[{"citation":{"short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624.","ieee":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, and O. Bachem, “On the fairness of disentangled representations,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14611–14624.","ama":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. On the fairness of disentangled representations. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14611–14624.","apa":"Locatello, F., Abbati, G., Rainforth, T., Bauer, S., Schölkopf, B., & Bachem, O. (2019). On the fairness of disentangled representations. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14611–14624). Vancouver, Canada.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14611–14624.","ista":"Locatello F, Abbati G, Rainforth T, Bauer S, Schölkopf B, Bachem O. 2019. On the fairness of disentangled representations. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14611–14624.","chicago":"Locatello, Francesco, Gabriele Abbati, Tom Rainforth, Stefan Bauer, Bernhard Schölkopf, and Olivier Bachem. “On the Fairness of Disentangled Representations.” In Advances in Neural Information Processing Systems, 32:14611–14624, 2019."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Gabriele","last_name":"Abbati","full_name":"Abbati, Gabriele"},{"last_name":"Rainforth","full_name":"Rainforth, Tom","first_name":"Tom"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"external_id":{"arxiv":["1905.13662"]},"article_processing_charge":"No","title":"On the fairness of disentangled representations","quality_controlled":"1","oa":1,"year":"2019","day":"08","publication":"Advances in Neural Information Processing Systems","page":"14611–14624","date_published":"2019-12-08T00:00:00Z","date_created":"2023-08-22T14:12:28Z","_id":"14197","type":"conference","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14","location":"Vancouver, Canada"},"status":"public","date_updated":"2023-09-12T09:37:22Z","extern":"1","department":[{"_id":"FrLo"}],"abstract":[{"lang":"eng","text":"Recently there has been a significant interest in learning disentangled\r\nrepresentations, as they promise increased interpretability, generalization to\r\nunseen scenarios and faster learning on downstream tasks. In this paper, we\r\ninvestigate the usefulness of different notions of disentanglement for\r\nimproving the fairness of downstream prediction tasks based on representations.\r\nWe consider the setting where the goal is to predict a target variable based on\r\nthe learned representation of high-dimensional observations (such as images)\r\nthat depend on both the target variable and an \\emph{unobserved} sensitive\r\nvariable. We show that in this setting both the optimal and empirical\r\npredictions can be unfair, even if the target variable and the sensitive\r\nvariable are independent. Analyzing the representations of more than\r\n\\num{12600} trained state-of-the-art disentangled models, we observe that\r\nseveral disentanglement scores are consistently correlated with increased\r\nfairness, suggesting that disentanglement may be a useful property to encourage\r\nfairness when sensitive variables are not observed."}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1905.13662","open_access":"1"}],"month":"12","intvolume":" 32","publication_identifier":{"isbn":["9781713807933"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":32},{"publication":"Advances in Neural Information Processing Systems","day":"29","year":"2019","date_created":"2023-08-22T14:09:35Z","date_published":"2019-12-29T00:00:00Z","page":"14291–14301","oa":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","ama":"Locatello F, Yurtsever A, Fercoq O, Cevher V. Stochastic Frank-Wolfe for composite convex minimization. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019:14291–14301.","apa":"Locatello, F., Yurtsever, A., Fercoq, O., & Cevher, V. (2019). Stochastic Frank-Wolfe for composite convex minimization. In Advances in Neural Information Processing Systems (Vol. 32, pp. 14291–14301). Vancouver, Canada.","ieee":"F. Locatello, A. Yurtsever, O. Fercoq, and V. Cevher, “Stochastic Frank-Wolfe for composite convex minimization,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32, pp. 14291–14301.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","chicago":"Locatello, Francesco, Alp Yurtsever, Olivier Fercoq, and Volkan Cevher. “Stochastic Frank-Wolfe for Composite Convex Minimization.” In Advances in Neural Information Processing Systems, 32:14291–14301, 2019.","ista":"Locatello F, Yurtsever A, Fercoq O, Cevher V. 2019. Stochastic Frank-Wolfe for composite convex minimization. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32, 14291–14301."},"title":"Stochastic Frank-Wolfe for composite convex minimization","external_id":{"arxiv":["1901.10348"]},"article_processing_charge":"No","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"first_name":"Alp","last_name":"Yurtsever","full_name":"Yurtsever, Alp"},{"full_name":"Fercoq, Olivier","last_name":"Fercoq","first_name":"Olivier"},{"first_name":"Volkan","last_name":"Cevher","full_name":"Cevher, Volkan"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781713807933"]},"volume":32,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"A broad class of convex optimization problems can be formulated as a semidefinite program (SDP), minimization of a convex function over the positive-semidefinite cone subject to some affine constraints. The majority of classical SDP solvers are designed for the deterministic setting where problem data is readily available. In this setting, generalized conditional gradient methods (aka Frank-Wolfe-type methods) provide scalable solutions by leveraging the so-called linear minimization oracle instead of the projection onto the semidefinite cone. Most problems in machine learning and modern engineering applications, however, contain some degree of stochasticity. In this work, we propose the first conditional-gradient-type method for solving stochastic optimization problems under affine constraints. Our method guarantees O(k−1/3) convergence rate in expectation on the objective residual and O(k−5/12) on the feasibility gap."}],"intvolume":" 32","month":"12","main_file_link":[{"url":"https://arxiv.org/abs/1901.10348","open_access":"1"}],"scopus_import":"1","extern":"1","date_updated":"2023-09-12T08:48:45Z","department":[{"_id":"FrLo"}],"_id":"14191","status":"public","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2019-12-08","end_date":"2019-12-14","location":"Vancouver, Canada"},"type":"conference"},{"status":"public","conference":{"start_date":"2019-12-08","end_date":"2019-12-14","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems"},"type":"conference","_id":"14193","title":"Are disentangled representations helpful for abstract visual reasoning?","department":[{"_id":"FrLo"}],"external_id":{"arxiv":["1905.12506"]},"article_processing_charge":"No","author":[{"first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste"},{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello"},{"full_name":"Schmidhuber, Jürgen","last_name":"Schmidhuber","first_name":"Jürgen"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","ieee":"S. van Steenkiste, F. Locatello, J. Schmidhuber, and O. Bachem, “Are disentangled representations helpful for abstract visual reasoning?,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32.","ama":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. Are disentangled representations helpful for abstract visual reasoning? In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","apa":"Steenkiste, S. van, Locatello, F., Schmidhuber, J., & Bachem, O. (2019). Are disentangled representations helpful for abstract visual reasoning? In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 2019.","ista":"Steenkiste S van, Locatello F, Schmidhuber J, Bachem O. 2019. Are disentangled representations helpful for abstract visual reasoning? Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","chicago":"Steenkiste, Sjoerd van, Francesco Locatello, Jürgen Schmidhuber, and Olivier Bachem. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” In Advances in Neural Information Processing Systems, Vol. 32, 2019."},"date_updated":"2023-09-12T09:02:43Z","intvolume":" 32","month":"05","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","abstract":[{"text":"A disentangled representation encodes information about the salient factors\r\nof variation in the data independently. Although it is often argued that this\r\nrepresentational format is useful in learning to solve many real-world\r\ndown-stream tasks, there is little empirical evidence that supports this claim.\r\nIn this paper, we conduct a large-scale study that investigates whether\r\ndisentangled representations are more suitable for abstract reasoning tasks.