signals, however, remains extremely challenging, especially on ultrafast timescales and in dilute media. Here, we describe the experimental realization of an all-optical and ultrafast scheme for detecting chiral dynamics in molecules. This technique is based on high-harmonic generation by a combination of two-color counterrotating femtosecond laser pulses with polarization states tunable from linear to circular. We demonstrate two different implementations of chiral-sensitive high-harmonic spectroscopy on an ensemble of randomly oriented methyloxirane molecules in the gas phase. Using two elliptically polarized fields, we observe that the ellipticities maximizing the harmonic signal reach up to \r\n4.4\r\n±\r\n0.2\r\n%\r\n (at 17.6 eV). Using two circularly polarized fields, we observe circular dichroisms ranging up to \r\n13\r\n±\r\n6\r\n%\r\n (28.3–33.1 eV). Our theoretical analysis confirms that the observed chiral response originates from subfemtosecond electron dynamics driven by the magnetic component of the driving laser field. This assignment is supported by the experimental observation of a strong intensity dependence of the chiral effects and its agreement with theory. We moreover report and explain a pronounced variation of the signal strength and dichroism with the driving-field ellipticities and harmonic orders. Finally, we demonstrate the sensitivity of the experimental observables to the shape of the electron hole. This technique for chiral discrimination will yield femtosecond temporal resolution when integrated in a pump-probe scheme and subfemtosecond resolution on chiral charge migration in a self-probing scheme."}],"doi":"10.1103/physrevx.8.031060","publication_identifier":{"eissn":["2160-3308"]},"publication_status":"published","status":"public"},{"oa":1,"year":"2018","alternative_title":["LNCS"],"date_updated":"2025-07-14T09:10:15Z","page":"178-197","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10199"}]},"publist_id":"7782","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"KrCh"}],"date_created":"2018-12-11T11:44:51Z","scopus_import":"1","external_id":{"isi":["000491469700013"]},"date_published":"2018-07-18T00:00:00Z","publisher":"Springer","intvolume":"     10982","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","isi":1,"_id":"141","title":"Symbolic algorithms for graphs and Markov decision processes with fairness objectives","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Henzinger","full_name":"Henzinger, Monika H","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"first_name":"Veronika","full_name":"Loitzenbauer, Veronika","last_name":"Loitzenbauer"},{"first_name":"Simin","last_name":"Oraee","full_name":"Oraee, Simin"},{"orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","last_name":"Toman","id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","first_name":"Viktor"}],"doi":"10.1007/978-3-319-96142-2_13","abstract":[{"text":"Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.","lang":"eng"}],"project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"ec_funded":1,"publication_status":"published","acknowledgement":"Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.","status":"public","ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","month":"07","citation":{"chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>.","mla":"Chatterjee, Krishnendu, et al. <i>Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives</i>. Vol. 10982, Springer, 2018, pp. 178–97, doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>.","apa":"Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., &#38; Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">https://doi.org/10.1007/978-3-319-96142-2_13</a>","ieee":"K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.","short":"K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197.","ama":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:<a href=\"https://doi.org/10.1007/978-3-319-96142-2_13\">10.1007/978-3-319-96142-2_13</a>","ista":"Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197."},"day":"18","oa_version":"Published Version","conference":{"location":"Oxford, United Kingdom","start_date":"2018-07-14","end_date":"2018-07-17","name":"CAV: Computer Aided Verification"},"file":[{"file_id":"5737","date_created":"2018-12-18T08:52:38Z","file_name":"2018_LNCS_Chatterjee.pdf","file_size":675606,"relation":"main_file","creator":"dernst","date_updated":"2020-07-14T12:44:53Z","access_level":"open_access","checksum":"1a6ffa4febe8bb8ac28be3adb3eafebc","content_type":"application/pdf"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":10982,"article_processing_charge":"No","has_accepted_license":"1"},{"publication":"International Conference on Learning Representations","date_updated":"2023-09-13T06:35:12Z","status":"public","publication_status":"published","oa":1,"title":"SOM-VAE: Interpretable discrete representation learning on time series","author":[{"first_name":"Vincent","last_name":"Fortuin","full_name":"Fortuin, Vincent"},{"first_name":"Matthias","last_name":"Hüser","full_name":"Hüser, Matthias"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco"},{"full_name":"Strathmann, Heiko","last_name":"Strathmann","first_name":"Heiko"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"}],"_id":"14198","abstract":[{"text":"High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data.","lang":"eng"}],"year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"arxiv":1,"article_processing_charge":"No","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"citation":{"mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” <i>International Conference on Learning Representations</i>, 2018.","chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In <i>International Conference on Learning Representations</i>, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018.","ista":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: <i>International Conference on Learning Representations</i>. ; 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., &#38; Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In <i>International Conference on Learning Representations</i>. New Orleans, LA, United States.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in <i>International Conference on Learning Representations</i>, New Orleans, LA, United States, 2018."