[{"department":[{"_id":"ScienComp"}],"conference":{"name":"AHPC: Austrian HPC Meeting","end_date":"2019-02-27","start_date":"2019-02-25","location":"Grundlsee, Austria"},"author":[{"orcid":"0000-0002-5621-8100","last_name":"Schlögl","full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois"},{"last_name":"Kiss","full_name":"Kiss, Janos","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87","first_name":"Janos"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano","full_name":"Elefante, Stefano","last_name":"Elefante"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_abstract","publication_status":"published","month":"02","publication":"AHPC19 - Austrian HPC Meeting 2019 ","day":"27","ddc":["000"],"article_processing_charge":"No","language":[{"iso":"eng"}],"year":"2019","oa_version":"Published Version","file_date_updated":"2023-05-16T07:27:09Z","page":"25","date_created":"2023-05-05T12:48:48Z","_id":"12901","date_published":"2019-02-27T00:00:00Z","oa":1,"date_updated":"2024-10-09T21:05:24Z","status":"public","citation":{"ama":"Schlögl A, Kiss J, Elefante S. Is Debian suitable for running an HPC Cluster? In: AHPC19 - Austrian HPC Meeting 2019 . Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz; 2019:25.","apa":"Schlögl, A., Kiss, J., & Elefante, S. (2019). Is Debian suitable for running an HPC Cluster? In AHPC19 - Austrian HPC Meeting 2019 (p. 25). Grundlsee, Austria: Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz.","short":"A. Schlögl, J. Kiss, S. Elefante, in:, AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","ieee":"A. Schlögl, J. Kiss, and S. Elefante, “Is Debian suitable for running an HPC Cluster?,” in AHPC19 - Austrian HPC Meeting 2019 , Grundlsee, Austria, 2019, p. 25.","chicago":"Schlögl, Alois, Janos Kiss, and Stefano Elefante. “Is Debian Suitable for Running an HPC Cluster?” In AHPC19 - Austrian HPC Meeting 2019 , 25. Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019.","mla":"Schlögl, Alois, et al. “Is Debian Suitable for Running an HPC Cluster?” AHPC19 - Austrian HPC Meeting 2019 , Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz, 2019, p. 25.","ista":"Schlögl A, Kiss J, Elefante S. 2019. Is Debian suitable for running an HPC Cluster? AHPC19 - Austrian HPC Meeting 2019 . AHPC: Austrian HPC Meeting, 25."},"corr_author":"1","main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf","open_access":"1"}],"title":"Is Debian suitable for running an HPC Cluster?","has_accepted_license":"1","publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","file":[{"file_size":1097603,"access_level":"open_access","creator":"dernst","relation":"main_file","date_created":"2023-05-16T07:27:09Z","file_name":"2019_AHPC_Schloegl.pdf","date_updated":"2023-05-16T07:27:09Z","checksum":"acc8272027faaf30709c51ac5c58ffa4","content_type":"application/pdf","file_id":"12970","success":1}]},{"month":"12","type":"research_data_reference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna","first_name":"Zuzanna"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","ddc":["570"],"day":"02","oa_version":"Published Version","year":"2019","date_published":"2019-12-02T00:00:00Z","_id":"13067","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-05-23T16:36:27Z","oa":1,"tmp":{"image":"/images/cc_0.png","short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"doi":"10.5061/DRYAD.TB2RBNZWK","status":"public","date_updated":"2025-07-10T11:54:22Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.tb2rbnzwk"}],"citation":{"ieee":"K. Johannesson, Z. Zagrodzka, R. Faria, A. M. Westram, and R. Butlin, “Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?” Dryad, 2019.","chicago":"Johannesson, Kerstin, Zuzanna Zagrodzka, Rui Faria, Anja M Westram, and Roger Butlin. “Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes?” Dryad, 2019. https://doi.org/10.5061/DRYAD.TB2RBNZWK.","mla":"Johannesson, Kerstin, et al. Data from: Is Embryo Abortion a Postzygotic Barrier to Gene Flow between Littorina Ecotypes? Dryad, 2019, doi:10.5061/DRYAD.TB2RBNZWK.","ista":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. 2019. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?, Dryad, 10.5061/DRYAD.TB2RBNZWK.","ama":"Johannesson K, Zagrodzka Z, Faria R, Westram AM, Butlin R. Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? 2019. doi:10.5061/DRYAD.TB2RBNZWK","apa":"Johannesson, K., Zagrodzka, Z., Faria, R., Westram, A. M., & Butlin, R. (2019). Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes? Dryad. https://doi.org/10.5061/DRYAD.TB2RBNZWK","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019)."},"related_material":{"record":[{"id":"7205","status":"public","relation":"used_in_publication"}]},"publisher":"Dryad","title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","abstract":[{"text":"Genetic incompatibilities contribute to reproductive isolation between many diverging populations, but it is still unclear to what extent they play a role if divergence happens with gene flow. In contact zones between the \"Crab\" and \"Wave\" ecotypes of the snail Littorina saxatilis divergent selection forms strong barriers to gene flow, while the role of postzygotic barriers due to selection against hybrids remains unclear. High embryo abortion rates in this species could indicate the presence of such barriers. Postzygotic barriers might include genetic incompatibilities (e.g. Dobzhansky-Muller incompatibilities) but also maladaptation, both expected to be most pronounced in contact zones. In addition, embryo abortion might reflect physiological stress on females and embryos independent of any genetic stress. We examined all embryos of >500 females sampled outside and inside contact zones of three populations in Sweden. Females' clutch size ranged from 0 to 1011 embryos (mean 130±123) and abortion rates varied between 0 and100% (mean 12%). We described female genotypes by using a hybrid index based on hundreds of SNPs differentiated between ecotypes with which we characterised female genotypes. We also calculated female SNP heterozygosity and inversion karyotype. Clutch size did not vary with female hybrid index and abortion rates were only weakly related to hybrid index in two sites but not at all in a third site. No additional variation in abortion rate was explained by female SNP heterozygosity, but increased female inversion heterozygosity added slightly to increased abortion. Our results show only weak and probably biologically insignificant postzygotic barriers contributing to ecotype divergence and the high and variable abortion rates were marginally, if at all, explained by hybrid index of females.","lang":"eng"}]},{"publication":"Current Genetics","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"Yes (via OA