\r\nUsing two new tasks similar to Raven's Progressive Matrices, we evaluate the\r\nusefulness of the representations learned by 360 state-of-the-art unsupervised\r\ndisentanglement models. Based on these representations, we train 3600 abstract\r\nreasoning models and observe that disentangled representations do in fact lead\r\nto better down-stream performance. In particular, they enable quicker learning\r\nusing fewer samples.","lang":"eng"}],"date_created":"2023-08-22T14:09:53Z","date_published":"2019-05-29T00:00:00Z","volume":32,"publication":"Advances in Neural Information Processing Systems","language":[{"iso":"eng"}],"day":"29","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781713807933"]}},{"status":"public","conference":{"name":"International Conference on Machine Learning","location":"Long Beach, CA, United States","end_date":"2019-06-15","start_date":"2019-06-10"},"type":"conference","_id":"14200","department":[{"_id":"FrLo"}],"extern":"1","date_updated":"2023-09-13T07:45:30Z","intvolume":" 97","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The key idea behind the unsupervised learning of disentangled representations\r\nis that real-world data is generated by a few explanatory factors of variation\r\nwhich can be recovered by unsupervised learning algorithms. In this paper, we\r\nprovide a sober look at recent progress in the field and challenge some common\r\nassumptions. We first theoretically show that the unsupervised learning of\r\ndisentangled representations is fundamentally impossible without inductive\r\nbiases on both the models and the data. Then, we train more than 12000 models\r\ncovering most prominent methods and evaluation metrics in a reproducible\r\nlarge-scale experimental study on seven different data sets. We observe that\r\nwhile the different methods successfully enforce properties ``encouraged'' by\r\nthe corresponding losses, well-disentangled models seemingly cannot be\r\nidentified without supervision. Furthermore, increased disentanglement does not\r\nseem to lead to a decreased sample complexity of learning for downstream tasks.\r\nOur results suggest that future work on disentanglement learning should be\r\nexplicit about the role of inductive biases and (implicit) supervision,\r\ninvestigate concrete benefits of enforcing disentanglement of the learned\r\nrepresentations, and consider a reproducible experimental setup covering\r\nseveral data sets."}],"volume":97,"language":[{"iso":"eng"}],"publication_status":"published","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","external_id":{"arxiv":["1811.12359"]},"article_processing_charge":"No","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” In Proceedings of the 36th International Conference on Machine Learning, 97:4114–24. ML Research Press, 2019.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2019. Challenging common assumptions in the unsupervised learning of disentangled representations. Proceedings of the 36th International Conference on Machine Learning. International Conference on Machine Learning vol. 97, 4114–4124.","mla":"Locatello, Francesco, et al. “Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations.” Proceedings of the 36th International Conference on Machine Learning, vol. 97, ML Research Press, 2019, pp. 4114–24.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2019). Challenging common assumptions in the unsupervised learning of disentangled representations. In Proceedings of the 36th International Conference on Machine Learning (Vol. 97, pp. 4114–4124). Long Beach, CA, United States: ML Research Press.","ama":"Locatello F, Bauer S, Lucic M, et al. Challenging common assumptions in the unsupervised learning of disentangled representations. In: Proceedings of the 36th International Conference on Machine Learning. Vol 97. ML Research Press; 2019:4114-4124.","ieee":"F. Locatello et al., “Challenging common assumptions in the unsupervised learning of disentangled representations,” in Proceedings of the 36th International Conference on Machine Learning, Long Beach, CA, United States, 2019, vol. 97, pp. 4114–4124.","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, Proceedings of the 36th International Conference on Machine Learning, ML Research Press, 2019, pp. 4114–4124."},"oa":1,"publisher":"ML Research Press","quality_controlled":"1","date_created":"2023-08-22T14:13:08Z","date_published":"2019-06-09T00:00:00Z","page":"4114-4124","publication":"Proceedings of the 36th International Conference on Machine Learning","day":"09","year":"2019"},{"has_accepted_license":"1","isi":1,"year":"2019","day":"10","publication":"Soft Matter","page":"602-614","date_published":"2019-01-10T00:00:00Z","doi":"10.1039/c8sm01956h","date_created":"2019-01-11T07:37:47Z","quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"citation":{"chicago":"Kavcic, Bor, A. Sakashita, H. Noguchi, and P. Ziherl. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter. Royal Society of Chemistry, 2019. https://doi.org/10.1039/c8sm01956h.","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614.","mla":"Kavcic, Bor, et al. “Limiting Shapes of Confined Lipid Vesicles.” Soft Matter, vol. 15, no. 4, Royal Society of Chemistry, 2019, pp. 602–14, doi:10.1039/c8sm01956h.","apa":"Kavcic, B., Sakashita, A., Noguchi, H., & Ziherl, P. (2019). Limiting shapes of confined lipid vesicles. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/c8sm01956h","ama":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. Limiting shapes of confined lipid vesicles. Soft Matter. 2019;15(4):602-614. doi:10.1039/c8sm01956h","short":"B. Kavcic, A. Sakashita, H. Noguchi, P. Ziherl, Soft Matter 15 (2019) 602–614.","ieee":"B. Kavcic, A. Sakashita, H. Noguchi, and P. Ziherl, “Limiting shapes of confined lipid vesicles,” Soft Matter, vol. 15, no. 4. Royal Society of Chemistry, pp. 602–614, 2019."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","last_name":"Kavcic","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"first_name":"A.","full_name":"Sakashita, A.","last_name":"Sakashita"},{"first_name":"H.","last_name":"Noguchi","full_name":"Noguchi, H."},{"full_name":"Ziherl, P.","last_name":"Ziherl","first_name":"P."}],"article_processing_charge":"No","external_id":{"isi":["000457329700003"],"pmid":["30629082"]},"title":"Limiting shapes of confined lipid vesicles","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"publication_status":"published","file":[{"file_id":"8641","checksum":"614c337d6424ccd3d48d1b1f9513510d","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-10-09T11:00:05Z","file_name":"lmt_sftmtr_V8.pdf","creator":"bkavcic","date_updated":"2020-10-09T11:00:05Z","file_size":5370762}],"language":[{"iso":"eng"}],"issue":"4","volume":15,"abstract":[{"lang":"eng","text":"We theoretically study the shapes of lipid vesicles confined to a spherical cavity, elaborating a framework based on the so-called limiting shapes constructed from geometrically simple structural elements such as double-membrane walls and edges. Partly inspired by numerical results, the proposed non-compartmentalized and compartmentalized limiting shapes are arranged in the bilayer-couple phase diagram which is then compared to its free-vesicle counterpart. We also compute the area-difference-elasticity phase diagram of the limiting shapes and we use it to interpret shape transitions experimentally observed in vesicles confined within another vesicle. The limiting-shape framework may be generalized to theoretically investigate the structure of certain cell organelles such as the mitochondrion."}],"oa_version":"Submitted Version","pmid":1,"scopus_import":"1","month":"01","intvolume":" 15","date_updated":"2023-09-13T08:47:16Z","ddc":["530"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-10-09T11:00:05Z","_id":"5817","type":"journal_article","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode","short":"CC BY-NC-ND (3.0)"},"status":"public"},{"abstract":[{"lang":"eng","text":"We consider the space of probability measures on a discrete set X, endowed with a dynamical optimal transport metric. Given two probability measures supported in a subset Y⊆X, it is natural to ask whether they can be connected by a constant speed geodesic with support in Y at all times. Our main result answers this question affirmatively, under a suitable geometric condition on Y introduced in this paper. The proof relies on an extension result for subsolutions to discrete Hamilton-Jacobi equations, which is of independent interest."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 58","publication_identifier":{"issn":["09442669"]},"publication_status":"published","file":[{"creator":"dernst","file_size":645565,"date_updated":"2020-07-14T12:47:55Z","file_name":"2018_Calculus_Erbar.pdf","date_created":"2019-01-28T15:37:11Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"ba05ac2d69de4c58d2cd338b63512798","file_id":"5895"}],"language":[{"iso":"eng"}],"issue":"1","volume":58,"ec_funded":1,"_id":"73","type":"journal_article","article_type":"original","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","date_updated":"2023-09-13T09:12:35Z","ddc":["510"],"department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:47:55Z","publisher":"Springer","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2019","day":"01","publication":"Calculus of Variations and Partial Differential Equations","doi":"10.1007/s00526-018-1456-1","date_published":"2019-02-01T00:00:00Z","date_created":"2018-12-11T11:44:29Z","article_number":"19","project":[{"grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"260482E2-B435-11E9-9278-68D0E5697425","name":"Taming Complexity in Partial Di erential Systems","grant_number":" F06504"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"citation":{"apa":"Erbar, M., Maas, J., & Wirth, M. (2019). On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. Springer. https://doi.org/10.1007/s00526-018-1456-1","ama":"Erbar M, Maas J, Wirth M. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 2019;58(1). doi:10.1007/s00526-018-1456-1","short":"M. Erbar, J. Maas, M. Wirth, Calculus of Variations and Partial Differential Equations 58 (2019).","ieee":"M. Erbar, J. Maas, and M. Wirth, “On the geometry of geodesics in discrete optimal transport,” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1. Springer, 2019.","mla":"Erbar, Matthias, et al. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations, vol. 58, no. 1, 19, Springer, 2019, doi:10.1007/s00526-018-1456-1.","ista":"Erbar M, Maas J, Wirth M. 2019. On the geometry of geodesics in discrete optimal transport. Calculus of Variations and Partial Differential Equations. 58(1), 19.","chicago":"Erbar, Matthias, Jan Maas, and Melchior Wirth. “On the Geometry of Geodesics in Discrete Optimal Transport.” Calculus of Variations and Partial Differential Equations. Springer, 2019. https://doi.org/10.1007/s00526-018-1456-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Matthias","full_name":"Erbar, Matthias","last_name":"Erbar"},{"last_name":"Maas","orcid":"0000-0002-0845-1338","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Wirth, Melchior","last_name":"Wirth","first_name":"Melchior"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["1805.06040"],"isi":["000452849400001"]},"title":"On the geometry of geodesics in discrete optimal transport"},{"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Learning meaningful and compact representations with disentangled semantic\r\naspects is considered to be of key importance in representation learning. Since\r\nreal-world data is notoriously costly to collect, many recent state-of-the-art\r\ndisentanglement models have heavily relied on synthetic toy data-sets. In this\r\npaper, we propose a novel data-set which consists of over one million images of\r\nphysical 3D objects with seven factors of variation, such as object color,\r\nshape, size and position. In order to be able to control all the factors of\r\nvariation precisely, we built an experimental platform where the objects are\r\nbeing moved by a robotic arm. In addition, we provide two more datasets which\r\nconsist of simulations of the experimental setup. These datasets provide for\r\nthe first time the possibility to systematically investigate how well different\r\ndisentanglement methods perform on real data in comparison to simulation, and\r\nhow simulated data can be leveraged to build better representations of the real\r\nworld. We provide a first experimental study of these questions and our results\r\nindicate that learned models transfer poorly, but that model and hyperparameter\r\nselection is an effective means of transferring information to the real world."}],"intvolume":" 32","month":"06","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"quality_controlled":"1","language":[{"iso":"eng"}],"publication":"Advances in Neural Information Processing Systems","day":"07","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781713807933"]},"date_created":"2023-08-22T14:09:13Z","date_published":"2019-06-07T00:00:00Z","volume":32,"_id":"14190","status":"public","conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","end_date":"2019-12-14","start_date":"2019-12-08"},"type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","extern":"1","date_updated":"2023-09-13T09:46:38Z","citation":{"chicago":"Gondal, Muhammad Waleed, Manuel Wüthrich, Đorđe Miladinović, Francesco Locatello, Martin Breidt, Valentin Volchkov, Joel Akpo, Olivier Bachem, Bernhard Schölkopf, and Stefan Bauer. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” In Advances in Neural Information Processing Systems, Vol. 32, 2019.","ista":"Gondal MW, Wüthrich M, Miladinović Đ, Locatello F, Breidt M, Volchkov V, Akpo J, Bachem O, Schölkopf B, Bauer S. 2019. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. Advances in Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 32.","mla":"Gondal, Muhammad Waleed, et al. “On the Transfer of Inductive Bias from Simulation to the Real World: A New Disentanglement Dataset.” Advances in Neural Information Processing Systems, vol. 32, 2019.","ama":"Gondal MW, Wüthrich M, Miladinović Đ, et al. On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In: Advances in Neural Information Processing Systems. Vol 32. ; 2019.","apa":"Gondal, M. W., Wüthrich, M., Miladinović, Đ., Locatello, F., Breidt, M., Volchkov, V., … Bauer, S. (2019). On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset. In Advances in Neural Information Processing Systems (Vol. 32). Vancouver, Canada.","short":"M.W. Gondal, M. Wüthrich, Đ. Miladinović, F. Locatello, M. Breidt, V. Volchkov, J. Akpo, O. Bachem, B. Schölkopf, S. Bauer, in:, Advances in Neural Information Processing Systems, 2019.","ieee":"M. W. Gondal et al., “On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset,” in Advances in Neural Information Processing Systems, Vancouver, Canada, 2019, vol. 32."},"department":[{"_id":"FrLo"}],"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","article_processing_charge":"No","external_id":{"arxiv":["1906.03292"]},"author":[{"first_name":"Muhammad Waleed","last_name":"Gondal","full_name":"Gondal, Muhammad Waleed"},{"first_name":"Manuel","full_name":"Wüthrich, Manuel","last_name":"Wüthrich"},{"first_name":"Đorđe","last_name":"Miladinović","full_name":"Miladinović, Đorđe"},{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"first_name":"Martin","last_name":"Breidt","full_name":"Breidt, Martin"},{"last_name":"Volchkov","full_name":"Volchkov, Valentin","first_name":"Valentin"},{"first_name":"Joel","full_name":"Akpo, Joel","last_name":"Akpo"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"},{"last_name":"Schölkopf","full_name":"Schölkopf, Bernhard","first_name":"Bernhard"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"}]},{"status":"public","type":"journal_article","article_type":"original","_id":"6982","department":[{"_id":"UlWa"}],"date_updated":"2023-09-15T12:19:31Z","month":"10","intvolume":" 15","scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.09209"}],"oa_version":"Preprint","abstract":[{"text":"We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding ϕ : G → M of a graph G into a 2-manifold M maps the vertices in V(G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to the same point or overlapping arcs due to data compression or low resolution. This raises the computational problem of deciding whether a given map ϕ : G → M comes from an embedding. A map ϕ : G → M is a weak embedding if it can be perturbed into an embedding ψ ϵ : G → M with ‖ ϕ − ψ ϵ ‖ < ϵ for every ϵ > 0, where ‖.‖ is the unform norm.\r\nA polynomial-time algorithm for recognizing weak embeddings has recently been found by Fulek and Kynčl. It reduces the problem to solving a system of linear equations over Z2. It runs in O(n2ω)≤ O(n4.75) time, where ω ∈ [2,2.373) is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler: We perform a sequence of local operations that gradually “untangles” the image ϕ(G) into an embedding ψ(G) or reports that ϕ is not a weak embedding. It combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.\r\n","lang":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"309","status":"public"}]},"issue":"4","volume":15,"language":[{"iso":"eng"}],"publication_status":"published","project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs"}],"article_number":"50","title":"Recognizing weak embeddings of graphs","author":[{"full_name":"Akitaya, Hugo","last_name":"Akitaya","first_name":"Hugo"},{"last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Csaba","full_name":"Tóth, Csaba","last_name":"Tóth"}],"external_id":{"arxiv":["1709.09209"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Akitaya, Hugo, et al. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms, vol. 15, no. 4, 50, ACM, 2019, doi:10.1145/3344549.","ama":"Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 2019;15(4). doi:10.1145/3344549","apa":"Akitaya, H., Fulek, R., & Tóth, C. (2019). Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. ACM. https://doi.org/10.1145/3344549","ieee":"H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” ACM Transactions on Algorithms, vol. 15, no. 4. ACM, 2019.","short":"H. Akitaya, R. Fulek, C. Tóth, ACM Transactions on Algorithms 15 (2019).","chicago":"Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs.” ACM Transactions on Algorithms. ACM, 2019. https://doi.org/10.1145/3344549.","ista":"Akitaya H, Fulek R, Tóth C. 2019. Recognizing weak embeddings of graphs. ACM Transactions on Algorithms. 15(4), 50."},"publisher":"ACM","quality_controlled":"1","oa":1,"doi":"10.1145/3344549","date_published":"2019-10-01T00:00:00Z","date_created":"2019-11-04T15:45:17Z","day":"01","publication":"ACM Transactions on Algorithms","year":"2019"},{"year":"2019","has_accepted_license":"1","day":"30","page":"132","date_created":"2019-09-22T14:08:44Z","doi":"10.15479/AT:ISTA:6894","date_published":"2019-09-30T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"ista":"Giacobbe M. 2019. Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria.","chicago":"Giacobbe, Mirco. “Automatic Time-Unbounded Reachability Analysis of Hybrid Systems.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6894.","apa":"Giacobbe, M. (2019). Automatic time-unbounded reachability analysis of hybrid systems. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6894","ama":"Giacobbe M. Automatic time-unbounded reachability analysis of hybrid systems. 2019. doi:10.15479/AT:ISTA:6894","short":"M. Giacobbe, Automatic Time-Unbounded Reachability Analysis of Hybrid Systems, Institute of Science and Technology Austria, 2019.","ieee":"M. Giacobbe, “Automatic time-unbounded reachability analysis of hybrid systems,” Institute of Science and Technology Austria, 2019.","mla":"Giacobbe, Mirco. Automatic Time-Unbounded Reachability Analysis of Hybrid Systems. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6894."