},"day":"06","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","external_id":{"arxiv":["1806.02199"]},"date_published":"2018-06-06T00:00:00Z","extern":"1","date_created":"2023-08-22T14:12:48Z","oa_version":"Preprint","conference":{"start_date":"2019-05-06","location":"New Orleans, LA, United States","end_date":"2019-05-09","name":"ICLR: International Conference on Learning Representations"}},{"department":[{"_id":"ToHe"}],"publist_id":"7781","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000491481600024"]},"date_published":"2018-07-18T00:00:00Z","date_created":"2018-12-11T11:44:51Z","scopus_import":"1","publisher":"Springer","intvolume":"     10981","isi":1,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","oa":1,"year":"2018","alternative_title":["LNCS"],"date_updated":"2023-09-15T12:12:08Z","page":"449 - 467","citation":{"apa":"Kong, H., Bartocci, E., &#38; Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>","ieee":"H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.","ama":"Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>","short":"H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467.","ista":"Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.","mla":"Kong, Hui, et al. <i>Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes</i>. Vol. 10981, Springer, 2018, pp. 449–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">10.1007/978-3-319-96145-3_24</a>.","chicago":"Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_24\">https://doi.org/10.1007/978-3-319-96145-3_24</a>."},"day":"18","month":"07","ddc":["000"],"file_date_updated":"2020-07-14T12:44:53Z","oa_version":"Published Version","conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, United Kingdom","end_date":"2018-07-17"},"file":[{"date_updated":"2020-07-14T12:44:53Z","checksum":"fd95e8026deacef3dc752a733bb9355f","content_type":"application/pdf","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":5591566,"file_name":"2018_LNCS_Kong.pdf","date_created":"2018-12-17T15:57:06Z","file_id":"5718"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","article_processing_charge":"No","volume":10981,"title":"Reachable set over-approximation for nonlinear systems using piecewise barrier tubes","author":[{"orcid":"0000-0002-3066-6941","last_name":"Kong","full_name":"Kong, Hui","first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","orcid":"0000−0002−2985−7724"}],"_id":"142","abstract":[{"lang":"eng","text":"We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective."}],"doi":"10.1007/978-3-319-96145-3_24","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"name":"The Wittgenstein Prize","call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"}],"status":"public","acknowledgement":"Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32","publication_status":"published"},{"volume":84,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","conference":{"end_date":"2018-04-11","start_date":"2018-04-09","location":"Playa Blanca, Lanzarote","name":"AISTATS: Conference on Artificial Intelligence and Statistics"},"citation":{"chicago":"Locatello, Francesco, Rajiv Khanna, Joydeep Ghosh, and Gunnar Rätsch. “Boosting Variational Inference: An Optimization Perspective.” In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, 84:464–72. ML Research Press, 2018.","mla":"Locatello, Francesco, et al. “Boosting Variational Inference: An Optimization Perspective.” <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, vol. 84, ML Research Press, 2018, pp. 464–72.","apa":"Locatello, F., Khanna, R., Ghosh, J., &#38; Rätsch, G. (2018). Boosting variational inference: An optimization perspective. In <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i> (Vol. 84, pp. 464–472). Playa Blanca, Lanzarote: ML Research Press.","ieee":"F. Locatello, R. Khanna, J. Ghosh, and G. Rätsch, “Boosting variational inference: An optimization perspective,” in <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>, Playa Blanca, Lanzarote, 2018, vol. 84, pp. 464–472.","short":"F. Locatello, R. Khanna, J. Ghosh, G. Rätsch, in:, Proceedings of the 21st International Conference on Artificial Intelligence and Statistics, ML Research Press, 2018, pp. 464–472.","ista":"Locatello F, Khanna R, Ghosh J, Rätsch G. 2018. Boosting variational inference: An optimization perspective. Proceedings of the 21st International Conference on Artificial Intelligence and Statistics. AISTATS: Conference on Artificial Intelligence and Statistics, PMLR, vol. 84, 464–472.","ama":"Locatello F, Khanna R, Ghosh J, Rätsch G. Boosting variational inference: An optimization perspective. In: <i>Proceedings of the 21st International Conference on Artificial Intelligence and Statistics</i>. Vol 84. ML Research Press; 2018:464-472."},"day":"15","month":"04","publication_status":"published","status":"public","abstract":[{"text":"Variational inference is a popular technique to approximate a possibly\r\nintractable Bayesian posterior with a more tractable one. Recently, boosting\r\nvariational inference has been proposed as a new paradigm to approximate the\r\nposterior by a mixture of densities by greedily adding components to the\r\nmixture. However, as is the case with many other variational inference\r\nalgorithms, its theoretical properties have not been studied. In the present\r\nwork, we study the convergence properties of this approach from a modern\r\noptimization viewpoint by establishing connections to the classic Frank-Wolfe\r\nalgorithm. Our analyses yields novel theoretical insights regarding the\r\nsufficient conditions for convergence, explicit rates, and algorithmic\r\nsimplifications. Since a lot of focus in previous works for variational\r\ninference has been on tractability, our work is especially important as a much\r\nneeded attempt to bridge the gap between probabilistic models and their\r\ncorresponding theoretical properties.","lang":"eng"}],"title":"Boosting variational inference: An optimization perspective","author":[{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"first_name":"Joydeep","last_name":"Ghosh","full_name":"Ghosh, Joydeep"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"}],"_id":"14201","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","publisher":"ML Research Press","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.01733"}],"intvolume":"        84","extern":"1","date_published":"2018-04-15T00:00:00Z","external_id":{"arxiv":["1708.01733"]},"date_created":"2023-08-22T14:15:20Z","scopus_import":"1","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"464-472","publication":"Proceedings of the 21st International Conference on Artificial Intelligence and Statistics","date_updated":"2023-09-13T07:52:40Z","year":"2018","alternative_title":["PMLR"],"oa":1},{"publication_identifier":{"eissn":["1049-5258"],"isbn":["9781510884472"]},"publication_status":"published","status":"public","title":"Boosting black box variational inference","author":[{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Gideon","full_name":"Dresdner, Gideon","last_name":"Dresdner"},{"first_name":"Rajiv","full_name":"Khanna, Rajiv","last_name":"Khanna"},{"first_name":"Isabel","full_name":"Valera, Isabel","last_name":"Valera"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"_id":"14202","abstract":[{"text":"Approximating a probability density in a tractable manner is a central task\r\nin Bayesian statistics. Variational Inference (VI) is a popular technique that\r\nachieves tractability by choosing a relatively simple variational family.