deal)","day":"01","file_date_updated":"2020-07-14T12:44:47Z","year":"2019","publist_id":"7785","date_published":"2019-02-01T00:00:00Z","external_id":{"isi":["000456958800017"]},"_id":"138","date_created":"2018-12-11T11:44:50Z","oa":1,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"status":"public","date_updated":"2025-04-15T06:50:19Z","doi":"10.1007/s00294-018-0879-8","file":[{"date_updated":"2020-07-14T12:44:47Z","checksum":"6779708b0b632a1a6ed28c56f5161142","content_type":"application/pdf","file_id":"5930","date_created":"2019-02-06T07:50:58Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":776399,"file_name":"2019_CurrentGenetics_Nikolic.pdf"}],"publisher":"Springer","abstract":[{"text":"Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin–antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin–antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin–antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.","lang":"eng"}],"title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","quality_controlled":"1","volume":65,"month":"02","isi":1,"publication_status":"published","department":[{"_id":"CaGu"}],"author":[{"id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","first_name":"Nela","orcid":"0000-0001-9068-6090","last_name":"Nikolic","full_name":"Nikolic, Nela"}],"ddc":["570"],"intvolume":" 65","scopus_import":"1","page":"133-138","oa_version":"Published Version","language":[{"iso":"eng"}],"issue":"1","citation":{"ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","ieee":"N. Nikolic, “Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system,” Current Genetics, vol. 65, no. 1. Springer, pp. 133–138, 2019.","chicago":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics. Springer, 2019. https://doi.org/10.1007/s00294-018-0879-8.","mla":"Nikolic, Nela. “Autoregulation of Bacterial Gene Expression: Lessons from the MazEF Toxin–Antitoxin System.” Current Genetics, vol. 65, no. 1, Springer, 2019, pp. 133–38, doi:10.1007/s00294-018-0879-8.","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","ama":"Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 2019;65(1):133-138. doi:10.1007/s00294-018-0879-8","apa":"Nikolic, N. (2019). Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. Springer. https://doi.org/10.1007/s00294-018-0879-8"},"ec_funded":1,"has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"Learning disentangled representations is considered a cornerstone problem in\r\nrepresentation learning. Recently, Locatello et al. (2019) demonstrated that\r\nunsupervised disentanglement learning without inductive biases is theoretically\r\nimpossible and that existing inductive biases and unsupervised methods do not\r\nallow to consistently learn disentangled representations. However, in many\r\npractical settings, one might have access to a limited amount of supervision,\r\nfor example through manual labeling of (some) factors of variation in a few\r\ntraining examples. In this paper, we investigate the impact of such supervision\r\non state-of-the-art disentanglement methods and perform a large scale study,\r\ntraining over 52000 models under well-defined and reproducible experimental\r\nconditions. We observe that a small number of labeled examples (0.01--0.5\\% of\r\nthe data set), with potentially imprecise and incomplete labels, is sufficient\r\nto perform model selection on state-of-the-art unsupervised models. Further, we\r\ninvestigate the benefit of incorporating supervision into the training process.\r\nOverall, we empirically validate that with little and imprecise supervision it\r\nis possible to reliably learn disentangled representations."}],"quality_controlled":"1","title":"Disentangling factors of variation using few labels","citation":{"short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019.","ama":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. Disentangling factors of variation using few labels. In: 8th International Conference on Learning Representations. ; 2019.","apa":"Locatello, F., Tschannen, M., Bauer, S., Rätsch, G., Schölkopf, B., & Bachem, O. (2019). Disentangling factors of variation using few labels. In 8th International Conference on Learning Representations. Virtual.","ista":"Locatello F, Tschannen M, Bauer S, Rätsch G, Schölkopf B, Bachem O. 2019. Disentangling factors of variation using few labels. 8th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","chicago":"Locatello, Francesco, Michael Tschannen, Stefan Bauer, Gunnar Rätsch, Bernhard Schölkopf, and Olivier Bachem. “Disentangling Factors of Variation Using Few Labels.” In 8th International Conference on Learning Representations, 2019.","ieee":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, and O. Bachem, “Disentangling factors of variation using few labels,” in 8th International Conference on Learning Representations, Virtual, 2019.","mla":"Locatello, Francesco, et al. “Disentangling Factors of Variation Using Few Labels.” 8th International Conference on Learning Representations, 2019."},"main_file_link":[{"url":"https://arxiv.org/abs/1905.01258","open_access":"1"}],"arxiv":1,"status":"public","date_updated":"2023-09-12T07:01:34Z","extern":"1","oa":1,"date_created":"2023-08-22T14:06:37Z","date_published":"2019-12-20T00:00:00Z","_id":"14184","external_id":{"arxiv":["1905.01258"]},"year":"2019","language":[{"iso":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","day":"20","scopus_import":"1","type":"conference","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","conference":{"name":"ICLR: International Conference on Learning Representations","start_date":"2020-04-26","location":"Virtual","end_date":"2020-05-01"},"author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"full_name":"Tschannen, Michael","last_name":"Tschannen","first_name":"Michael"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"department":[{"_id":"FrLo"}],"month":"12","publication":"8th International Conference on Learning Representations"},{"language":[{"iso":"eng"}],"oa_version":"Preprint","page":"217-227","author":[{"full_name":"Gresele, Luigi","last_name":"Gresele","first_name":"Luigi"},{"first_name":"Paul K.","last_name":"Rubenstein","full_name":"Rubenstein, Paul K."},{"first_name":"Arash","full_name":"Mehrjou, Arash","last_name":"Mehrjou"},{"full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"}],"conference":{"name":"UAI: Uncertainty in Artificial Intelligence","end_date":"2019-07-25","start_date":"2019-07-22","location":"Tel Aviv, Israel"},"department":[{"_id":"FrLo"}],"publication_status":"published","volume":115,"month":"05","scopus_import":"1","intvolume":" 115","citation":{"ama":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In: Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. Vol 115. ML Research Press; 2019:217-227.","apa":"Gresele, L., Rubenstein, P. K., Mehrjou, A., Locatello, F., & Schölkopf, B. (2019). The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence (Vol. 115, pp. 217–227). Tel Aviv, Israel: ML Research Press.","short":"L. Gresele, P.K. Rubenstein, A. Mehrjou, F. Locatello, B. Schölkopf, in:, Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, ML Research Press, 2019, pp. 217–227.","ieee":"L. Gresele, P. K. Rubenstein, A. Mehrjou, F. Locatello, and B. Schölkopf, “The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA,” in Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, Tel Aviv, Israel, 2019, vol. 115, pp. 217–227.","chicago":"Gresele, Luigi, Paul K. Rubenstein, Arash Mehrjou, Francesco Locatello, and Bernhard Schölkopf. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” In Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, 115:217–27. ML Research Press, 2019.","mla":"Gresele, Luigi, et al. “The Incomplete Rosetta Stone Problem: Identifiability Results for Multi-View Nonlinear ICA.” Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence, vol. 115, ML Research Press, 2019, pp. 217–27.","ista":"Gresele L, Rubenstein PK, Mehrjou A, Locatello F, Schölkopf B. 2019. The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA. Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence. UAI: Uncertainty in Artificial Intelligence, PMLR, vol. 115, 217–227."},"alternative_title":["PMLR"],"extern":"1","year":"2019","date_created":"2023-08-22T14:08:35Z","external_id":{"arxiv":["1905.06642"]},"_id":"14189","date_published":"2019-05-16T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","day":"16","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1905.06642","open_access":"1"}],"abstract":[{"text":"We consider the problem of recovering a common latent source with independent\r\ncomponents from multiple views. This applies to settings in which a variable is\r\nmeasured with multiple experimental modalities, and where the goal is to\r\nsynthesize the disparate measurements into a single unified representation. We\r\nconsider the case that the observed views are a nonlinear mixing of\r\ncomponent-wise corruptions of the sources. When the views are considered\r\nseparately, this reduces to nonlinear Independent Component Analysis (ICA) for\r\nwhich it is provably impossible to undo the mixing. We present novel\r\nidentifiability proofs that this is possible when the multiple views are\r\nconsidered jointly, showing that the mixing can theoretically be undone using\r\nfunction approximators such as deep neural networks. In contrast to known\r\nidentifiability results for nonlinear ICA, we prove that independent latent\r\nsources with arbitrary mixing can be recovered as long as multiple,\r\nsufficiently different noisy views are available.","lang":"eng"}],"title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","quality_controlled":"1","publisher":"ML Research Press","oa":1,"arxiv":1,"date_updated":"2023-09-12T08:07:38Z","status":"public"},{"article_processing_charge":"No","intvolume":" 32","day":"07","type":"conference","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","department":[{"_id":"FrLo"}],"author":[{"full_name":"Gondal, Muhammad Waleed","last_name":"Gondal","first_name":"Muhammad Waleed"},{"last_name":"Wüthrich","full_name":"Wüthrich, Manuel","first_name":"Manuel"},{"first_name":"Đorđe","full_name":"Miladinović, Đorđe","last_name":"Miladinović"},{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Breidt, Martin","last_name":"Breidt","first_name":"Martin"},{"first_name":"Valentin","full_name":"Volchkov, Valentin","last_name":"Volchkov"},{"first_name":"Joel","full_name":"Akpo, Joel","last_name":"Akpo"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"}],"conference":{"end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems"},"publication":"Advances in Neural Information Processing Systems","volume":32,"month":"06","date_created":"2023-08-22T14:09:13Z","date_published":"2019-06-07T00:00:00Z","_id":"14190","external_id":{"arxiv":["1906.03292"]},"year":"2019","language":[{"iso":"eng"}],"oa_version":"Preprint","arxiv":1,"date_updated":"2023-09-13T09:46:38Z","status":"public","extern":"1","oa":1,"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."}],"quality_controlled":"1","title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","citation":{"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.","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.","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.","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.","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."},"publication_identifier":{"isbn":["9781713807933"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}]},{"arxiv":1,"status":"public","date_updated":"2023-09-12T08:48:45Z","oa":1,"abstract":[{"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.","lang":"eng"}],"title":"Stochastic Frank-Wolfe for composite convex minimization","quality_controlled":"1","publication_identifier":{"isbn":["9781713807933"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"article_processing_charge":"No","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publication":"Advances in Neural Information Processing Systems","date_created":"2023-08-22T14:09:35Z","date_published":"2019-12-29T00:00:00Z","external_id":{"arxiv":["1901.10348"]},"_id":"14191","year":"2019","extern":"1","citation":{"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.","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.","short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 14291–14301.","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.","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."},"intvolume":" 32","scopus_import":"1","publication_status":"published","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"last_name":"Yurtsever","full_name":"Yurtsever, Alp","first_name":"Alp"},{"full_name":"Fercoq, Olivier","last_name":"Fercoq","first_name":"Olivier"},{"last_name":"Cevher","full_name":"Cevher, Volkan","first_name":"Volkan"}],"conference":{"end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems"},"department":[{"_id":"FrLo"}],"volume":32,"month":"12","language":[{"iso":"eng"}],"page":"14291–14301","oa_version":"Preprint"},{"intvolume":" 32","article_processing_charge":"No","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","type":"conference","author":[{"first_name":"Sjoerd van","full_name":"Steenkiste, Sjoerd van","last_name":"Steenkiste"},{"orcid":"0000-0002-4850-0683","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Jürgen","last_name":"Schmidhuber","full_name":"Schmidhuber, Jürgen"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"department":[{"_id":"FrLo"}],"conference":{"end_date":"2019-12-14","location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems"},"volume":32,"publication":"Advances in Neural Information Processing Systems","month":"05","date_created":"2023-08-22T14:09:53Z","date_published":"2019-05-29T00:00:00Z","_id":"14193","external_id":{"arxiv":["1905.12506"]},"year":"2019","language":[{"iso":"eng"}],"oa_version":"Preprint","arxiv":1,"status":"public","date_updated":"2024-10-14T12:28:15Z","extern":"1","oa":1,"title":"Are disentangled representations helpful for abstract visual reasoning?","quality_controlled":"1","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"}],"publication_identifier":{"isbn":["9781713807933"]},"citation":{"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.","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.","mla":"Steenkiste, Sjoerd van, et al. “Are Disentangled Representations Helpful for Abstract Visual Reasoning?” Advances in Neural Information Processing Systems, vol. 32, 2019.