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","author":[{"last_name":"Giacobbe","full_name":"Giacobbe, Mirco","orcid":"0000-0001-8180-0904","id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","first_name":"Mirco"}],"title":"Automatic time-unbounded reachability analysis of hybrid systems","degree_awarded":"PhD","publication_status":"published","publication_identifier":{"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"773beaf4a85dc2acc2c12b578fbe1965","file_id":"6916","creator":"mgiacobbe","file_size":4100685,"date_updated":"2020-07-14T12:47:43Z","file_name":"giacobbe_thesis.pdf","date_created":"2019-09-27T14:15:05Z"},{"file_size":7959732,"date_updated":"2020-07-14T12:47:43Z","creator":"mgiacobbe","file_name":"giacobbe_thesis_src.tar.gz","date_created":"2019-09-27T14:22:04Z","content_type":"application/gzip","relation":"source_file","access_level":"closed","file_id":"6917","checksum":"97f1c3da71feefd27e6e625d32b4c75b"}],"related_material":{"record":[{"status":"public","id":"631","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"647"},{"relation":"part_of_dissertation","id":"140","status":"public"}]},"abstract":[{"text":"Hybrid automata combine finite automata and dynamical systems, and model the interaction of digital with physical systems. Formal analysis that can guarantee the safety of all behaviors or rigorously witness failures, while unsolvable in general, has been tackled algorithmically using, e.g., abstraction, bounded model-checking, assisted theorem proving.\r\nNevertheless, very few methods have addressed the time-unbounded reachability analysis of hybrid automata and, for current sound and automatic tools, scalability remains critical. We develop methods for the polyhedral abstraction of hybrid automata, which construct coarse overapproximations and tightens them incrementally, in a CEGAR fashion. We use template polyhedra, i.e., polyhedra whose facets are normal to a given set of directions.\r\nWhile, previously, directions were given by the user, we introduce (1) the first method\r\nfor computing template directions from spurious counterexamples, so as to generalize and\r\neliminate them. The method applies naturally to convex hybrid automata, i.e., hybrid\r\nautomata with (possibly non-linear) convex constraints on derivatives only, while for linear\r\nODE requires further abstraction. Specifically, we introduce (2) the conic abstractions,\r\nwhich, partitioning the state space into appropriate (possibly non-uniform) cones, divide\r\ncurvy trajectories into relatively straight sections, suitable for polyhedral abstractions.\r\nFinally, we introduce (3) space-time interpolation, which, combining interval arithmetic\r\nand template refinement, computes appropriate (possibly non-uniform) time partitioning\r\nand template directions along spurious trajectories, so as to eliminate them.\r\nWe obtain sound and automatic methods for the reachability analysis over dense\r\nand unbounded time of convex hybrid automata and hybrid automata with linear ODE.\r\nWe build prototype tools and compare—favorably—our methods against the respective\r\nstate-of-the-art tools, on several benchmarks.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","date_updated":"2023-09-19T09:30:43Z","supervisor":[{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"ddc":["000"],"file_date_updated":"2020-07-14T12:47:43Z","department":[{"_id":"ToHe"}],"_id":"6894","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)"},"type":"dissertation","status":"public"},{"article_processing_charge":"No","author":[{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H"}],"department":[{"_id":"NiBa"}],"title":"Data from: The consequences of an introgression event","citation":{"ista":"Barton NH. 2019. Data from: The consequences of an introgression event, Dryad, 10.5061/dryad.2kb6fh4.","chicago":"Barton, Nicholas H. “Data from: The Consequences of an Introgression Event.” Dryad, 2019. https://doi.org/10.5061/dryad.2kb6fh4.","short":"N.H. Barton, (2019).","ieee":"N. H. Barton, “Data from: The consequences of an introgression event.” Dryad, 2019.","apa":"Barton, N. H. (2019). Data from: The consequences of an introgression event. Dryad. https://doi.org/10.5061/dryad.2kb6fh4","ama":"Barton NH. Data from: The consequences of an introgression event. 2019. doi:10.5061/dryad.2kb6fh4","mla":"Barton, Nicholas H. Data from: The Consequences of an Introgression Event. Dryad, 2019, doi:10.5061/dryad.2kb6fh4."},"date_updated":"2023-09-19T10:06:07Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"research_data_reference","status":"public","_id":"9805","date_created":"2021-08-06T12:03:50Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"40"}]},"doi":"10.5061/dryad.2kb6fh4","date_published":"2019-01-09T00:00:00Z","year":"2019","day":"09","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.2kb6fh4","open_access":"1"}],"publisher":"Dryad","month":"01","abstract":[{"lang":"eng","text":"The spread of adaptive alleles is fundamental to evolution, and in theory, this process is well‐understood. However, only rarely can we follow this process—whether it originates from the spread of a new mutation, or by introgression from another population. In this issue of Molecular Ecology, Hanemaaijer et al. (2018) report on a 25‐year long study of the mosquitoes Anopheles gambiae (Figure 1) and Anopheles coluzzi in Mali, based on genotypes at 15 single‐nucleotide polymorphism (SNP). The species are usually reproductively isolated from each other, but in 2002 and 2006, bursts of hybridization were observed, when F1 hybrids became abundant. Alleles backcrossed from A. gambiae into A. coluzzi, but after the first event, these declined over the following years. In contrast, after 2006, an insecticide resistance allele that had established in A. gambiae spread into A. coluzzi, and rose to high frequency there, over 6 years (~75 generations). Whole genome sequences of 74 individuals showed that A. gambiae SNP from across the genome had become common in the A. coluzzi population, but that most of these were clustered in 34 genes around the resistance locus. A new set of SNP from 25 of these genes were assayed over time; over the 4 years since near‐fixation of the resistance allele; some remained common, whereas others declined. What do these patterns tell us about this introgression event?"}],"oa_version":"Published Version"},{"page":"238-255","date_published":"2019-01-09T00:00:00Z","doi":"10.1523/JNEUROSCI.1059-18.2018","date_created":"2018-12-11T11:44:07Z","has_accepted_license":"1","isi":1,"year":"2019","day":"09","publication":"Journal of Neuroscience","publisher":"Society for Neuroscience","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by INSERM, CNRS, UDS, Ligue Régionale contre le Cancer, Hôpital de Strasbourg, Association pour la Recherche sur le Cancer (ARC) and Agence Nationale de la Recherche (ANR) grants. P.B.C. was funded by the ANR and by the ARSEP (Fondation pour l'Aide à la Recherche sur la Sclérose en Plaques), and G.T. by governmental and ARC fellowships. This work was also supported by grants from the Ataxia UK (2491) and the NC3R (NC/L000199/1) awarded to M.F. The Institut de Génétique et de Biologie Moléculaire et Cellulaire was also supported by a French state fund through the ANR labex. D.E.S. was funded by Marie Curie Grant CIG 334077/IRTIM. We thank B. Altenhein, K. Brückner, M. Crozatier, L. Waltzer, M. Logan, E. Kurant, R. Reuter, E. Kurucz, J.L Dimarcq, J. Hoffmann, C. Goodman, the DHSB, and the BDSC for reagents and flies. We also thank all of the laboratory members for comments on the manuscript; C. Diebold, C. Delaporte, M. Pezze, the fly, and imaging and antibody facilities for technical assistance; and D. Dembele for help with statistics. In addition, we thank Alison Brewer for help with Luciferase assays.","author":[{"first_name":"Guillaume","full_name":"Trébuchet, Guillaume","last_name":"Trébuchet"},{"full_name":"Cattenoz, Pierre B","last_name":"Cattenoz","first_name":"Pierre B"},{"last_name":"Zsámboki","full_name":"Zsámboki, János","first_name":"János"},{"first_name":"David","full_name":"Mazaud, David","last_name":"Mazaud"},{"orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Manolis","last_name":"Fanto","full_name":"Fanto, Manolis"},{"first_name":"Angela","last_name":"Giangrande","full_name":"Giangrande, Angela"}],"publist_id":"8048","article_processing_charge":"No","external_id":{"pmid":["30504274"],"isi":["000455189900006"]},"title":"The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate","citation":{"mla":"Trébuchet, Guillaume, et al. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience, vol. 39, no. 2, Society for Neuroscience, 2019, pp. 238–55, doi:10.1523/JNEUROSCI.1059-18.2018.","short":"G. Trébuchet, P.B. Cattenoz, J. Zsámboki, D. Mazaud, D.E. Siekhaus, M. Fanto, A. Giangrande, Journal of Neuroscience 39 (2019) 238–255.","ieee":"G. Trébuchet et al., “The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate,” Journal of Neuroscience, vol. 39, no. 2. Society for Neuroscience, pp. 238–255, 2019.","ama":"Trébuchet G, Cattenoz PB, Zsámboki J, et al. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 2019;39(2):238-255. doi:10.1523/JNEUROSCI.1059-18.2018","apa":"Trébuchet, G., Cattenoz, P. B., Zsámboki, J., Mazaud, D., Siekhaus, D. E., Fanto, M., & Giangrande, A. (2019). The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.1059-18.2018","chicago":"Trébuchet, Guillaume, Pierre B Cattenoz, János Zsámboki, David Mazaud, Daria E Siekhaus, Manolis Fanto, and Angela Giangrande. “The Repo Homeodomain Transcription Factor Suppresses Hematopoiesis in Drosophila and Preserves the Glial Fate.” Journal of Neuroscience. Society for Neuroscience, 2019. https://doi.org/10.1523/JNEUROSCI.1059-18.2018.","ista":"Trébuchet G, Cattenoz PB, Zsámboki J, Mazaud D, Siekhaus DE, Fanto M, Giangrande A. 2019. The Repo homeodomain transcription factor suppresses hematopoiesis in Drosophila and preserves the glial fate. Journal of Neuroscience. 