\r\nBorrowing ideas from the classic boosting framework, recent approaches attempt\r\nto \\emph{boost} VI by replacing the selection of a single density with a\r\ngreedily constructed mixture of densities. In order to guarantee convergence,\r\nprevious works impose stringent assumptions that require significant effort for\r\npractitioners. Specifically, they require a custom implementation of the greedy\r\nstep (called the LMO) for every probabilistic model with respect to an\r\nunnatural variational family of truncated distributions. Our work fixes these\r\nissues with novel theoretical and algorithmic insights. On the theoretical\r\nside, we show that boosting VI satisfies a relaxed smoothness assumption which\r\nis sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm.\r\nFurthermore, we rephrase the LMO problem and propose to maximize the Residual\r\nELBO (RELBO) which replaces the standard ELBO optimization in VI. These\r\ntheoretical enhancements allow for black box implementation of the boosting\r\nsubroutine. Finally, we present a stopping criterion drawn from the duality gap\r\nin the classic FW analyses and exhaustive experiments to illustrate the\r\nusefulness of our theoretical and algorithmic contributions.","lang":"eng"}],"arxiv":1,"volume":31,"article_processing_charge":"No","citation":{"chicago":"Locatello, Francesco, Gideon Dresdner, Rajiv Khanna, Isabel Valera, and Gunnar Rätsch. “Boosting Black Box Variational Inference.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 31. Neural Information Processing Systems Foundation, 2018.","mla":"Locatello, Francesco, et al. “Boosting Black Box Variational Inference.” <i>Advances in Neural Information Processing Systems</i>, vol. 31, Neural Information Processing Systems Foundation, 2018.","apa":"Locatello, F., Dresdner, G., Khanna, R., Valera, I., &#38; Rätsch, G. (2018). Boosting black box variational inference. In <i>Advances in Neural Information Processing Systems</i> (Vol. 31). Montreal, Canada: Neural Information Processing Systems Foundation.","ieee":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, and G. Rätsch, “Boosting black box variational inference,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2018, vol. 31.","ista":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. 2018. Boosting black box variational inference. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 31.","ama":"Locatello F, Dresdner G, Khanna R, Valera I, Rätsch G. Boosting black box variational inference. In: <i>Advances in Neural Information Processing Systems</i>. Vol 31. Neural Information Processing Systems Foundation; 2018.","short":"F. Locatello, G. Dresdner, R. Khanna, I. Valera, G. Rätsch, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2018."},"day":"06","month":"06","oa_version":"Preprint","conference":{"end_date":"2018-12-08","start_date":"2018-12-03","location":"Montreal, Canada","name":"NeurIPS: Neural Information Processing Systems"},"publication":"Advances in Neural Information Processing Systems","date_updated":"2023-09-13T07:38:24Z","oa":1,"year":"2018","publisher":"Neural Information Processing Systems Foundation","intvolume":"        31","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.02185"}],"type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1806.02185"]},"extern":"1","date_published":"2018-06-06T00:00:00Z","date_created":"2023-08-22T14:15:40Z","scopus_import":"1"},{"extern":"1","external_id":{"arxiv":["1804.08544"]},"date_published":"2018-07-15T00:00:00Z","date_created":"2023-08-22T14:16:01Z","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"publisher":"ML Research Press","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"intvolume":"        80","alternative_title":["PMLR"],"year":"2018","oa":1,"page":"5727-5736","publication":"Proceedings of the 35th International Conference on Machine Learning","date_updated":"2023-09-13T08:13:39Z","oa_version":"Preprint","conference":{"name":"ICML: International Conference on Machine Learning","location":"Stockholm, Sweden","start_date":"2018-07-10","end_date":"2018-07-15"},"citation":{"ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:5727-5736.","short":"A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736.","ista":"Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., &#38; Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736.","chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:5727–36. ML Research Press, 2018.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 5727–36."},"day":"15","month":"07","volume":80,"article_processing_charge":"No","arxiv":1,"abstract":[{"text":"We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework.","lang":"eng"}],"title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","author":[{"full_name":"Yurtsever, Alp","last_name":"Yurtsever","first_name":"Alp"},{"last_name":"Fercoq","full_name":"Fercoq, Olivier","first_name":"Olivier"},{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello"},{"full_name":"Cevher, Volkan","last_name":"Cevher","first_name":"Volkan"}],"_id":"14203","publication_status":"published","status":"public"},{"abstract":[{"lang":"eng","text":"Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives."}],"author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"full_name":"Raj, Anant","last_name":"Raj","first_name":"Anant"},{"last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth","first_name":"Sai Praneeth"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"last_name":"Stich","full_name":"Stich, Sebastian U.","first_name":"Sebastian U."},{"first_name":"Martin","full_name":"Jaggi, Martin","last_name":"Jaggi"}],"title":"On matching pursuit and coordinate descent","_id":"14204","publication_status":"published","status":"public","oa_version":"Preprint","day":"01","citation":{"ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: <i>Proceedings of the 35th International Conference on Machine Learning</i>. Vol 80. ML Research Press; 2018:3198-3207.","short":"F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207.","ista":"Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., &#38; Jaggi, M. (2018). On matching pursuit and coordinate descent. In <i>Proceedings of the 35th International Conference on Machine Learning</i> (Vol. 80, pp. 3198–3207). ML Research Press.","ieee":"F. Locatello <i>et al.</i>, “On matching pursuit and coordinate descent,” in <i>Proceedings of the 35th International Conference on Machine Learning</i>, 2018, vol. 80, pp. 3198–3207.","chicago":"Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In <i>Proceedings of the 35th International Conference on Machine Learning</i>, 80:3198–3207. ML Research Press, 2018.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” <i>Proceedings of the 35th International Conference on Machine Learning</i>, vol. 80, ML Research Press, 2018, pp. 3198–207."