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019.","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."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}]},{"arxiv":1,"status":"public","date_updated":"2024-10-14T12:29:05Z","oa":1,"quality_controlled":"1","title":"On the fairness of disentangled representations","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."}],"publication_identifier":{"isbn":["9781713807933"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13662"}],"article_processing_charge":"No","day":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publication":"Advances in Neural Information Processing Systems","date_created":"2023-08-22T14:12:28Z","date_published":"2019-12-08T00:00:00Z","_id":"14197","external_id":{"arxiv":["1905.13662"]},"year":"2019","extern":"1","citation":{"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.","mla":"Locatello, Francesco, et al. “On the Fairness of Disentangled Representations.” Advances in Neural Information Processing Systems, vol. 32, 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.","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.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 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.","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."},"intvolume":" 32","scopus_import":"1","publication_status":"published","author":[{"first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","orcid":"0000-0002-4850-0683"},{"first_name":"Gabriele","full_name":"Abbati, Gabriele","last_name":"Abbati"},{"first_name":"Tom","last_name":"Rainforth","full_name":"Rainforth, Tom"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Vancouver, Canada","start_date":"2019-12-08","end_date":"2019-12-14"},"department":[{"_id":"FrLo"}],"volume":32,"month":"12","language":[{"iso":"eng"}],"page":"14611–14624","oa_version":"Preprint"},{"day":"09","article_processing_charge":"No","publication":"Proceedings of the 36th International Conference on Machine Learning","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14200","external_id":{"arxiv":["1811.12359"]},"date_published":"2019-06-09T00:00:00Z","date_created":"2023-08-22T14:13:08Z","year":"2019","date_updated":"2024-10-14T12:29:16Z","status":"public","arxiv":1,"oa":1,"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","title":"Challenging common assumptions in the unsupervised learning of disentangled representations","publisher":"ML Research Press","main_file_link":[{"url":"https://arxiv.org/abs/1811.12359","open_access":"1"}],"scopus_import":"1","intvolume":" 97","month":"06","volume":97,"author":[{"last_name":"Locatello","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"last_name":"Rätsch","full_name":"Rätsch, Gunnar","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","last_name":"Gelly","first_name":"Sylvain"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"department":[{"_id":"FrLo"}],"conference":{"end_date":"2019-06-15","location":"Long Beach, CA, United States","start_date":"2019-06-10","name":"International Conference on Machine Learning"},"publication_status":"published","oa_version":"Preprint","page":"4114-4124","language":[{"iso":"eng"}],"extern":"1","citation":{"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.","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.","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.","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.","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.","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."}},{"citation":{"ista":"Fischer JL, Kneuss O. 2019. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 266(1), 257–311.","mla":"Fischer, Julian L., and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations, vol. 266, no. 1, Elsevier, 2019, pp. 257–311, doi:10.1016/j.jde.2018.07.045.","ieee":"J. L. Fischer and O. Kneuss, “Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity,” Journal of Differential Equations, vol. 266, no. 1. Elsevier, pp. 257–311, 2019.","chicago":"Fischer, Julian L, and Olivier Kneuss. “Bi-Sobolev Solutions to the Prescribed Jacobian Inequality in the Plane with L p Data and Applications to Nonlinear Elasticity.” Journal of Differential Equations. Elsevier, 2019. https://doi.org/10.1016/j.jde.2018.07.045.","short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.","apa":"Fischer, J. L., & Kneuss, O. (2019). Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2018.07.045","ama":"Fischer JL, Kneuss O. Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity. Journal of Differential Equations. 2019;266(1):257-311. doi:10.1016/j.jde.2018.07.045"},"issue":"1","language":[{"iso":"eng"}],"page":"257 - 311","oa_version":"Preprint","isi":1,"publication_status":"published","department":[{"_id":"JuFi"}],"author":[{"orcid":"0000-0002-0479-558X","last_name":"Fischer","full_name":"Fischer, Julian L","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olivier","last_name":"Kneuss","full_name":"Kneuss, Olivier"}],"volume":266,"month":"01","intvolume":" 266","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1408.1587","open_access":"1"}],"publisher":"Elsevier","quality_controlled":"1","abstract":[{"text":"We construct planar bi-Sobolev mappings whose local volume distortion is bounded from below by a given function f∈Lp with p>1. More precisely, for any 1<q<(p+1)/2 we construct W1,q-bi-Sobolev maps with identity boundary conditions; for f∈L∞, we provide bi-Lipschitz maps. The basic building block of our construction are bi-Lipschitz maps which stretch a given compact subset of the unit square by a given factor while preserving the boundary. The construction of these stretching maps relies on a slight strengthening of the celebrated covering result of Alberti, Csörnyei, and Preiss for measurable planar sets in the case of compact sets. We apply our result to a model functional in nonlinear elasticity, the integrand of which features fast blowup as the Jacobian determinant of the deformation becomes small. For such functionals, the derivation of the equilibrium equations for minimizers requires an additional regularization of test functions, which our maps provide.","lang":"eng"}],"title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","oa":1,"arxiv":1,"status":"public","doi":"10.1016/j.jde.2018.07.045","date_updated":"2023-09-08T13:25:35Z","year":"2019","publist_id":"7770","date_created":"2018-12-11T11:44:54Z","date_published":"2019-01-05T00:00:00Z","external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"_id":"151","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Journal of Differential Equations","article_processing_charge":"No","day":"05"},{"publisher":"National Academy of Sciences","title":"Harmonic dynamics of the Abelian sandpile","quality_controlled":"1","abstract":[{"text":"The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. ","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1812015116","open_access":"1"}],"publication_identifier":{"eissn":["1091-6490"]},"doi":"10.1073/pnas.1812015116","status":"public","date_updated":"2026-06-18T18:17:35Z","arxiv":1,"oa":1,"article_type":"original","date_published":"2019-02-19T00:00:00Z","external_id":{"arxiv":["1806.10823"],"pmid":[" 30728300"],"isi":["000459074400013"]},"_id":"196","date_created":"2018-12-11T11:45:08Z","pmid":1,"year":"2019","article_processing_charge":"No","day":"19","publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"link":[{"relation":"press_release","description":"News on IST Webpage","url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/"}]},"issue":"8","corr_author":"1","citation":{"ista":"Lang M, Shkolnikov M. 2019. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences of the United States of America. 116(8), 2821–2830.","chicago":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1812015116.","ieee":"M. Lang and M. Shkolnikov, “Harmonic dynamics of the Abelian sandpile,” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 8. National Academy of Sciences, pp. 2821–2830, 2019.","mla":"Lang, Moritz, and Mikhail Shkolnikov. “Harmonic Dynamics of the Abelian Sandpile.” Proceedings of the National Academy of Sciences of the United States of America, vol. 116, no. 8, National Academy of Sciences, 2019, pp. 2821–30, doi:10.1073/pnas.1812015116.","short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 2821–2830.","ama":"Lang M, Shkolnikov M. Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences of the United States of America. 2019;116(8):2821-2830. doi:10.1073/pnas.1812015116","apa":"Lang, M., & Shkolnikov, M. (2019). Harmonic dynamics of the Abelian sandpile. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1812015116"},"page":"2821-2830","oa_version":"Published Version","language":[{"iso":"eng"}],"acknowledgement":"M.L. is grateful to the members of the C Guet and G Tkacik groups for valuable comments and support. M.S. is grateful to Nikita Kalinin for inspiring communications.\r\n","intvolume":" 116","ddc":["500","570"],"scopus_import":"1","month":"02","volume":116,"isi":1,"publication_status":"published","author":[{"first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","full_name":"Lang, Moritz"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","orcid":"0000-0002-4310-178X"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}]},{"language":[{"iso":"eng"}],"page":"909–928","oa_version":"Preprint","intvolume":" 5","scopus_import":1,"publication_status":"published","department":[{"_id":"TaHa"}],"author":[{"full_name":"Kalinin, Nikita","last_name":"Kalinin","first_name":"Nikita"},{"first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","full_name":"Shkolnikov, Mikhail","last_name":"Shkolnikov"}],"month":"09","volume":5,"ec_funded":1,"citation":{"apa":"Kalinin, N., & Shkolnikov, M. (2019). Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s40879-018-0218-0","ama":"Kalinin N, Shkolnikov M. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 2019;5(3):909–928. doi:10.1007/s40879-018-0218-0","short":"N. Kalinin, M. Shkolnikov, European Journal of Mathematics 5 (2019) 909–928.","mla":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics, vol. 5, no. 3, Springer Nature, 2019, pp. 909–928, doi:10.1007/s40879-018-0218-0.","chicago":"Kalinin, Nikita, and Mikhail Shkolnikov. “Tropical Formulae for Summation over a Part of SL(2,Z).” European Journal of Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40879-018-0218-0.","ieee":"N. Kalinin and M. Shkolnikov, “Tropical formulae for summation over a part of SL(2,Z),” European Journal of Mathematics, vol. 5, no. 3. Springer Nature, pp. 909–928, 2019.","ista":"Kalinin N, Shkolnikov M. 2019. Tropical formulae for summation over a part of SL(2,Z). European Journal of Mathematics. 5(3), 909–928."},"issue":"3","date_created":"2018-12-11T11:46:29Z","date_published":"2019-09-15T00:00:00Z","_id":"441","external_id":{"arxiv":["1711.02089"]},"year":"2019","publist_id":"7382","article_processing_charge":"No","day":"15","type":"journal_article","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication":"European Journal of Mathematics","publisher":"Springer Nature","title":"Tropical formulae for summation over a part of SL(2,Z)","quality_controlled":"1","publication_identifier":{"eissn":["2199-6768"],"issn":["2199-675X"]},"main_file_link":[{"url":"https://arxiv.org/abs/1711.02089","open_access":"1"}],"arxiv":1,"project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"date_updated":"2021-01-12T07:56:46Z","doi":"10.1007/s40879-018-0218-0","status":"public","article_type":"original","oa":1},{"day":"01","article_processing_charge":"Yes (via OA deal)","type":"journal_article","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Journal of the London Mathematical Society","date_created":"2018-12-11T11:44:06Z","external_id":{"isi":["000470025900008"]},"_id":"5","date_published":"2019-06-01T00:00:00Z","publist_id":"8052","year":"2019","file_date_updated":"2020-07-14T12:46:35Z","doi":"10.1112/jlms.12193","status":"public","date_updated":"2023-09-19T10:13:08Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"quality_controlled":"1","title":"The wonderful compactification for quantum groups","abstract":[{"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.","lang":"eng"}],"publisher":"Wiley","file":[{"date_updated":"2020-07-14T12:46:35Z","content_type":"application/pdf","checksum":"1be56239b2cd740a0e9a084f773c22f6","file_id":"7238","access_level":"open_access","file_size":431754,"creator":"kschuh","date_created":"2020-01-07T13:31:53Z","relation":"main_file","file_name":"2019_Wiley_Ganev.pdf"}],"scopus_import":"1","intvolume":" 99","ddc":["510"],"author":[{"first_name":"Iordan V","id":"447491B8-F248-11E8-B48F-1D18A9856A87","full_name":"Ganev, Iordan V","last_name":"Ganev"}],"department":[{"_id":"TaHa"}],"publication_status":"published","isi":1,"month":"06","volume":99,"language":[{"iso":"eng"}],"oa_version":"Published Version","page":"778-806","has_accepted_license":"1","citation":{"ista":"Ganev IV. 2019. The wonderful compactification for quantum groups. Journal of the London Mathematical Society. 