39(2), 238–255."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"}],"volume":39,"issue":"2","ec_funded":1,"publication_status":"published","file":[{"success":1,"file_id":"8596","checksum":"8f6925eb4cd1e8747d8ea25929c68de6","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2019_JournNeuroscience_Trebuchet.pdf","date_created":"2020-10-02T09:33:28Z","file_size":9455414,"date_updated":"2020-10-02T09:33:28Z","creator":"dernst"}],"language":[{"iso":"eng"}],"scopus_import":"1","month":"01","intvolume":" 39","abstract":[{"text":"Despite their different origins, Drosophila glia and hemocytes are related cell populations that provide an immune function. Drosophila hemocytes patrol the body cavity and act as macrophages outside the nervous system whereas glia originate from the neuroepithelium and provide the scavenger population of the nervous system. Drosophila glia are hence the functional orthologs of vertebrate microglia, even though the latter are cells of immune origin that subsequently move into the brain during development. Interestingly, the Drosophila immune cells within (glia) and outside the nervous system (hemocytes) require the same transcription factor Glide/Gcm for their development. This raises the issue of how do glia specifically differentiate in the nervous system and hemocytes in the procephalic mesoderm. The Repo homeodomain transcription factor and pan-glial direct target of Glide/Gcm is known to ensure glial terminal differentiation. Here we show that Repo also takes center stage in the process that discriminates between glia and hemocytes. First, Repo expression is repressed in the hemocyte anlagen by mesoderm-specific factors. Second, Repo ectopic activation in the procephalic mesoderm is sufficient to repress the expression of hemocyte-specific genes. Third, the lack of Repo triggers the expression of hemocyte markers in glia. Thus, a complex network of tissue-specific cues biases the potential of Glide/Gcm. These data allow us to revise the concept of fate determinants and help us understand the bases of cell specification. Both sexes were analyzed.SIGNIFICANCE STATEMENTDistinct cell types often require the same pioneer transcription factor, raising the issue of how does one factor trigger different fates. In Drosophila, glia and hemocytes provide a scavenger activity within and outside the nervous system, respectively. While they both require the Glide/Gcm transcription factor, glia originate from the ectoderm, hemocytes from the mesoderm. Here we show that tissue-specific factors inhibit the gliogenic potential of Glide/Gcm in the mesoderm by repressing the expression of the homeodomain protein Repo, a major glial-specific target of Glide/Gcm. Repo expression in turn inhibits the expression of hemocyte-specific genes in the nervous system. These cell-specific networks secure the establishment of the glial fate only in the nervous system and allow cell diversification.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"DaSi"}],"file_date_updated":"2020-10-02T09:33:28Z","date_updated":"2023-09-19T10:10:55Z","ddc":["570"],"article_type":"original","type":"journal_article","status":"public","_id":"8"},{"date_published":"2019-06-01T00:00:00Z","doi":"10.1112/jlms.12193","date_created":"2018-12-11T11:44:06Z","page":"778-806","day":"01","publication":"Journal of the London Mathematical Society","isi":1,"has_accepted_license":"1","year":"2019","quality_controlled":"1","publisher":"Wiley","oa":1,"title":"The wonderful compactification for quantum groups","author":[{"last_name":"Ganev","full_name":"Ganev, Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","first_name":"Iordan V"}],"publist_id":"8052","external_id":{"isi":["000470025900008"]},"article_processing_charge":"Yes (via OA deal)","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 778–806, doi:10.1112/jlms.12193.","ieee":"I. V. Ganev, “The wonderful compactification for quantum groups,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 778–806, 2019.","short":"I.V. Ganev, Journal of the London Mathematical Society 99 (2019) 778–806.","apa":"Ganev, I. V. (2019). The wonderful compactification for quantum groups. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12193","ama":"Ganev IV. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 2019;99(3):778-806. doi:10.1112/jlms.12193","chicago":"Ganev, Iordan V. “The Wonderful Compactification for Quantum Groups.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12193.","ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806."},"volume":99,"issue":"3","file":[{"creator":"kschuh","date_updated":"2020-07-14T12:46:35Z","file_size":431754,"date_created":"2020-01-07T13:31:53Z","file_name":"2019_Wiley_Ganev.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"7238","checksum":"1be56239b2cd740a0e9a084f773c22f6"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"06","intvolume":" 99","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this paper, we introduce a quantum version of the wonderful compactification of a group as a certain noncommutative projective scheme. Our approach stems from the fact that the wonderful compactification encodes the asymptotics of matrix coefficients, and from its realization as a GIT quotient of the Vinberg semigroup. In order to define the wonderful compactification for a quantum group, we adopt a generalized formalism of Proj categories in the spirit of Artin and Zhang. Key to our construction is a quantum version of the Vinberg semigroup, which we define as a q-deformation of a certain Rees algebra, compatible with a standard Poisson structure. Furthermore, we discuss quantum analogues of the stratification of the wonderful compactification by orbits for a certain group action, and provide explicit computations in the case of SL2."}],"department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:46:35Z","ddc":["510"],"date_updated":"2023-09-19T10:13:08Z","status":"public","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)"},"_id":"5"},{"title":"Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana","author":[{"last_name":"Vasileva","full_name":"Vasileva, Mina K","first_name":"Mina K","id":"3407EB18-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Vasileva MK. 2019. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria.","chicago":"Vasileva, Mina K. “Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7172.","apa":"Vasileva, M. K. (2019). Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7172","ama":"Vasileva MK. Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana. 2019. doi:10.15479/AT:ISTA:7172","ieee":"M. K. Vasileva, “Molecular mechanisms of endomembrane trafficking in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2019.","short":"M.K. Vasileva, Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2019.","mla":"Vasileva, Mina K. Molecular Mechanisms of Endomembrane Trafficking in Arabidopsis Thaliana. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7172."},"publisher":"Institute of Science and Technology Austria","oa":1,"doi":"10.15479/AT:ISTA:7172","date_published":"2019-12-12T00:00:00Z","date_created":"2019-12-11T21:24:39Z","page":"192","day":"12","has_accepted_license":"1","year":"2019","status":"public","type":"dissertation","_id":"7172","department":[{"_id":"JiFr"}],"file_date_updated":"2020-07-14T12:47:51Z","ddc":["570"],"supervisor":[{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"date_updated":"2023-09-19T10:39:33Z","month":"12","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"abstract":[{"text":"The development and growth of Arabidopsis thaliana is regulated by a combination of genetic programing and also by the environmental influences. An important role in these processes play the phytohormones and among them, auxin is crucial as it controls many important functions. It is transported through the whole plant body by creating local and temporal concentration maxima and minima, which have an impact on the cell status, tissue and organ identity. Auxin has the property to undergo a directional and finely regulated cell-to-cell transport, which is enabled by the transport proteins, localized on the plasma membrane. An important role in this process have the PIN auxin efflux proteins, which have an asymmetric/polar subcellular localization and determine the directionality of the auxin transport. During the last years, there were significant advances in understanding how the trafficking molecular machineries function, including studies on molecular interactions, function, subcellular localization and intracellular distribution. However, there is still a lack of detailed characterization on the steps of endocytosis, exocytosis, endocytic recycling and degradation. Due to this fact, I focused on the identification of novel trafficking factors and better characterization of the intracellular trafficking pathways. My PhD thesis consists of an introductory chapter, three experimental chapters, a chapter containing general discussion, conclusions and perspectives and also an appendix chapter with published collaborative papers.