},"month":"07","volume":80,"article_processing_charge":"No","arxiv":1,"year":"2018","alternative_title":["PMLR"],"oa":1,"page":"3198-3207","publication":"Proceedings of the 35th International Conference on Machine Learning","date_updated":"2023-09-13T08:19:05Z","external_id":{"arxiv":["1803.09539"]},"date_published":"2018-07-01T00:00:00Z","extern":"1","scopus_import":"1","date_created":"2023-08-22T14:16:25Z","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"        80","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"publisher":"ML Research Press"},{"article_processing_charge":"No","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1804.11130","open_access":"1"}],"arxiv":1,"external_id":{"arxiv":["1804.11130"]},"extern":"1","date_published":"2018-05-01T00:00:00Z","date_created":"2023-08-22T14:25:34Z","oa_version":"Preprint","conference":{"end_date":"2018-05-03","start_date":"2018-04-30","location":"Vancouver, Canada","name":"International Conference on Machine Learning"},"scopus_import":"1","citation":{"short":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018.","ista":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning.","ama":"Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: <i>6th International Conference on Learning Representations</i>. ; 2018.","apa":"Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., &#38; Scholkopf, B. (2018). Clustering meets implicit generative models. In <i>6th International Conference on Learning Representations</i>. Vancouver, Canada.","ieee":"F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in <i>6th International Conference on Learning Representations</i>, Vancouver, Canada, 2018.","mla":"Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” <i>6th International Conference on Learning Representations</i>, 2018.","chicago":"Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In <i>6th International Conference on Learning Representations</i>, 2018."},"department":[{"_id":"FrLo"}],"day":"01","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","publication":"6th International Conference on Learning Representations","date_updated":"2023-09-13T09:08:24Z","abstract":[{"lang":"eng","text":"Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples."}],"year":"2018","oa":1,"title":"Clustering meets implicit generative models","author":[{"full_name":"Locatello, Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Damien","last_name":"Vincent","full_name":"Vincent, Damien"},{"full_name":"Tolstikhin, Ilya","last_name":"Tolstikhin","first_name":"Ilya"},{"first_name":"Gunnar","last_name":"Ratsch","full_name":"Ratsch, Gunnar"},{"last_name":"Gelly","full_name":"Gelly, Sylvain","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Scholkopf, Bernhard","last_name":"Scholkopf"}],"_id":"14224"},{"date_published":"2018-05-04T00:00:00Z","external_id":{"pmid":["29728606"]},"extern":"1","date_created":"2023-09-06T12:07:33Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Springer Nature","main_file_link":[{"url":"https://doi.org/10.1038/s41467-018-04139-2","open_access":"1"}],"intvolume":"         9","year":"2018","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry","Multidisciplinary"],"oa":1,"article_number":"1806","article_type":"original","publication":"Nature Communications","date_updated":"2023-11-07T11:46:12Z","oa_version":"Published Version","citation":{"ama":"Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. <i>Nature Communications</i>. 2018;9. doi:<a href=\"https://doi.org/10.1038/s41467-018-04139-2\">10.1038/s41467-018-04139-2</a>","ista":"Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.","short":"B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler, K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).","ieee":"B. Bräuning <i>et al.</i>, “Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB,” <i>Nature Communications</i>, vol. 9. Springer Nature, 2018.","apa":"Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler, A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-04139-2\">https://doi.org/10.1038/s41467-018-04139-2</a>","mla":"Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming Toxin YaxAB.” <i>Nature Communications</i>, vol. 9, 1806, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-04139-2\">10.1038/s41467-018-04139-2</a>.","chicago":"Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling, Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming Toxin YaxAB.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-04139-2\">https://doi.org/10.1038/s41467-018-04139-2</a>."},"day":"04","pmid":1,"month":"05","article_processing_charge":"No","volume":9,"abstract":[{"lang":"eng","text":"Pore-forming toxins (PFT) are virulence factors that transform from soluble to membrane-bound states. The Yersinia YaxAB system represents a family of binary α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures. YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the molecular basis for its two-component lytic mechanism remains elusive. Here, we present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy map of the YaxAB complex. Our structures reveal a pore predominantly composed of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties, but only YaxA is capable of binding to membranes by itself. YaxB can subsequently be recruited to membrane-associated YaxA and induced to present its lytic transmembrane helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers. Our results allow for a comparison between pore assemblies belonging to the wider ClyA-like family of α-PFTs, highlighting diverse pore architectures."}],"doi":"10.1038/s41467-018-04139-2","title":"Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB","author":[{"first_name":"Bastian","full_name":"Bräuning, Bastian","last_name":"Bräuning"},{"last_name":"Bertosin","full_name":"Bertosin, Eva","first_name":"Eva"},{"last_name":"Praetorius","full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"first_name":"Christian","full_name":"Ihling, Christian","last_name":"Ihling"},{"last_name":"Schatt","full_name":"Schatt, Alexandra","first_name":"Alexandra"},{"first_name":"Agnes","last_name":"Adler","full_name":"Adler, Agnes"},{"first_name":"Klaus","full_name":"Richter, Klaus","last_name":"Richter"},{"last_name":"Sinz","full_name":"Sinz, Andrea","first_name":"Andrea"},{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"},{"first_name":"Michael","full_name":"Groll, Michael","last_name":"Groll"}],"_id":"14284","publication_status":"published","status":"public","publication_identifier":{"issn":["2041-1723"]}},{"scopus_import":"1","date_created":"2018-12-11T11:44:51Z","external_id":{"isi":["000545262800020"]},"date_published":"2018-07-09T00:00:00Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7780","department":[{"_id":"KrCh"}],"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","isi":1,"main_file_link":[{"url":"https://arxiv.org/abs/1804.10985","open_access":"1"}],"publisher":"IEEE","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"year":"2018","oa":1,"page":"185 - 194","date_updated":"2025-06-02T08:53:48Z","conference":{"name":"LICS: Logic in Computer Science","end_date":"2018-07-12","start_date":"2018-07-09","location":"Oxford, United Kingdom"},"oa_version":"Preprint","month":"07","day":"09","citation":{"mla":"Brázdil, Tomáš, et al. <i>Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS</i>. Vol. F138033, IEEE, 2018, pp. 185–94, doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>.","chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., &#38; Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. <a href=\"https://doi.org/10.1145/3209108.3209191\">https://doi.org/10.1145/3209108.3209191</a>","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:<a href=\"https://doi.org/10.1145/3209108.3209191\">10.1145/3209108.3209191</a>","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194."