99(3), 778–806.","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.","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.","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"},"issue":"3"},{"date_published":"2019-02-01T00:00:00Z","external_id":{"pmid":["30559456"],"isi":["000457468300011"]},"_id":"5789","acknowledged_ssus":[{"_id":"Bio"}],"date_created":"2018-12-30T22:59:15Z","pmid":1,"file_date_updated":"2020-10-21T07:18:35Z","year":"2019","article_processing_charge":"No","day":"01","publication":"Nature Cell Biology","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_updated":"2020-10-21T07:18:35Z","success":1,"checksum":"e38523787b3bc84006f2793de99ad70f","content_type":"application/pdf","file_id":"8685","relation":"main_file","date_created":"2020-10-21T07:18:35Z","file_size":71590590,"creator":"dernst","access_level":"open_access","file_name":"2018_NatureCellBio_Petridou_accepted.pdf"}],"publisher":"Nature Publishing Group","abstract":[{"lang":"eng","text":"Tissue morphogenesis is driven by mechanical forces that elicit changes in cell size, shape and motion. The extent by which forces deform tissues critically depends on the rheological properties of the recipient tissue. Yet, whether and how dynamic changes in tissue rheology affect tissue morphogenesis and how they are regulated within the developing organism remain unclear. Here, we show that blastoderm spreading at the onset of zebrafish morphogenesis relies on a rapid, pronounced and spatially patterned tissue fluidization. Blastoderm fluidization is temporally controlled by mitotic cell rounding-dependent cell–cell contact disassembly during the last rounds of cell cleavages. Moreover, fluidization is spatially restricted to the central blastoderm by local activation of non-canonical Wnt signalling within the blastoderm margin, increasing cell cohesion and thereby counteracting the effect of mitotic rounding on contact disassembly. Overall, our results identify a fluidity transition mediated by loss of cell cohesion as a critical regulator of embryo morphogenesis."}],"title":"Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling","quality_controlled":"1","publication_identifier":{"issn":["1465-7392"]},"project":[{"name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"ALTF710-2016","name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425"}],"status":"public","doi":"10.1038/s41556-018-0247-4","date_updated":"2025-07-10T11:52:59Z","oa":1,"article_type":"original","page":"169–178","oa_version":"Submitted Version","language":[{"iso":"eng"}],"intvolume":" 21","ddc":["570"],"scopus_import":"1","month":"02","volume":21,"isi":1,"publication_status":"published","author":[{"id":"2A003F6C-F248-11E8-B48F-1D18A9856A87","first_name":"Nicoletta","orcid":"0000-0002-8451-1195","last_name":"Petridou","full_name":"Petridou, Nicoletta"},{"first_name":"Silvia","last_name":"Grigolon","full_name":"Grigolon, Silvia"},{"first_name":"Guillaume","full_name":"Salbreux, Guillaume","last_name":"Salbreux"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B"},{"first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"department":[{"_id":"CaHe"},{"_id":"EdHa"}],"ec_funded":1,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/when-a-fish-becomes-fluid/","description":"News on IST Homepage","relation":"press_release"}]},"has_accepted_license":"1","citation":{"mla":"Petridou, Nicoletta, et al. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology, vol. 21, Nature Publishing Group, 2019, pp. 169–178, doi:10.1038/s41556-018-0247-4.","chicago":"Petridou, Nicoletta, Silvia Grigolon, Guillaume Salbreux, Edouard B Hannezo, and Carl-Philipp J Heisenberg. “Fluidization-Mediated Tissue Spreading by Mitotic Cell Rounding and Non-Canonical Wnt Signalling.” Nature Cell Biology. Nature Publishing Group, 2019. https://doi.org/10.1038/s41556-018-0247-4.","ieee":"N. Petridou, S. Grigolon, G. Salbreux, E. B. Hannezo, and C.-P. J. Heisenberg, “Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling,” Nature Cell Biology, vol. 21. Nature Publishing Group, pp. 169–178, 2019.","ista":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. 2019. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 21, 169–178.","apa":"Petridou, N., Grigolon, S., Salbreux, G., Hannezo, E. B., & Heisenberg, C.-P. J. (2019). Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0247-4","ama":"Petridou N, Grigolon S, Salbreux G, Hannezo EB, Heisenberg C-PJ. Fluidization-mediated tissue spreading by mitotic cell rounding and non-canonical Wnt signalling. Nature Cell Biology. 2019;21:169–178. doi:10.1038/s41556-018-0247-4","short":"N. Petridou, S. Grigolon, G. Salbreux, E.B. Hannezo, C.-P.J. Heisenberg, Nature Cell Biology 21 (2019) 169–178."}},{"page":"365-394","oa_version":"Preprint","language":[{"iso":"eng"}],"volume":91,"month":"08","publication_status":"published","isi":1,"department":[{"_id":"UlWa"}],"author":[{"first_name":"Steven","last_name":"Chaplick","full_name":"Chaplick, Steven"},{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774"},{"last_name":"Klavík","full_name":"Klavík, Pavel","first_name":"Pavel"}],"intvolume":" 91","scopus_import":"1","issue":"4","citation":{"ieee":"S. Chaplick, R. Fulek, and P. Klavík, “Extending partial representations of circle graphs,” Journal of Graph Theory, vol. 91, no. 4. Wiley, pp. 365–394, 2019.","chicago":"Chaplick, Steven, Radoslav Fulek, and Pavel Klavík. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory. Wiley, 2019. https://doi.org/10.1002/jgt.22436.","mla":"Chaplick, Steven, et al. “Extending Partial Representations of Circle Graphs.” Journal of Graph Theory, vol. 91, no. 4, Wiley, 2019, pp. 365–94, doi:10.1002/jgt.22436.","ista":"Chaplick S, Fulek R, Klavík P. 2019. Extending partial representations of circle graphs. Journal of Graph Theory. 91(4), 365–394.","ama":"Chaplick S, Fulek R, Klavík P. Extending partial representations of circle graphs. Journal of Graph Theory. 2019;91(4):365-394. doi:10.1002/jgt.22436","apa":"Chaplick, S., Fulek, R., & Klavík, P. (2019). Extending partial representations of circle graphs. Journal of Graph Theory. Wiley. https://doi.org/10.1002/jgt.22436","short":"S. Chaplick, R. Fulek, P. Klavík, Journal of Graph Theory 91 (2019) 365–394."},"ec_funded":1,"year":"2019","date_published":"2019-08-01T00:00:00Z","_id":"5790","external_id":{"isi":["000485392800004"],"arxiv":["1309.2399"]},"date_created":"2018-12-30T22:59:15Z","publication":"Journal of Graph Theory","type":"journal_article","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","day":"01","main_file_link":[{"url":"https://arxiv.org/abs/1309.2399","open_access":"1"}],"publication_identifier":{"issn":["0364-9024"]},"publisher":"Wiley","quality_controlled":"1","abstract":[{"text":"The partial representation extension problem is a recently introduced generalization of the recognition problem. A circle graph is an intersection graph of chords of a circle. We study the partial representation extension problem for circle graphs, where the input consists of a graph G and a partial representation R′ giving some predrawn chords that represent an induced subgraph of G. The question is whether one can extend R′ to a representation R of the entire graph G, that is, whether one can draw the remaining chords into a partially predrawn representation to obtain a representation of G. Our main result is an O(n3) time algorithm for partial representation extension of circle graphs, where n is the number of vertices. To show this, we describe the structure of all representations of a circle