\r\nThe first chapter is separated in two different parts: I start by a general introduction to auxin biology and then I introduce the trafficking pathways in the model plant Arabidopsis thaliana. Then, I explain also the phosphorylation-signals for polar targeting and also the roles of the phytohormone strigolactone.\r\nThe second chapter includes the characterization of bar1/sacsin mutant, which was identified in a forward genetic screen for novel trafficking components in Arabidopsis thaliana, where by the implementation of an EMS-treated pPIN1::PIN1-GFP marker line and by using the established inhibitor of ARF-GEFs, Brefeldin A (BFA) as a tool to study trafficking processes, we identified a novel factor, which is mediating the adaptation of the plant cell to ARF-GEF inhibition. The mutation is in a previously uncharacterized gene, encoding a very big protein that we, based on its homologies, called SACSIN with domains suggesting roles as a molecular chaperon or as a component of the ubiquitin-proteasome system. Our physiology and imaging studies revealed that SACSIN is a crucial plant cell component of the adaptation to the ARF-GEF inhibition.\r\nThe third chapter includes six subchapters, where I focus on the role of the phytohormone strigolactone, which interferes with auxin feedback on PIN internalization. Strigolactone moderates the polar auxin transport by increasing the internalization of the PIN auxin efflux carriers, which reduces the canalization related growth responses. In addition, I also studied the role of phosphorylation in the strigolactone regulation of auxin feedback on PIN internalization. In this chapter I also present my results on the MAX2-dependence of strigolactone-mediated root growth inhibition and I also share my results on the auxin metabolomics profiling after application of GR24.\r\nIn the fourth chapter I studied the effect of two small molecules ES-9 and ES9-17, which were identified from a collection of small molecules with the property to impair the clathrin-mediated endocytosis.\r\nIn the fifth chapter, I discuss all my observations and experimental findings and suggest alternative hypothesis to interpret my results.\r\nIn the appendix there are three collaborative published projects. In the first, I participated in the characterization of the role of ES9 as a small molecule, which is inhibitor of clathrin- mediated endocytosis in different model organisms. In the second paper, I contributed to the characterization of another small molecule ES9-17, which is a non-protonophoric analog of ES9 and also impairs the clathrin-mediated endocytosis not only in plant cells, but also in mammalian HeLa cells. Last but not least, I also attach another paper, where I tried to establish the grafting method as a technique in our lab to study canalization related processes.","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1346"},{"id":"6377","status":"public","relation":"part_of_dissertation"},{"id":"449","status":"public","relation":"part_of_dissertation"}]},"file":[{"date_created":"2019-12-12T09:32:36Z","file_name":"Thesis_Mina_final_upload_7.docx","creator":"mvasilev","date_updated":"2020-07-14T12:47:51Z","file_size":20454014,"checksum":"ef981c1a3b1d9da0edcbedcff4970d37","file_id":"7175","access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"},{"file_id":"7176","checksum":"3882c4585e46c9cfb486e4225cad54ab","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-12-12T09:33:10Z","file_name":"Thesis_Mina_final_upload_7.pdf","date_updated":"2020-07-14T12:47:51Z","file_size":11565025,"creator":"mvasilev"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD"},{"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)"},"type":"dissertation","keyword":["Information estimation","Time-series","data analysis"],"status":"public","_id":"6473","department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:47:31Z","date_updated":"2023-09-19T15:13:26Z","supervisor":[{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper"}],"ddc":["004"],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"lang":"eng","text":"Single cells are constantly interacting with their environment and each other, more importantly, the accurate perception of environmental cues is crucial for growth, survival, and reproduction. This communication between cells and their environment can be formalized in mathematical terms and be quantified as the information flow between them, as prescribed by information theory. \r\nThe recent availability of real–time dynamical patterns of signaling molecules in single cells has allowed us to identify encoding about the identity of the environment in the time–series. However, efficient estimation of the information transmitted by these signals has been a data–analysis challenge due to the high dimensionality of the trajectories and the limited number of samples. In the first part of this thesis, we develop and evaluate decoding–based estimation methods to lower bound the mutual information and derive model–based precise information estimates for biological reaction networks governed by the chemical master equation. This is followed by applying the decoding-based methods to study the intracellular representation of extracellular changes in budding yeast, by observing the transient dynamics of nuclear translocation of 10 transcription factors in response to 3 stress conditions. Additionally, we apply these estimators to previously published data on ERK and Ca2+ signaling and yeast stress response. We argue that this single cell decoding-based measure of information provides an unbiased, quantitative and interpretable measure for the fidelity of biological signaling processes. \r\nFinally, in the last section, we deal with gene regulation which is primarily controlled by transcription factors (TFs) that bind to the DNA to activate gene expression. The possibility that non-cognate TFs activate transcription diminishes the accuracy of regulation with potentially disastrous effects for the cell. This ’crosstalk’ acts as a previously unexplored source of noise in biochemical networks and puts a strong constraint on their performance. To mitigate erroneous initiation we propose an out of equilibrium scheme that implements kinetic proofreading. We show that such architectures are favored over their equilibrium counterparts for complex organisms despite introducing noise in gene expression. "}],"oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"1576"},{"relation":"dissertation_contains","id":"6900","status":"public"},{"relation":"dissertation_contains","id":"281","status":"public"},{"status":"public","id":"2016","relation":"dissertation_contains"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2019-05-23T11:18:16Z","file_name":"Thesis_Cepeda.zip","date_updated":"2020-07-14T12:47:31Z","file_size":23937464,"creator":"scepeda","checksum":"75f9184c1346e10a5de5f9cc7338309a","file_id":"6480","content_type":"application/zip","access_level":"closed","relation":"source_file"},{"checksum":"afdc0633ddbd71d5b13550d7fb4f4454","file_id":"6481","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-23T11:18:13Z","file_name":"CepedaThesis.pdf","creator":"scepeda","date_updated":"2020-07-14T12:47:31Z","file_size":16646985}],"article_processing_charge":"No","author":[{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"}],"title":"Estimating information flow in single cells","citation":{"chicago":"Cepeda Humerez, Sarah A. “Estimating Information Flow in Single Cells.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6473.","ista":"Cepeda Humerez SA. 2019. Estimating information flow in single cells. Institute of Science and Technology Austria.","mla":"Cepeda Humerez, Sarah A. Estimating Information Flow in Single Cells. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6473.","ieee":"S. A. Cepeda Humerez, “Estimating information flow in single cells,” Institute of Science and Technology Austria, 2019.","short":"S.A. Cepeda Humerez, Estimating Information Flow in Single Cells, Institute of Science and Technology Austria, 2019.","ama":"Cepeda Humerez SA. Estimating information flow in single cells. 2019. doi:10.15479/AT:ISTA:6473","apa":"Cepeda Humerez, S. A. (2019). Estimating information flow in single cells. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6473"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"135","date_created":"2019-05-21T00:11:23Z","doi":"10.15479/AT:ISTA:6473","date_published":"2019-05-23T00:00:00Z","year":"2019","has_accepted_license":"1","day":"23"},{"ddc":["576"],"date_updated":"2023-09-22T10:00:48Z","supervisor":[{"first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:18Z","_id":"6071","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"checksum":"e60a72de35d270b31f1a23d50f224ec0","file_id":"6072","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-03-06T16:05:07Z","file_name":"Thesis_final_PDFA_RoshanPrizak.pdf","date_updated":"2020-07-14T12:47:18Z","file_size":20995465,"creator":"rprizak"},{"checksum":"67c2630333d05ebafef5f018863a8465","file_id":"6073","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"thesis_v2_merge.zip","title":"Latex files","date_created":"2019-03-06T16:09:39Z","file_size":85705272,"date_updated":"2020-07-14T12:47:18Z","creator":"rprizak"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"1358","relation":"part_of_dissertation"},{"id":"955","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","abstract":[{"text":"Transcription factors, by binding to specific sequences on the DNA, control the precise spatio-temporal expression of genes inside a cell. However, this specificity is limited, leading to frequent incorrect binding of transcription factors that might have