},"article_processing_charge":"No","volume":"F138033","doi":"10.1145/3209108.3209191","abstract":[{"text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.","lang":"eng"}],"_id":"143","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","full_name":"Novotny, Petr"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"},{"last_name":"Zuleger","full_name":"Zuleger, Florian","first_name":"Florian"}],"title":"Efficient algorithms for asymptotic bounds on termination time in VASS","ec_funded":1,"publication_status":"published","status":"public","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"publication_identifier":{"isbn":["978-1-4503-5583-4"]}},{"year":"2018","abstract":[{"lang":"eng","text":"Function and activity of biomolecules often depend on their spatial arrangement. The method introduced here allows genetically encoding the spatial arrangement of proteins and DNA. The approach relies on staple proteins that fold double-stranded DNA into user-defined shapes. This thesis describes the development of staple proteins based on the DNA recognition of TAL effectors and presents experimentally derived rules for designing a variety of self-assembling nanoscale shapes featuring structural motifs such as curvature, vertices, corners, and multilayer helix packing. "}],"author":[{"full_name":"Praetorius, Florian M","last_name":"Praetorius","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62","first_name":"Florian M"}],"title":"Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures","oa":1,"supervisor":[{"first_name":"Hendrik","full_name":"Dietz, Hendrik","last_name":"Dietz"}],"_id":"14306","status":"public","publication_status":"published","date_updated":"2023-11-07T11:43:38Z","extern":"1","date_published":"2018-01-16T00:00:00Z","date_created":"2023-09-06T13:11:22Z","oa_version":"Published Version","day":"16","citation":{"ieee":"F. M. Praetorius, “Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures,” Technische Universität München, 2018.","apa":"Praetorius, F. M. (2018). <i>Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures</i>. Technische Universität München.","short":"F.M. Praetorius, Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures, Technische Universität München, 2018.","ista":"Praetorius FM. 2018. Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. Technische Universität München.","ama":"Praetorius FM. Genetically encoding the spatial arrangement of DNA and proteins in self-assembling nanostructures. 2018.","chicago":"Praetorius, Florian M. “Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures.” Technische Universität München, 2018.","mla":"Praetorius, Florian M. <i>Genetically Encoding the Spatial Arrangement of DNA and Proteins in Self-Assembling Nanostructures</i>. Technische Universität München, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","language":[{"iso":"eng"}],"type":"dissertation","article_processing_charge":"No","degree_awarded":"PhD","main_file_link":[{"url":"https://mediatum.ub.tum.de/1398662","open_access":"1"}],"publisher":"Technische Universität München"},{"year":"2018","keyword":["General Chemistry","Condensed Matter Physics"],"oa":1,"article_type":"original","page":"9577-9588","publication":"Soft Matter","date_updated":"2023-02-23T13:47:43Z","extern":"1","date_published":"2018-12-21T00:00:00Z","external_id":{"arxiv":["1909.11121"],"pmid":["30456407"]},"scopus_import":"1","date_created":"2021-02-01T13:44:41Z","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","intvolume":"        14","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.11121"}],"publisher":"Royal Society of Chemistry ","issue":"47","abstract":[{"text":"The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena.","lang":"eng"}],"doi":"10.1039/c8sm01760c","author":[{"first_name":"Antoine","full_name":"Aubret, Antoine","last_name":"Aubret"},{"orcid":"0000-0002-7253-9465","last_name":"Palacci","full_name":"Palacci, Jérémie A","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"}],"title":"Diffusiophoretic design of self-spinning microgears from colloidal microswimmers","_id":"9053","publication_status":"published","status":"public","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"oa_version":"Preprint","day":"21","citation":{"mla":"Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>.","chicago":"Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>. Royal Society of Chemistry , 2018. <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>.","short":"A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588.","ama":"Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. 2018;14(47):9577-9588. doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>","ista":"Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588.","apa":"Aubret, A., &#38; Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>","ieee":"A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” <i>Soft Matter</i>, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018."},"month":"12","pmid":1,"article_processing_charge":"No","volume":14,"arxiv":1},{"volume":14,"article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","citation":{"chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” <i>Nature Physics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0227-4\">https://doi.org/10.1038/s41567-018-0227-4</a>.","mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” <i>Nature Physics</i>, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:<a href=\"https://doi.org/10.1038/s41567-018-0227-4\">10.1038/s41567-018-0227-4</a>.","ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. <i>Nature Physics</i>. 2018;14(11):1114-1118. doi:<a href=\"https://doi.org/10.1038/s41567-018-0227-4\">10.1038/s41567-018-0227-4</a>","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118.","apa":"Aubret, A., Youssef, M., Sacanna, S., &#38; Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-018-0227-4\">https://doi.org/10.1038/s41567-018-0227-4</a>","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” <i>Nature Physics</i>, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018."},"day":"01","month":"11","status":"public","publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"abstract":[{"text":"Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery.","lang":"eng"}],"issue":"11","doi":"10.1038/s41567-018-0227-4","title":"Targeted assembly and synchronization of self-spinning microgears","author":[{"first_name":"Antoine","last_name":"Aubret","full_name":"Aubret, Antoine"},{"last_name":"Youssef","full_name":"Youssef, Mena","first_name":"Mena"},{"first_name":"Stefano","last_name":"Sacanna","full_name":"Sacanna, Stefano"},{"full_name":"Palacci, Jérémie A","last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465"}],"_id":"9062","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1","publisher":"Springer Nature","intvolume":"        14","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.01033"}],"date_published":"2018-11-01T00:00:00Z","external_id":{"arxiv":["1810.01033"]},"extern":"1","date_created":"2021-02-02T13:52:49Z","scopus_import":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","page":"1114-1118","article_type":"original","publication":"Nature Physics","date_updated":"2023-02-23T13:48:02Z","year":"2018","oa":1},{"month":"10","citation":{"ista":"Lee N, Ko E, Choi HY, Hong YJ, Nauman M, Kang W, Choi HJ, Choi YJ, Jo Y. 2018. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. Advanced Materials. 30(52), 1805564.","short":"N. Lee, E. Ko, H.Y. Choi, Y.J. Hong, M. Nauman, W. Kang, H.J. Choi, Y.J. Choi, Y. Jo, Advanced Materials 30 (2018).","ama":"Lee N, Ko E, Choi HY, et al. Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. <i>Advanced Materials</i>. 2018;30(52). doi:<a href=\"https://doi.org/10.1002/adma.201805564\">10.1002/adma.201805564</a>","ieee":"N. Lee <i>et al.</i>, “Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate,” <i>Advanced Materials</i>, vol. 30, no. 52. Wiley, 2018.","apa":"Lee, N., Ko, E., Choi, H. Y., Hong, Y. J., Nauman, M., Kang, W., … Jo, Y. (2018). Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate. <i>Advanced Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adma.201805564\">https://doi.org/10.1002/adma.201805564</a>","chicago":"Lee, Nara, Eunjung Ko, Hwan Young Choi, Yun Jeong Hong, Muhammad Nauman, Woun Kang, Hyoung Joon Choi, Young Jai Choi, and Younjung Jo. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” <i>Advanced Materials</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/adma.201805564\">https://doi.org/10.1002/adma.201805564</a>.","mla":"Lee, Nara, et al. “Antiferromagnet‐based Spintronic Functionality by Controlling Isospin Domains in a Layered Perovskite Iridate.” <i>Advanced Materials</i>, vol. 30, no. 52, 1805564, Wiley, 2018, doi:<a href=\"https://doi.org/10.1002/adma.201805564\">10.1002/adma.201805564</a>."},"day":"29","oa_version":"Preprint","arxiv":1,"volume":30,"article_processing_charge":"No","_id":"9066","title":"Antiferromagnet‐based spintronic functionality by controlling isospin domains in a layered perovskite iridate","author":[{"first_name":"Nara","full_name":"Lee, Nara","last_name":"Lee"},{"first_name":"Eunjung","full_name":"Ko, Eunjung","last_name":"Ko"},{"full_name":"Choi, Hwan Young","last_name":"Choi","first_name":"Hwan Young"},{"last_name":"Hong","full_name":"Hong, Yun Jeong","first_name":"Yun Jeong"},{"orcid":"0000-0002-2111-4846","full_name":"Nauman, Muhammad","last_name":"Nauman","id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad"},{"first_name":"Woun","full_name":"Kang, Woun","last_name":"Kang"},{"last_name":"Choi","full_name":"Choi, Hyoung Joon","first_name":"Hyoung Joon"},{"first_name":"Young Jai","last_name":"Choi","full_name":"Choi, Young Jai"},{"first_name":"Younjung","full_name":"Jo, Younjung","last_name":"Jo"}],"doi":"10.1002/adma.201805564","abstract":[{"text":"The novel electronic state of the canted antiferromagnetic (AFM) insulator, strontium iridate (Sr2IrO4) has been well described by the spin-orbit-entangled isospin Jeff = 1/2, but the role of isospin in transport phenomena remains poorly understood. In this study, antiferromagnet-based spintronic functionality is demonstrated by combining unique characteristics of the isospin state in Sr2IrO4. Based on magnetic and transport measurements, large and highly anisotropic magnetoresistance (AMR) is obtained by manipulating the antiferromagnetic isospin domains. First-principles calculations suggest that electrons whose isospin directions are strongly coupled to in-plane net magnetic moment encounter the isospin mismatch when moving across antiferromagnetic domain boundaries, which generates a high resistance state. By rotating a magnetic field that aligns in-plane net moments and removes domain boundaries, the macroscopically-ordered isospins govern dynamic transport through the system, which leads to the extremely angle-sensitive AMR. As with this work that establishes a link between isospins and magnetotransport in strongly spin-orbit-coupled AFM Sr2IrO4, the peculiar AMR effect provides a beneficial foundation for fundamental and applied research on AFM spintronics.","lang":"eng"}],"issue":"52","publication_identifier":{"issn":["0935-9648","1521-4095"]},"publication_status":"published","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-02-02T15:50:58Z","extern":"1","external_id":{"arxiv":["1811.04562"]},"date_published":"2018-10-29T00:00:00Z","publisher":"Wiley","intvolume":"        30","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"keyword":["Mechanical Engineering","General Materials Science","Mechanics of Materials"],"year":"2018","date_updated":"2021-02-03T13:58:39Z","publication":"Advanced Materials","article_number":"1805564","article_type":"original"},{"publisher":"Elsevier","intvolume":"       536","volume":536,"article_processing_charge":"No","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"citation":{"apa":"Hussain, T., Oh, M., Nauman, M., Jo, Y., Han, G., Kim, C., &#38; Kang, W. (2018). Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. <i>Physica B: Condensed Matter</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">https://doi.org/10.1016/j.physb.2017.11.032</a>","ieee":"T. Hussain <i>et al.</i>, “Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se,” <i>Physica B: Condensed Matter</i>, vol. 536. Elsevier, pp. 235–238, 2018.","short":"T. Hussain, M. Oh, M. Nauman, Y. Jo, G. Han, C. Kim, W. Kang, Physica B: Condensed Matter 536 (2018) 235–238.","ista":"Hussain T, Oh M, Nauman M, Jo Y, Han G, Kim C, Kang W. 2018. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. Physica B: Condensed Matter. 536, 235–238.","ama":"Hussain T, Oh M, Nauman M, et al. Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se. <i>Physica B: Condensed Matter</i>. 2018;536:235-238. doi:<a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">10.1016/j.physb.2017.11.032</a>","mla":"Hussain, Tayyaba, et al. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” <i>Physica B: Condensed Matter</i>, vol. 536, Elsevier, 2018, pp. 235–38, doi:<a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">10.1016/j.physb.2017.11.032</a>.","chicago":"Hussain, Tayyaba, Myeong-jun Oh, Muhammad Nauman, Younjung Jo, Garam Han, Changyoung Kim, and Woun Kang. “Pressure-Induced Metal–Insulator Transitions in Chalcogenide NiS2-Se.” <i>Physica B: Condensed Matter</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.physb.2017.11.032\">https://doi.org/10.1016/j.physb.2017.11.032</a>."