graph using split decomposition. This can be of independent interest.","lang":"eng"}],"title":"Extending partial representations of circle graphs","oa":1,"article_type":"original","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"date_updated":"2026-04-16T09:47:19Z","doi":"10.1002/jgt.22436","status":"public","arxiv":1},{"intvolume":" 1893","day":"01","scopus_import":1,"publication":"The hippo pathway","month":"01","volume":1893,"type":"book_chapter","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"author":[{"full_name":"Asaoka, Yoichi","last_name":"Asaoka","first_name":"Yoichi"},{"full_name":"Morita, Hitoshi","last_name":"Morita","first_name":"Hitoshi"},{"last_name":"Furumoto","full_name":"Furumoto, Hiroko","first_name":"Hiroko"},{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"Makoto","full_name":"Furutani-Seiki, Makoto","last_name":"Furutani-Seiki"}],"date_published":"2019-01-01T00:00:00Z","_id":"5793","editor":[{"first_name":"Alexander","full_name":"Hergovich, Alexander","last_name":"Hergovich"}],"date_created":"2019-01-06T22:59:11Z","page":"167-181","oa_version":"None","year":"2019","language":[{"iso":"eng"}],"date_updated":"2021-01-12T08:03:30Z","status":"public","doi":"10.1007/978-1-4939-8910-2_14","alternative_title":["MIMB"],"publisher":"Springer","abstract":[{"lang":"eng","text":"The transcription coactivator, Yes-associated protein (YAP), which is a nuclear effector of the Hippo signaling pathway, has been shown to be a mechano-transducer. By using mutant fish and human 3D spheroids, we have recently demonstrated that YAP is also a mechano-effector. YAP functions in three-dimensional (3D) morphogenesis of organ and global body shape by controlling actomyosin-mediated tissue tension. In this chapter, we present a platform that links the findings in fish embryos with human cells. The protocols for analyzing tissue tension-mediated global body shape/organ morphogenesis in vivo and ex vivo using medaka fish embryos and in vitro using human cell spheroids represent useful tools for unraveling the molecular mechanisms by which YAP functions in regulating global body/organ morphogenesis."}],"title":"Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids","quality_controlled":"1","series_title":"Methods in Molecular Biology","citation":{"apa":"Asaoka, Y., Morita, H., Furumoto, H., Heisenberg, C.-P. J., & Furutani-Seiki, M. (2019). Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In A. Hergovich (Ed.), The hippo pathway (Vol. 1893, pp. 167–181). Springer. https://doi.org/10.1007/978-1-4939-8910-2_14","ama":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: Hergovich A, ed. The Hippo Pathway. Vol 1893. Methods in Molecular Biology. Springer; 2019:167-181. doi:10.1007/978-1-4939-8910-2_14","short":"Y. Asaoka, H. Morita, H. Furumoto, C.-P.J. Heisenberg, M. Furutani-Seiki, in:, A. Hergovich (Ed.), The Hippo Pathway, Springer, 2019, pp. 167–181.","mla":"Asaoka, Yoichi, et al. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” The Hippo Pathway, edited by Alexander Hergovich, vol. 1893, Springer, 2019, pp. 167–81, doi:10.1007/978-1-4939-8910-2_14.","chicago":"Asaoka, Yoichi, Hitoshi Morita, Hiroko Furumoto, Carl-Philipp J Heisenberg, and Makoto Furutani-Seiki. “Studying YAP-Mediated 3D Morphogenesis Using Fish Embryos and Human Spheroids.” In The Hippo Pathway, edited by Alexander Hergovich, 1893:167–81. Methods in Molecular Biology. Springer, 2019. https://doi.org/10.1007/978-1-4939-8910-2_14.","ieee":"Y. Asaoka, H. Morita, H. Furumoto, C.-P. J. Heisenberg, and M. Furutani-Seiki, “Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids,” in The hippo pathway, vol. 1893, A. Hergovich, Ed. Springer, 2019, pp. 167–181.","ista":"Asaoka Y, Morita H, Furumoto H, Heisenberg C-PJ, Furutani-Seiki M. 2019.Studying YAP-mediated 3D morphogenesis using fish embryos and human spheroids. In: The hippo pathway. MIMB, vol. 1893, 167–181."},"publication_identifier":{"isbn":["978-1-4939-8909-6"]}},{"_id":"5817","external_id":{"pmid":["30629082"],"isi":["000457329700003"]},"date_published":"2019-01-10T00:00:00Z","pmid":1,"license":"https://creativecommons.org/licenses/by-nc-nd/3.0/","date_created":"2019-01-11T07:37:47Z","file_date_updated":"2020-10-09T11:00:05Z","year":"2019","day":"10","article_processing_charge":"No","publication":"Soft Matter","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","file":[{"relation":"main_file","date_created":"2020-10-09T11:00:05Z","access_level":"open_access","file_size":5370762,"creator":"bkavcic","file_name":"lmt_sftmtr_V8.pdf","date_updated":"2020-10-09T11:00:05Z","success":1,"file_id":"8641","checksum":"614c337d6424ccd3d48d1b1f9513510d","content_type":"application/pdf"}],"title":"Limiting shapes of confined lipid vesicles","quality_controlled":"1","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."}],"publisher":"Royal Society of Chemistry","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"status":"public","doi":"10.1039/c8sm01956h","date_updated":"2024-10-09T20:58:29Z","oa":1,"tmp":{"short":"CC BY-NC-ND (3.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/3.0/legalcode"},"article_type":"original","oa_version":"Submitted Version","page":"602-614","language":[{"iso":"eng"}],"scopus_import":"1","ddc":["530"],"intvolume":" 15","volume":15,"month":"01","department":[{"_id":"GaTk"}],"author":[{"orcid":"0000-0001-6041-254X","last_name":"Kavcic","full_name":"Kavcic, Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","first_name":"Bor"},{"full_name":"Sakashita, A.","last_name":"Sakashita","first_name":"A."},{"last_name":"Noguchi","full_name":"Noguchi, H.","first_name":"H."},{"first_name":"P.","full_name":"Ziherl, P.","last_name":"Ziherl"}],"publication_status":"published","isi":1,"has_accepted_license":"1","issue":"4","citation":{"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","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","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.","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.","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.","ista":"Kavcic B, Sakashita A, Noguchi H, Ziherl P. 2019. Limiting shapes of confined lipid vesicles. Soft Matter. 15(4), 602–614."