[{"month":"06","quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.02199","open_access":"1"}],"oa_version":"Preprint","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"}],"date_published":"2018-06-06T00:00:00Z","date_created":"2023-08-22T14:12:48Z","day":"06","language":[{"iso":"eng"}],"publication":"International Conference on Learning Representations","year":"2018","publication_status":"published","status":"public","type":"conference","conference":{"end_date":"2019-05-09","location":"New Orleans, LA, United States","start_date":"2019-05-06","name":"ICLR: International Conference on Learning Representations"},"_id":"14198","department":[{"_id":"FrLo"}],"title":"SOM-VAE: Interpretable discrete representation learning on time series","author":[{"full_name":"Fortuin, Vincent","last_name":"Fortuin","first_name":"Vincent"},{"last_name":"Hüser","full_name":"Hüser, Matthias","first_name":"Matthias"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"first_name":"Heiko","last_name":"Strathmann","full_name":"Strathmann, Heiko"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"}],"article_processing_charge":"No","external_id":{"arxiv":["1806.02199"]},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” 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.","mla":"Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.","apa":"Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.","ama":"Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.","ieee":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.","short":"V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018."},"date_updated":"2023-09-13T06:35:12Z"},{"alternative_title":["PMLR"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.08544"}],"month":"07","intvolume":" 80","abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","volume":80,"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"location":"Stockholm, Sweden","end_date":"2018-07-15","start_date":"2018-07-10","name":"ICML: International Conference on Machine Learning"},"status":"public","_id":"14203","department":[{"_id":"FrLo"}],"date_updated":"2023-09-13T08:13:39Z","extern":"1","publisher":"ML Research Press","quality_controlled":"1","oa":1,"page":"5727-5736","date_published":"2018-07-15T00:00:00Z","date_created":"2023-08-22T14:16:01Z","year":"2018","day":"15","publication":"Proceedings of the 35th International Conference on Machine Learning","author":[{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"first_name":"Olivier","full_name":"Fercoq, Olivier","last_name":"Fercoq"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello"},{"last_name":"Cevher","full_name":"Cevher, Volkan","first_name":"Volkan"}],"article_processing_charge":"No","external_id":{"arxiv":["1804.08544"]},"title":"A conditional gradient framework for composite convex minimization with applications to semidefinite programming","citation":{"chicago":"Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018.","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.","mla":"Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36.","ieee":"A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 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.","apa":"Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.","ama":"Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"publication_status":"published","volume":209,"issue":"4","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci."}],"intvolume":" 209","month":"08","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/early/2017/11/30/227082"}],"scopus_import":"1","date_updated":"2023-09-13T08:22:32Z","department":[{"_id":"NiBa"}],"_id":"282","status":"public","type":"journal_article","publication":"Genetics","day":"01","year":"2018","isi":1,"date_created":"2018-12-11T11:45:36Z","date_published":"2018-08-01T00:00:00Z","doi":"10.1534/genetics.118.301018","page":"1279 - 1303","oa":1,"publisher":"Genetics Society of America","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018","apa":"Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018","short":"H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303.","ieee":"H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018.","mla":"Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018.","ista":"Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303.","chicago":"Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018."},"title":"Introgression of a block of genome under infinitesimal selection","external_id":{"isi":["000440014100020"]},"article_processing_charge":"No","author":[{"id":"42377A0A-F248-11E8-B48F-1D18A9856A87","first_name":"Himani","full_name":"Sachdeva, Himani","last_name":"Sachdeva"},{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7617"},{"_id":"108","status":"public","type":"conference","conference":{"end_date":"2018-06-22","location":"Vail, CO, USA","start_date":"2018-06-17 ","name":"ISIT: International Symposium on Information Theory"},"date_updated":"2023-09-13T08:23:18Z","department":[{"_id":"KrPi"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"month":"08","intvolume":" 2018","scopus_import":"1","alternative_title":["ISIT Proceedings"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2017/507"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":2018,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654."