},"day":"01","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","date_published":"2018-05-01T00:00:00Z","date_created":"2021-02-02T15:52:43Z","oa_version":"None","publication":"Physica B: Condensed Matter","publication_identifier":{"issn":["0921-4526"]},"date_updated":"2021-02-04T07:18:57Z","status":"public","publication_status":"published","page":"235-238","article_type":"original","title":"Pressure-induced metal–insulator transitions in chalcogenide NiS2-Se","author":[{"first_name":"Tayyaba","full_name":"Hussain, Tayyaba","last_name":"Hussain"},{"last_name":"Oh","full_name":"Oh, Myeong-jun","first_name":"Myeong-jun"},{"id":"32c21954-2022-11eb-9d5f-af9f93c24e71","first_name":"Muhammad","full_name":"Nauman, Muhammad","last_name":"Nauman","orcid":"0000-0002-2111-4846"},{"last_name":"Jo","full_name":"Jo, Younjung","first_name":"Younjung"},{"first_name":"Garam","full_name":"Han, Garam","last_name":"Han"},{"first_name":"Changyoung","full_name":"Kim, Changyoung","last_name":"Kim"},{"last_name":"Kang","full_name":"Kang, Woun","first_name":"Woun"}],"_id":"9068","abstract":[{"lang":"eng","text":"We report the temperature-dependent resistivity ρ(T) of chalcogenide NiS2-xSex (x = 0.1) using hydrostatic pressure as a control parameter in the temperature range of 4–300 K. The insulating behavior of ρ(T) survives at low temperatures in the pressure regime below 7.5 kbar, whereas a clear insulator-to-metallic transition is observed above 7.5 kbar. Two types of magnetic transitions, from the paramagnetic (PM) to the antiferromagnetic (AFM) state and from the AFM state to the weak ferromagnetic (WF) state, were evaluated and confirmed by magnetization measurement. According to the temperature–pressure phase diagram, the WF phase survives up to 7.5 kbar, and the transition temperature of the WF transition decreases as the pressure increases, whereas the metal–insulator transition temperature increases up to 9.4 kbar. We analyzed the metallic behavior and proposed Fermi-liquid behavior of NiS1.9Se0.1."}],"year":"2018","doi":"10.1016/j.physb.2017.11.032"},{"publist_id":"6530","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"date_created":"2018-12-11T11:49:10Z","scopus_import":"1","external_id":{"isi":["000424842400019"]},"date_published":"2018-01-29T00:00:00Z","publisher":"Company of Biologists","intvolume":"       131","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","isi":1,"oa":1,"year":"2018","date_updated":"2025-05-07T11:12:29Z","publication":"Journal of Cell Science","article_number":"jcs.204198","ddc":["581"],"file_date_updated":"2020-07-14T12:48:15Z","month":"01","citation":{"mla":"Tejos, Ricardo, et al. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>, vol. 131, no. 2, jcs. 204198, Company of Biologists, 2018, doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>.","chicago":"Tejos, Ricardo, Cecilia Rodríguez Furlán, Maciek Adamowski, Michael Sauer, Lorena Norambuena, and Jiří Friml. “PATELLINS Are Regulators of Auxin Mediated PIN1 Relocation and Plant Development in Arabidopsis Thaliana.” <i>Journal of Cell Science</i>. Company of Biologists, 2018. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>.","ieee":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, and J. Friml, “PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana,” <i>Journal of Cell Science</i>, vol. 131, no. 2. Company of Biologists, 2018.","apa":"Tejos, R., Rodríguez Furlán, C., Adamowski, M., Sauer, M., Norambuena, L., &#38; Friml, J. (2018). PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.204198\">https://doi.org/10.1242/jcs.204198</a>","ama":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. <i>Journal of Cell Science</i>. 2018;131(2). doi:<a href=\"https://doi.org/10.1242/jcs.204198\">10.1242/jcs.204198</a>","ista":"Tejos R, Rodríguez Furlán C, Adamowski M, Sauer M, Norambuena L, Friml J. 2018. PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana. Journal of Cell Science. 131(2), jcs. 204198.","short":"R. Tejos, C. Rodríguez Furlán, M. Adamowski, M. Sauer, L. Norambuena, J. Friml, Journal of Cell Science 131 (2018)."},"pubrep_id":"988","day":"29","oa_version":"Published Version","file":[{"file_id":"6299","date_created":"2019-04-12T08:46:32Z","file_name":"2017_adamowski_PATELLINS_are.pdf","creator":"dernst","file_size":14925985,"relation":"main_file","access_level":"open_access","checksum":"bf156c20a4f117b4b932370d54cbac8c","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z"}],"volume":131,"article_processing_charge":"No","has_accepted_license":"1","_id":"913","title":"PATELLINS are regulators of auxin mediated PIN1 relocation and plant development in Arabidopsis thaliana","author":[{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"full_name":"Rodríguez Furlán, Cecilia","last_name":"Rodríguez Furlán","first_name":"Cecilia"},{"orcid":"0000-0001-6463-5257","full_name":"Adamowski, Maciek","last_name":"Adamowski","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"last_name":"Sauer","full_name":"Sauer, Michael","first_name":"Michael"},{"first_name":"Lorena","full_name":"Norambuena, Lorena","last_name":"Norambuena"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596"}],"doi":"10.1242/jcs.204198","abstract":[{"lang":"eng","text":"Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We performed a microarray-based approach to find regulators of the auxin-induced PIN relocation in the Arabidopsis thaliana root. We identified a subset of a family of phosphatidylinositol transfer proteins (PITP), the PATELLINs (PATL). Here, we show that PATLs are expressed in partially overlapping cells types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia, and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests PATLs redundantly play a crucial role in polarity and patterning in Arabidopsis."}],"issue":"2","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants"}],"publication_identifier":{"issn":["00219533"]},"ec_funded":1,"publication_status":"published","status":"public"},{"extern":"1","date_published":"2018-09-01T00:00:00Z","date_created":"2021-02-15T14:17:25Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":"       123","main_file_link":[{"url":"https://doi.org/10.1029/2017JC013591","open_access":"1"}],"publisher":"American Geophysical Union","year":"2018","oa":1,"article_type":"original","page":"6136-6155","publication":"Journal of Geophysical Research: Oceans","date_updated":"2022-01-24T12:39:03Z","oa_version":"Published Version","day":"01","citation":{"ieee":"O. Richet, J.-M. Chomaz, and C. J. Muller, “Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude,” <i>Journal of Geophysical Research: Oceans</i>, vol. 123, no. 9. American Geophysical Union, pp. 6136–6155, 2018.","apa":"Richet, O., Chomaz, J.-M., &#38; Muller, C. J. (2018). Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2017jc013591\">https://doi.org/10.1029/2017jc013591</a>","ama":"Richet O, Chomaz J-M, Muller CJ. Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. <i>Journal of Geophysical Research: Oceans</i>. 2018;123(9):6136-6155. doi:<a href=\"https://doi.org/10.1029/2017jc013591\">10.1029/2017jc013591</a>","short":"O. Richet, J.-M. Chomaz, C.J. Muller, Journal of Geophysical Research: Oceans 123 (2018) 6136–6155.","ista":"Richet O, Chomaz J-M, Muller CJ. 2018. Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude. Journal of Geophysical Research: Oceans. 