},"corr_author":"1"},{"publisher":"Elsevier","abstract":[{"text":"Hippocampus is needed for both spatial working and reference memories. Here, using a radial eight-arm maze, we examined how the combined demand on these memories influenced CA1 place cell assemblies while reference memories were partially updated. This was contrasted with control tasks requiring only working memory or the update of reference memory. Reference memory update led to the reward-directed place field shifts at newly rewarded arms and to the gradual strengthening of firing in passes between newly rewarded arms but not between those passes that included a familiar-rewarded arm. At the maze center, transient network synchronization periods preferentially replayed trajectories of the next chosen arm in reference memory tasks but the previously visited arm in the working memory task. Hence, reference memory demand was uniquely associated with a gradual, goal novelty-related reorganization of place cell assemblies and with trajectory replay that reflected the animal's decision of which arm to visit next.","lang":"eng"}],"quality_controlled":"1","title":"Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze","publication_identifier":{"issn":["1097-4199"]},"main_file_link":[{"url":"https://www.doi.org/10.1016/j.neuron.2018.11.015","open_access":"1"}],"project":[{"call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511"}],"doi":"10.1016/j.neuron.2018.11.015","date_updated":"2026-06-18T18:56:25Z","status":"public","article_type":"original","oa":1,"date_created":"2019-01-13T22:59:10Z","date_published":"2019-01-02T00:00:00Z","_id":"5828","external_id":{"isi":["000454791500014"]},"year":"2019","article_processing_charge":"No","day":"02","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Neuron","ec_funded":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"837"}],"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/reading-rats-minds/","description":"News on IST Homepage"}]},"citation":{"ama":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 2019;101(1):119-132.e4. doi:10.1016/j.neuron.2018.11.015","apa":"Xu, H., Baracskay, P., O’Neill, J., & Csicsvari, J. L. (2019). Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.11.015","short":"H. Xu, P. Baracskay, J. O’Neill, J.L. Csicsvari, Neuron 101 (2019) 119–132.e4.","ieee":"H. Xu, P. Baracskay, J. O’Neill, and J. L. Csicsvari, “Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze,” Neuron, vol. 101, no. 1. Elsevier, p. 119–132.e4, 2019.","chicago":"Xu, Haibing, Peter Baracskay, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2018.11.015.","mla":"Xu, Haibing, et al. “Assembly Responses of Hippocampal CA1 Place Cells Predict Learned Behavior in Goal-Directed Spatial Tasks on the Radial Eight-Arm Maze.” Neuron, vol. 101, no. 1, Elsevier, 2019, p. 119–132.e4, doi:10.1016/j.neuron.2018.11.015.","ista":"Xu H, Baracskay P, O’Neill J, Csicsvari JL. 2019. Assembly responses of hippocampal CA1 place cells predict learned behavior in goal-directed spatial tasks on the radial eight-arm maze. Neuron. 101(1), 119–132.e4."},"issue":"1","language":[{"iso":"eng"}],"page":"119-132.e4","oa_version":"Published Version","ddc":["570"],"intvolume":" 101","scopus_import":"1","isi":1,"publication_status":"published","author":[{"full_name":"Xu, Haibing","last_name":"Xu","id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing"},{"last_name":"Baracskay","full_name":"Baracskay, Peter","id":"361CC00E-F248-11E8-B48F-1D18A9856A87","first_name":"Peter"},{"id":"426376DC-F248-11E8-B48F-1D18A9856A87","first_name":"Joseph","last_name":"O'Neill","full_name":"O'Neill, Joseph"},{"first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036"}],"department":[{"_id":"JoCs"}],"month":"01","volume":101},{"publication":"Plant Cell and Environment","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","day":"01","article_processing_charge":"No","year":"2019","external_id":{"pmid":["30378140"],"isi":["000459014800021"]},"_id":"5830","date_published":"2019-03-01T00:00:00Z","pmid":1,"date_created":"2019-01-13T22:59:11Z","oa":1,"article_type":"original","date_updated":"2026-06-18T18:56:52Z","status":"public","doi":"10.1111/pce.13475","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"publication_identifier":{"issn":["0140-7791"]},"abstract":[{"lang":"eng","text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants."}],"title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","quality_controlled":"1","publisher":"Wiley","volume":42,"month":"03","department":[{"_id":"JiFr"}],"author":[{"first_name":"Luosha","full_name":"Zhang, Luosha","last_name":"Zhang"},{"last_name":"Shi","full_name":"Shi, Xiong","first_name":"Xiong"},{"first_name":"Yutao","last_name":"Zhang","full_name":"Zhang, Yutao"},{"full_name":"Wang, Jiajing","last_name":"Wang","first_name":"Jiajing"},{"first_name":"Jingwei","full_name":"Yang, Jingwei","last_name":"Yang"},{"last_name":"Ishida","full_name":"Ishida, Takashi","first_name":"Takashi"},{"first_name":"Wenqian","full_name":"Jiang, Wenqian","last_name":"Jiang"},{"first_name":"Xiangyu","full_name":"Han, Xiangyu","last_name":"Han"},{"full_name":"Kang, Jingke","last_name":"Kang","first_name":"Jingke"},{"first_name":"Xuening","full_name":"Wang, Xuening","last_name":"Wang"},{"last_name":"Pan","full_name":"Pan, Lixia","first_name":"Lixia"},{"first_name":"Shuo","last_name":"Lv","full_name":"Lv, Shuo"},{"first_name":"Bing","last_name":"Cao","full_name":"Cao, Bing"},{"last_name":"Zhang","full_name":"Zhang, Yonghong","first_name":"Yonghong"},{"last_name":"Wu","full_name":"Wu, Jinbin","first_name":"Jinbin"},{"last_name":"Han","full_name":"Han, Huibin","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"first_name":"Zhubing","last_name":"Hu","full_name":"Hu, Zhubing"},{"full_name":"Cui, Langjun","last_name":"Cui","first_name":"Langjun"},{"last_name":"Sawa","full_name":"Sawa, Shinichiro","first_name":"Shinichiro"},{"first_name":"Junmin","full_name":"He, Junmin","last_name":"He"},{"last_name":"Wang","full_name":"Wang, Guodong","first_name":"Guodong"}],"isi":1,"publication_status":"published","acknowledgement":"We thank Drs. Juan Xu, Yongfeng Guo, and Annie Marion-Poll for sharing materials. We are grateful to Profs. Xiaoping She for helpful discussion and Zhezhi Wang for his generosity in providing laboratory facilities. The study is supported by the National Natural Science Foundation of China (31771556, 31271575, and 31200902 to G. W.), by the 100-Talent Program of Shaanxi Province (to G. W.), by the Fundamental Research Funds for the Central Universities (GK201702016 to G. W.; GK201603110 to L. C.), partly by the open funds of the State Key Laboratory of Plant Physiology and Biochemistry (SKLPPBKF1805), and by the Initial Project for Post-Graduates of Hubei University of Medicine (2016QDJZR14 to Y. Z.).","scopus_import":"1","intvolume":" 42","ddc":["580"],"oa_version":"Published Version","page":"1033-1044","language":[{"iso":"eng"}],"OA_place":"publisher","issue":"3","OA_type":"free access","citation":{"ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2019. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 42(3), 1033–1044.","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment, vol. 42, no. 3. Wiley, pp. 1033–1044, 2019.","chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2019. https://doi.org/10.1111/pce.13475.","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, vol. 42, no. 3, Wiley, 2019, pp. 1033–44, doi:10.1111/pce.13475.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment 42 (2019) 1033–1044.","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2019;42(3):1033-1044. doi:10.1111/pce.13475","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2019). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475"}}]