deleterious consequences on the cell. By constructing a biophysical model of TF-DNA binding in the context of gene regulation, I will first explore how regulatory constraints can strongly shape the distribution of a population in sequence space. Then, by directly linking this to a picture of multiple types of transcription factors performing their functions simultaneously inside the cell, I will explore the extent of regulatory crosstalk -- incorrect binding interactions between transcription factors and binding sites that lead to erroneous regulatory states -- and understand the constraints this places on the design of regulatory systems. I will then develop a generic theoretical framework to investigate the coevolution of multiple transcription factors and multiple binding sites, in the context of a gene regulatory network that performs a certain function. As a particular tractable version of this problem, I will consider the evolution of two transcription factors when they transmit upstream signals to downstream target genes. Specifically, I will describe the evolutionary steady states and the evolutionary pathways involved, along with their timescales, of a system that initially undergoes a transcription factor duplication event. To connect this important theoretical model to the prominent biological event of transcription factor duplication giving rise to paralogous families, I will then describe a bioinformatics analysis of C2H2 Zn-finger transcription factors, a major family in humans, and focus on the patterns of evolution that paralogs have undergone in their various protein domains in the recent past. ","lang":"eng"}],"month":"03","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Prizak, Roshan. “Coevolution of Transcription Factors and Their Binding Sites in Sequence Space.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/at:ista:th6071.","ista":"Prizak R. 2019. Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria.","mla":"Prizak, Roshan. Coevolution of Transcription Factors and Their Binding Sites in Sequence Space. Institute of Science and Technology Austria, 2019, doi:10.15479/at:ista:th6071.","apa":"Prizak, R. (2019). Coevolution of transcription factors and their binding sites in sequence space. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:th6071","ama":"Prizak R. Coevolution of transcription factors and their binding sites in sequence space. 2019. doi:10.15479/at:ista:th6071","short":"R. Prizak, Coevolution of Transcription Factors and Their Binding Sites in Sequence Space, Institute of Science and Technology Austria, 2019.","ieee":"R. Prizak, “Coevolution of transcription factors and their binding sites in sequence space,” Institute of Science and Technology Austria, 2019."},"title":"Coevolution of transcription factors and their binding sites in sequence space","article_processing_charge":"No","author":[{"first_name":"Roshan","id":"4456104E-F248-11E8-B48F-1D18A9856A87","last_name":"Prizak","full_name":"Prizak, Roshan"}],"project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"day":"11","year":"2019","has_accepted_license":"1","date_created":"2019-03-06T16:16:10Z","date_published":"2019-03-11T00:00:00Z","doi":"10.15479/at:ista:th6071","page":"189","oa":1,"publisher":"Institute of Science and Technology Austria"},{"publisher":"EMS Press","quality_controlled":"1","oa":1,"page":"1135-1177","doi":"10.25537/dm.2019v24.1135-1177","date_published":"2019-05-20T00:00:00Z","date_created":"2020-02-02T23:01:06Z","has_accepted_license":"1","isi":1,"year":"2019","day":"20","publication":"Documenta Mathematica","author":[{"first_name":"Tanya K","id":"4D046628-F248-11E8-B48F-1D18A9856A87","full_name":"Srivastava, Tanya K","last_name":"Srivastava"}],"article_processing_charge":"No","external_id":{"isi":["000517806400019"],"arxiv":["1809.08970"]},"title":"On derived equivalences of k3 surfaces in positive characteristic","citation":{"ista":"Srivastava TK. 2019. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 24, 1135–1177.","chicago":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica. EMS Press, 2019. https://doi.org/10.25537/dm.2019v24.1135-1177.","apa":"Srivastava, T. K. (2019). On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. EMS Press. https://doi.org/10.25537/dm.2019v24.1135-1177","ama":"Srivastava TK. On derived equivalences of k3 surfaces in positive characteristic. Documenta Mathematica. 2019;24:1135-1177. doi:10.25537/dm.2019v24.1135-1177","ieee":"T. K. Srivastava, “On derived equivalences of k3 surfaces in positive characteristic,” Documenta Mathematica, vol. 24. EMS Press, pp. 1135–1177, 2019.","short":"T.K. Srivastava, Documenta Mathematica 24 (2019) 1135–1177.","mla":"Srivastava, Tanya K. “On Derived Equivalences of K3 Surfaces in Positive Characteristic.” Documenta Mathematica, vol. 24, EMS Press, 2019, pp. 1135–77, doi:10.25537/dm.2019v24.1135-1177."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"05","intvolume":" 24","abstract":[{"text":"For an ordinary K3 surface over an algebraically closed field of positive characteristic we show that every automorphism lifts to characteristic zero. Moreover, we show that the Fourier-Mukai partners of an ordinary K3 surface are in one-to-one correspondence with the Fourier-Mukai partners of the geometric generic fiber of its canonical lift. We also prove that the explicit counting formula for Fourier-Mukai partners of the K3 surfaces with Picard rank two and with discriminant equal to minus of a prime number, in terms of the class number of the prime, holds over a field of positive characteristic as well. We show that the image of the derived autoequivalence group of a K3 surface of finite height in the group of isometries of its crystalline cohomology has index at least two. Moreover, we provide a conditional upper bound on the kernel of this natural cohomological descent map. Further, we give an extended remark in the appendix on the possibility of an F-crystal structure on the crystalline cohomology of a K3 surface over an algebraically closed field of positive characteristic and show that the naive F-crystal structure fails in being compatible with inner product. ","lang":"eng"}],"oa_version":"Published Version","volume":24,"publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"publication_status":"published","file":[{"checksum":"9a1a64bd49ab03fa4f738fb250fc4f90","file_id":"7438","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-02-03T06:26:12Z","file_name":"2019_DocumMath_Srivastava.pdf","date_updated":"2020-07-14T12:47:58Z","file_size":469730,"creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","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":"7436","department":[{"_id":"TaHa"}],"file_date_updated":"2020-07-14T12:47:58Z","date_updated":"2023-10-17T07:42:21Z","ddc":["510"]},{"oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","date_created":"2018-12-11T11:44:29Z","date_published":"2019-09-25T00:00:00Z","doi":"10.1214/18-AIHP916","page":"1203-1225","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","day":"25","year":"2019","isi":1,"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics"}],"title":"Limit law of a second class particle in TASEP with non-random initial condition","external_id":{"isi":["000487763200001"],"arxiv":["1710.02323"]},"article_processing_charge":"No","author":[{"first_name":"Patrick","last_name":"Ferrari","full_name":"Ferrari, Patrick"},{"full_name":"Ghosal, Promit","last_name":"Ghosal","first_name":"Promit"},{"full_name":"Nejjar, Peter","last_name":"Nejjar","first_name":"Peter","id":"4BF426E2-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ferrari P, Ghosal P, Nejjar P. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 2019;55(3):1203-1225. doi:10.1214/18-AIHP916","apa":"Ferrari, P., Ghosal, P., & Nejjar, P. (2019). Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AIHP916","ieee":"P. Ferrari, P. Ghosal, and P. Nejjar, “Limit law of a second class particle in TASEP with non-random initial condition,” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3. Institute of Mathematical Statistics, pp. 1203–1225, 2019.","short":"P. Ferrari, P. Ghosal, P. Nejjar, Annales de l’institut Henri Poincare (B) Probability and Statistics 55 (2019) 1203–1225.","mla":"Ferrari, Patrick, et al. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics, vol. 55, no. 3, Institute of Mathematical Statistics, 2019, pp. 1203–25, doi:10.1214/18-AIHP916.","ista":"Ferrari P, Ghosal P, Nejjar P. 2019. Limit law of a second class particle in TASEP with non-random initial condition. Annales de l’institut Henri Poincare (B) Probability and Statistics. 55(3), 1203–1225.","chicago":"Ferrari, Patrick, Promit Ghosal, and Peter Nejjar. “Limit Law of a Second Class Particle in TASEP with Non-Random Initial Condition.” Annales de l’institut Henri Poincare (B) Probability and Statistics. Institute of Mathematical Statistics, 2019. https://doi.org/10.1214/18-AIHP916."