123(9), 6136–6155.","mla":"Richet, O., et al. “Internal Tide Dissipation at Topography: Triadic Resonant Instability Equatorward and Evanescent Waves Poleward of the Critical Latitude.” <i>Journal of Geophysical Research: Oceans</i>, vol. 123, no. 9, American Geophysical Union, 2018, pp. 6136–55, doi:<a href=\"https://doi.org/10.1029/2017jc013591\">10.1029/2017jc013591</a>.","chicago":"Richet, O., J.-M. Chomaz, and Caroline J Muller. “Internal Tide Dissipation at Topography: Triadic Resonant Instability Equatorward and Evanescent Waves Poleward of the Critical Latitude.” <i>Journal of Geophysical Research: Oceans</i>. American Geophysical Union, 2018. <a href=\"https://doi.org/10.1029/2017jc013591\">https://doi.org/10.1029/2017jc013591</a>."},"month":"09","article_processing_charge":"No","volume":123,"issue":"9","abstract":[{"lang":"eng","text":"Several studies have shown the existence of a critical latitude where the dissipation of internal tides is strongly enhanced. Internal tides are internal waves generated by barotropic tidal currents impinging rough topography at the seafloor. Their dissipation and concomitant diapycnal mixing are believed to be important for water masses and the large‐scale ocean circulation. The purpose of this study is to clarify the physical processes at the origin of this strong latitudinal dependence of tidal energy dissipation. We find that different mechanisms are involved equatorward and poleward of the critical latitude. Triadic resonant instabilities are responsible for the dissipation of internal tides equatorward of the critical latitude. In particular, a dominant triad involving the primary internal tide and near‐inertial waves is key. At the critical latitude, the peak of energy dissipation is explained by both increased instability growth rates, and smaller scales of secondary waves thus more prone to break and dissipate their energy. Surprisingly, poleward of the critical latitude, the generation of evanescent waves appears to be crucial. Triadic instabilities have been widely studied, but the transfer of energy to evanescent waves has received comparatively little attention. Our work suggests that the nonlinear transfer of energy from the internal tide to evanescent waves (corresponding to the 2f‐pump mechanism described by Young et al., 2008, https://doi.org/10.1017/S0022112008001742) is an efficient mechanism to dissipate internal tide energy near and poleward of the critical latitude. The theoretical results are confirmed in idealized high‐resolution numerical simulations of a barotropic M2 tide impinging sinusoidal topography in a linearly stratified fluid."}],"doi":"10.1029/2017jc013591","author":[{"first_name":"O.","full_name":"Richet, O.","last_name":"Richet"},{"last_name":"Chomaz","full_name":"Chomaz, J.-M.","first_name":"J.-M."},{"orcid":"0000-0001-5836-5350","last_name":"Muller","full_name":"Muller, Caroline J","first_name":"Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b"}],"title":"Internal tide dissipation at topography: Triadic resonant instability equatorward and evanescent waves poleward of the critical latitude","_id":"9134","status":"public","publication_status":"published","publication_identifier":{"issn":["2169-9275"]}},{"oa_version":"Published Version","day":"20","citation":{"chicago":"Muller, Caroline J, and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1719967115\">https://doi.org/10.1073/pnas.1719967115</a>.","mla":"Muller, Caroline J., and David M. Romps. “Acceleration of Tropical Cyclogenesis by Self-Aggregation Feedbacks.” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 12, Proceedings of the National Academy of Sciences, 2018, pp. 2930–35, doi:<a href=\"https://doi.org/10.1073/pnas.1719967115\">10.1073/pnas.1719967115</a>.","ieee":"C. J. Muller and D. M. Romps, “Acceleration of tropical cyclogenesis by self-aggregation feedbacks,” <i>Proceedings of the National Academy of Sciences</i>, vol. 115, no. 12. Proceedings of the National Academy of Sciences, pp. 2930–2935, 2018.","apa":"Muller, C. J., &#38; Romps, D. M. (2018). Acceleration of tropical cyclogenesis by self-aggregation feedbacks. <i>Proceedings of the National Academy of Sciences</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1719967115\">https://doi.org/10.1073/pnas.1719967115</a>","short":"C.J. Muller, D.M. Romps, Proceedings of the National Academy of Sciences 115 (2018) 2930–2935.","ama":"Muller CJ, Romps DM. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. <i>Proceedings of the National Academy of Sciences</i>. 2018;115(12):2930-2935. doi:<a href=\"https://doi.org/10.1073/pnas.1719967115\">10.1073/pnas.1719967115</a>","ista":"Muller CJ, Romps DM. 2018. Acceleration of tropical cyclogenesis by self-aggregation feedbacks. Proceedings of the National Academy of Sciences. 115(12), 2930–2935."},"month":"03","article_processing_charge":"No","volume":115,"issue":"12","abstract":[{"lang":"eng","text":"Idealized simulations of tropical moist convection have revealed that clouds can spontaneously clump together in a process called self-aggregation. This results in a state where a moist cloudy region with intense deep convection is surrounded by extremely dry subsiding air devoid of deep convection. Because of the idealized settings of the simulations where it was discovered, the relevance of self-aggregation to the real world is still debated. Here, we show that self-aggregation feedbacks play a leading-order role in the spontaneous genesis of tropical cyclones in cloud-resolving simulations. Those feedbacks accelerate the cyclogenesis process by a factor of 2, and the feedbacks contributing to the cyclone formation show qualitative and quantitative agreement with the self-aggregation process. Once the cyclone is formed, wind-induced surface heat exchange (WISHE) effects dominate, although we find that self-aggregation feedbacks have a small but nonnegligible contribution to the maintenance of the mature cyclone. Our results suggest that self-aggregation, and the framework developed for its study, can help shed more light into the physical processes leading to cyclogenesis and cyclone intensification. In particular, our results point out the importance of the longwave radiative cooling outside the cyclone."}],"doi":"10.1073/pnas.1719967115","author":[{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"full_name":"Romps, David M.","last_name":"Romps","first_name":"David M."}],"title":"Acceleration of tropical cyclogenesis by self-aggregation feedbacks","_id":"9135","publication_status":"published","status":"public","publication_identifier":{"issn":["0027-8424","1091-6490"]},"extern":"1","date_published":"2018-03-20T00:00:00Z","date_created":"2021-02-15T14:18:16Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1073/pnas.1719967115"}],"intvolume":"       115","publisher":"Proceedings of the National Academy of Sciences","year":"2018","keyword":["Multidisciplinary"],"oa":1,"article_type":"original","page":"2930-2935","publication":"Proceedings of the National Academy of Sciences","date_updated":"2022-01-24T12:39:49Z"}]