},"title":"Inverted leftover hash lemma","author":[{"full_name":"Obremski, Marciej","last_name":"Obremski","first_name":"Marciej"},{"last_name":"Skorski","full_name":"Skorski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"}],"publist_id":"7946","article_processing_charge":"No","external_id":{"isi":["000448139300368"]},"quality_controlled":"1","publisher":"IEEE","oa":1,"day":"16","isi":1,"year":"2018","date_published":"2018-08-16T00:00:00Z","doi":"10.1109/ISIT.2018.8437654","date_created":"2018-12-11T11:44:40Z"},{"_id":"14204","type":"conference","status":"public","date_updated":"2023-09-13T08:19:05Z","extern":"1","department":[{"_id":"FrLo"}],"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.09539"}],"alternative_title":["PMLR"],"scopus_import":"1","intvolume":" 80","month":"07","publication_status":"published","language":[{"iso":"eng"}],"volume":80,"citation":{"ieee":"F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 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.","ama":"Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.","apa":"Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press.","mla":"Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207.","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.","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 Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1803.09539"]},"article_processing_charge":"No","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"last_name":"Raj","full_name":"Raj, Anant","first_name":"Anant"},{"first_name":"Sai Praneeth","last_name":"Karimireddy","full_name":"Karimireddy, Sai Praneeth"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Sebastian U.","last_name":"Stich","full_name":"Stich, Sebastian U."},{"first_name":"Martin","last_name":"Jaggi","full_name":"Jaggi, Martin"}],"title":"On matching pursuit and coordinate descent","oa":1,"quality_controlled":"1","publisher":"ML Research Press","year":"2018","publication":"Proceedings of the 35th International Conference on Machine Learning","day":"01","page":"3198-3207","date_created":"2023-08-22T14:16:25Z","date_published":"2018-07-01T00:00:00Z"},{"related_material":{"record":[{"id":"8332","status":"public","relation":"dissertation_contains"}]},"volume":10981,"file":[{"date_updated":"2020-07-14T12:45:04Z","file_size":1603844,"creator":"dernst","date_created":"2018-12-17T12:52:12Z","file_name":"2018_LNCS_Kragl.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"5705","checksum":"c64fff560fe5a7532ec10626ad1c215e"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 10981","scopus_import":"1","alternative_title":["LNCS"],"oa_version":"Published Version","abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:04Z","ddc":["000"],"date_updated":"2023-09-13T08:45:09Z","status":"public","type":"conference","conference":{"location":"Oxford, UK","end_date":"2018-07-17","start_date":"2018-07-14","name":"CAV: Computer Aided Verification"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"160","date_published":"2018-07-18T00:00:00Z","doi":"10.1007/978-3-319-96145-3_5","date_created":"2018-12-11T11:44:57Z","page":"79 - 102","day":"18","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"title":"Layered Concurrent Programs","publist_id":"7761","author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","full_name":"Kragl, Bernhard","orcid":"0000-0001-7745-9117","last_name":"Kragl"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"article_processing_charge":"No","external_id":{"isi":["000491481600005"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5","apa":"Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5."},"project":[{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z211","name":"The Wittgenstein Prize"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}]},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","ieee":"Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018.","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7.","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7."},"title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","author":[{"full_name":"Gao, Zhen","last_name":"Gao","first_name":"Zhen"},{"last_name":"Daneva","full_name":"Daneva, Anna","first_name":"Anna"},{"full_name":"Salanenka, Yuliya","last_name":"Salanenka","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Van Durme","full_name":"Van Durme, Matthias","first_name":"Matthias"},{"full_name":"Huysmans, Marlies","last_name":"Huysmans","first_name":"Marlies"},{"first_name":"Zongcheng","full_name":"Lin, Zongcheng","last_name":"Lin"},{"first_name":"Freya","full_name":"De Winter, Freya","last_name":"De Winter"},{"first_name":"Steffen","full_name":"Vanneste, Steffen","last_name":"Vanneste"},{"first_name":"Mansour","last_name":"Karimi","full_name":"Karimi, Mansour"},{"last_name":"Van De Velde","full_name":"Van De Velde, Jan","first_name":"Jan"},{"first_name":"Klaas","full_name":"Vandepoele, Klaas","last_name":"Vandepoele"},{"last_name":"Van De Walle","full_name":"Van De Walle, Davy","first_name":"Davy"},{"first_name":"Koen","full_name":"Dewettinck, Koen","last_name":"Dewettinck"},{"first_name":"Bart","last_name":"Lambrecht","full_name":"Lambrecht, Bart"},{"full_name":"Nowack, Moritz","last_name":"Nowack","first_name":"Moritz"}],"publist_id":"7619","article_processing_charge":"No","external_id":{"isi":["000435571000017"]},"acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","publisher":"Nature Publishing Group","quality_controlled":"1","day":"28","publication":"Nature Plants","isi":1,"year":"2018","doi":"10.1038/s41477-018-0160-7","date_published":"2018-05-28T00:00:00Z","date_created":"2018-12-11T11:45:35Z","page":"365 - 375","_id":"280","status":"public","type":"journal_article","date_updated":"2023-09-13T08:24:17Z","department":[{"_id":"JiFr"}],"oa_version":"None","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"month":"05","intvolume":" 4","scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","issue":"6","volume":4},{"status":"public","type":"journal_article","_id":"503","department":[{"_id":"CaGu"}],"date_updated":"2023-09-13T08:24:51Z","month":"02","intvolume":" 