},"intvolume":" 55","month":"09","main_file_link":[{"url":"https://arxiv.org/abs/1710.02323","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We consider the totally asymmetric simple exclusion process (TASEP) with non-random initial condition having density ρ on ℤ− and λ on ℤ+, and a second class particle initially at the origin. For ρ<λ, there is a shock and the second class particle moves with speed 1−λ−ρ. For large time t, we show that the position of the second class particle fluctuates on a t1/3 scale and determine its limiting law. We also obtain the limiting distribution of the number of steps made by the second class particle until time t.","lang":"eng"}],"ec_funded":1,"issue":"3","volume":55,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0246-0203"]},"status":"public","article_type":"original","type":"journal_article","_id":"72","department":[{"_id":"LaEr"},{"_id":"JaMa"}],"date_updated":"2023-10-17T08:53:45Z"},{"date_published":"2019-05-01T00:00:00Z","doi":"10.1364/cleo_at.2019.jtu2a.52","date_created":"2019-07-17T09:40:44Z","publication_identifier":{"isbn":["9781943580576"]},"publication_status":"published","year":"2019","day":"01","publication":"CLEO: Applications and Technology","language":[{"iso":"eng"}],"publisher":"Optica Publishing Group","scopus_import":"1","quality_controlled":"1","month":"05","abstract":[{"text":"We demonstrate robust retention of valley coherence and its control via polariton pseudospin precession through the optical TE-TM splitting in bilayer WS2 microcavity exciton polaritons at room temperature.","lang":"eng"}],"oa_version":"None","author":[{"first_name":"Mandeep","last_name":"Khatoniar","full_name":"Khatoniar, Mandeep"},{"full_name":"Yama, Nicholas","last_name":"Yama","first_name":"Nicholas"},{"last_name":"Ghazaryan","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg"},{"full_name":"Guddala, Sriram","last_name":"Guddala","first_name":"Sriram"},{"first_name":"Pouyan","last_name":"Ghaemi","full_name":"Ghaemi, Pouyan"},{"first_name":"Vinod","last_name":"Menon","full_name":"Menon, Vinod"}],"article_processing_charge":"No","department":[{"_id":"MiLe"}],"title":"Room temperature control of valley coherence in bilayer WS2 exciton polaritons","citation":{"chicago":"Khatoniar, Mandeep, Nicholas Yama, Areg Ghazaryan, Sriram Guddala, Pouyan Ghaemi, and Vinod Menon. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” In CLEO: Applications and Technology. Optica Publishing Group, 2019. https://doi.org/10.1364/cleo_at.2019.jtu2a.52.","ista":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. 2019. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. CLEO: Applications and Technology. CLEO: Conference on Lasers and Electro-Optics, paper JTu2A.52.","mla":"Khatoniar, Mandeep, et al. “Room Temperature Control of Valley Coherence in Bilayer WS2 Exciton Polaritons.” CLEO: Applications and Technology, paper JTu2A.52, Optica Publishing Group, 2019, doi:10.1364/cleo_at.2019.jtu2a.52.","ieee":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, and V. Menon, “Room temperature control of valley coherence in bilayer WS2 exciton polaritons,” in CLEO: Applications and Technology, San Jose, CA, United States, 2019.","short":"M. Khatoniar, N. Yama, A. Ghazaryan, S. Guddala, P. Ghaemi, V. Menon, in:, CLEO: Applications and Technology, Optica Publishing Group, 2019.","apa":"Khatoniar, M., Yama, N., Ghazaryan, A., Guddala, S., Ghaemi, P., & Menon, V. (2019). Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In CLEO: Applications and Technology. San Jose, CA, United States: Optica Publishing Group. https://doi.org/10.1364/cleo_at.2019.jtu2a.52","ama":"Khatoniar M, Yama N, Ghazaryan A, Guddala S, Ghaemi P, Menon V. Room temperature control of valley coherence in bilayer WS2 exciton polaritons. In: CLEO: Applications and Technology. Optica Publishing Group; 2019. doi:10.1364/cleo_at.2019.jtu2a.52"},"date_updated":"2023-10-17T12:14:29Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","conference":{"location":"San Jose, CA, United States","end_date":"2019-05-10","start_date":"2019-05-05","name":"CLEO: Conference on Lasers and Electro-Optics"},"status":"public","_id":"6646","article_number":"paper JTu2A.52"},{"_id":"7233","article_number":"NM2A.5","conference":{"name":"NLO: Nonlinear Optics","start_date":"2019-07-15","end_date":"2019-07-19","location":"Waikoloa Beach, Hawaii (HI), United States"},"type":"conference","status":"public","citation":{"ista":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. 2019. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. Nonlinear Optics, OSA Technical Digest. NLO: Nonlinear Optics, NM2A.5.","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kumari, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” In Nonlinear Optics, OSA Technical Digest. Optica Publishing Group, 2019. https://doi.org/10.1364/NLO.2019.NM2A.5.","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, and H. G. L. Schwefel, “Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity,” in Nonlinear Optics, OSA Technical Digest, Waikoloa Beach, Hawaii (HI), United States, 2019.","short":"A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kumari, H.G.L. Schwefel, in:, Nonlinear Optics, OSA Technical Digest, Optica Publishing Group, 2019.","ama":"Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kumari M, Schwefel HGL. Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In: Nonlinear Optics, OSA Technical Digest. Optica Publishing Group; 2019. doi:10.1364/NLO.2019.NM2A.5","apa":"Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kumari, M., & Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity. In Nonlinear Optics, OSA Technical Digest. Waikoloa Beach, Hawaii (HI), United States: Optica Publishing Group. https://doi.org/10.1364/NLO.2019.NM2A.5","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb Generation in Lithium Niobate Disk Resonator inside a Microwave Cavity.” Nonlinear Optics, OSA Technical Digest, NM2A.5, Optica Publishing Group, 2019, doi:10.1364/NLO.2019.NM2A.5."},"date_updated":"2023-10-17T12:14:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Leuchs","full_name":"Leuchs, Gerd","first_name":"Gerd"},{"full_name":"Kumari, Madhuri","last_name":"Kumari","first_name":"Madhuri"},{"first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L.","last_name":"Schwefel"}],"department":[{"_id":"JoFi"}],"title":"Resonant electro-optic frequency comb generation in lithium niobate disk resonator inside a microwave cavity","abstract":[{"lang":"eng","text":"We demonstrate electro-optic frequency comb generation using a doubly resonant system comprising a whispering gallery mode disk resonator made of lithium niobate mounted inside a three dimensional copper cavity. We observe 180 sidebands centred at 1550 nm."}],"oa_version":"None","scopus_import":"1","publisher":"Optica Publishing Group","quality_controlled":"1","month":"07","year":"2019","publication_status":"published","publication_identifier":{"isbn":["9781557528209"]},"publication":"Nonlinear Optics, OSA Technical Digest","language":[{"iso":"eng"}],"day":"15","date_created":"2020-01-05T23:00:48Z","date_published":"2019-07-15T00:00:00Z","doi":"10.1364/NLO.2019.NM2A.5"},{"department":[{"_id":"LaEr"}],"date_updated":"2023-10-17T12:20:20Z","status":"public","type":"journal_article","_id":"6240","issue":"2","volume":55,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"149"}]},"ec_funded":1,"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0246-0203"]},"publication_status":"published","month":"05","intvolume":" 55","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.08343"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"For a general class of large non-Hermitian random block matrices X we prove that there are no eigenvalues away from a deterministic set with very high probability. This set is obtained from the Dyson equation of the Hermitization of X as the self-consistent approximation of the pseudospectrum. We demonstrate that the analysis of the matrix Dyson equation from (Probab. Theory Related Fields (2018)) offers a unified treatment of many structured matrix ensembles."}],"title":"Location of the spectrum of Kronecker random matrices","author":[{"last_name":"Alt","full_name":"Alt, Johannes","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","last_name":"Erdös"},{"last_name":"Krüger","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297","first_name":"Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Nemish","full_name":"Nemish, Yuriy","orcid":"0000-0002-7327-856X","first_name":"Yuriy","id":"4D902E6A-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"arxiv":["1706.08343"],"isi":["000467793600003"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"J. Alt, L. Erdös, T. H. Krüger, and Y. Nemish, “Location of the spectrum of Kronecker random matrices,” Annales de l’institut Henri Poincare, vol. 55, no. 2. Institut Henri Poincaré, pp. 661–696, 2019.","short":"J. Alt, L. Erdös, T.H. Krüger, Y. Nemish, Annales de l’institut Henri Poincare 55 (2019) 661–696.","ama":"Alt J, Erdös L, Krüger TH, Nemish Y. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 2019;55(2):661-696. doi:10.1214/18-AIHP894","apa":"Alt, J., Erdös, L., Krüger, T. H., & Nemish, Y. (2019). Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. Institut Henri Poincaré. https://doi.org/10.1214/18-AIHP894","mla":"Alt, Johannes, et al. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare, vol. 55, no. 2, Institut Henri Poincaré, 2019, pp. 661–96, doi:10.1214/18-AIHP894.","ista":"Alt J, Erdös L, Krüger TH, Nemish Y. 2019. Location of the spectrum of Kronecker random matrices. Annales de l’institut Henri Poincare. 55(2), 661–696.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Yuriy Nemish. “Location of the Spectrum of Kronecker Random Matrices.” Annales de l’institut Henri Poincare. Institut Henri Poincaré, 2019. https://doi.org/10.1214/18-AIHP894."},"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems"}],"doi":"10.1214/18-AIHP894","date_published":"2019-05-01T00:00:00Z","date_created":"2019-04-08T14:05:04Z","page":"661-696","day":"01","publication":"Annales de l'institut Henri Poincare","isi":1,"year":"2019","quality_controlled":"1","publisher":"Institut Henri Poincaré","oa":1}]