268","scopus_import":"1","oa_version":"None","acknowledged_ssus":[{"_id":"Bio"}],"abstract":[{"text":"Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry.","lang":"eng"}],"volume":268,"language":[{"iso":"eng"}],"publication_status":"published","title":"Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains","author":[{"last_name":"Tomasek","orcid":"0000-0003-3768-877X","full_name":"Tomasek, Kathrin","first_name":"Kathrin","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"publist_id":"7317","article_processing_charge":"No","external_id":{"isi":["000425715100006"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008.","ista":"Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52.","mla":"Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008.","short":"K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52.","ieee":"K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018.","apa":"Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008","ama":"Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008"},"quality_controlled":"1","publisher":"Elsevier","acknowledgement":"We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n","doi":"10.1016/j.jbiotec.2018.01.008","date_published":"2018-02-20T00:00:00Z","date_created":"2018-12-11T11:46:50Z","page":"40 - 52","day":"20","publication":"Journal of Biotechnology","isi":1,"year":"2018"},{"article_number":"2005971","author":[{"first_name":"Waqas","full_name":"Chaudhry, Waqas","last_name":"Chaudhry"},{"orcid":"0000-0001-7460-7479","full_name":"Pleska, Maros","last_name":"Pleska","id":"4569785E-F248-11E8-B48F-1D18A9856A87","first_name":"Maros"},{"full_name":"Shah, Nilang","last_name":"Shah","first_name":"Nilang"},{"first_name":"Howard","last_name":"Weiss","full_name":"Weiss, Howard"},{"first_name":"Ingrid","full_name":"Mccall, Ingrid","last_name":"Mccall"},{"first_name":"Justin","last_name":"Meyer","full_name":"Meyer, Justin"},{"full_name":"Gupta, Animesh","last_name":"Gupta","first_name":"Animesh"},{"last_name":"Guet","full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bruce","last_name":"Levin","full_name":"Levin, Bruce"}],"publist_id":"7972","article_processing_charge":"Yes","external_id":{"isi":["000443383300024"]},"title":"Leaky resistance and the conditions for the existence of lytic bacteriophage","citation":{"chicago":"Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.","ista":"Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971.","mla":"Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.","short":"W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018).","ieee":"W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018.","ama":"Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971","apa":"Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"doi":"10.1371/journal.pbio.2005971","date_published":"2018-08-16T00:00:00Z","date_created":"2018-12-11T11:44:32Z","has_accepted_license":"1","isi":1,"year":"2018","day":"16","publication":"PLoS Biology","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"82","department":[{"_id":"CaGu"}],"file_date_updated":"2020-07-14T12:48:10Z","date_updated":"2023-09-13T08:45:41Z","ddc":["570"],"scopus_import":"1","month":"08","intvolume":" 16","abstract":[{"lang":"eng","text":"In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”."}],"oa_version":"Published Version","related_material":{"record":[{"relation":"research_data","id":"9810","status":"public"}]},"volume":16,"issue":"8","publication_status":"published","file":[{"file_size":4007095,"date_updated":"2020-07-14T12:48:10Z","creator":"dernst","file_name":"2018_Plos_Chaudhry.pdf","date_created":"2018-12-17T12:55:31Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5706","checksum":"527076f78265cd4ea192cd1569851587"}],"language":[{"iso":"eng"}]},{"date_updated":"2023-09-13T08:46:15Z","ddc":["003","004"],"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"BeBi"}],"_id":"4","type":"journal_article","status":"public","pubrep_id":"1049","publication_status":"published","file":[{"file_name":"IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf","date_created":"2018-12-12T10:16:28Z","file_size":22803163,"date_updated":"2020-07-14T12:46:22Z","creator":"system","file_id":"5216","checksum":"7a2243668f215821bc6aecad0320079a","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"4","volume":37,"ec_funded":1,"abstract":[{"text":"We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body.","lang":"eng"}],"oa_version":"Submitted Version","scopus_import":"1","month":"08","intvolume":" 37","citation":{"mla":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325.","ama":"Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325","apa":"Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325","ieee":"N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.","short":"N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018).","chicago":"Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325.","ista":"Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Umetani, Nobuyuki","last_name":"Umetani","first_name":"Nobuyuki"},{"last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"publist_id":"8053","external_id":{"isi":["000448185000050"]},"article_processing_charge":"No","title":"Learning three-dimensional flow for interactive aerodynamic design","article_number":"89","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"04","publication":"ACM Trans. Graph.","date_published":"2018-08-04T00:00:00Z","doi":"10.1145/3197517.3201325","date_created":"2018-12-11T11:44:06Z","quality_controlled":"1","publisher":"ACM","oa":1}]