[{"doi":"10.1016/j.cub.2019.06.084","acknowledgement":"We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.).","intvolume":" 29","date_updated":"2025-01-14T14:31:02Z","status":"public","publisher":"Elsevier","type":"journal_article","keyword":["General Agricultural and Biological Sciences","General Biochemistry","Genetics and Molecular Biology"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","year":"2019","pmid":1,"_id":"12190","page":"2676-2686.e3","publication_identifier":{"issn":["0960-9822"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2023-01-16T09:16:33Z","citation":{"apa":"Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2019.06.084","mla":"Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.","ieee":"E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier, p. 2676–2686.e3, 2019.","chicago":"Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier, 2019. https://doi.org/10.1016/j.cub.2019.06.084.","ama":"Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084","ista":"Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.","short":"E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3."},"volume":29,"article_processing_charge":"No","month":"08","date_published":"2019-08-19T00:00:00Z","scopus_import":"1","publication_status":"published","extern":"1","abstract":[{"lang":"eng","text":"Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor."}],"day":"19","issue":"16","publication":"Current Biology","oa_version":"None","author":[{"last_name":"Lawrence","first_name":"Emma J.","full_name":"Lawrence, Emma J."},{"full_name":"Gao, Hongbo","last_name":"Gao","first_name":"Hongbo"},{"last_name":"Tock","first_name":"Andrew J.","full_name":"Tock, Andrew J."},{"last_name":"Lambing","first_name":"Christophe","full_name":"Lambing, Christophe"},{"first_name":"Alexander R.","full_name":"Blackwell, Alexander R.","last_name":"Blackwell"},{"orcid":"0000-0002-4008-1234","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","first_name":"Xiaoqi","full_name":"Feng, Xiaoqi"},{"last_name":"Henderson","first_name":"Ian R.","full_name":"Henderson, Ian R."}],"external_id":{"pmid":["31378616"]},"department":[{"_id":"XiFe"}],"title":"Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis"},{"publication":"eLife","abstract":[{"lang":"eng","text":"Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation."}],"day":"28","ddc":["580"],"oa_version":"Published Version","article_number":"42530","has_accepted_license":"1","publication_status":"published","extern":"1","scopus_import":"1","file":[{"date_created":"2023-02-07T09:42:46Z","date_updated":"2023-02-07T09:42:46Z","access_level":"open_access","relation":"main_file","checksum":"ea6b89c20d59e5eb3646916fe5d568ad","creator":"alisjak","file_id":"12525","success":1,"file_name":"2019_elife_He.pdf","file_size":2493837,"content_type":"application/pdf"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"XiFe"}],"title":"Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation","author":[{"full_name":"He, Shengbo","last_name":"He","first_name":"Shengbo"},{"first_name":"Martin","full_name":"Vickers, Martin","last_name":"Vickers"},{"last_name":"Zhang","first_name":"Jingyi","full_name":"Zhang, Jingyi"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","last_name":"Feng","first_name":"Xiaoqi"}],"license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"unknown":["31135340"]},"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12192","year":"2019","acknowledgement":"We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF).","doi":"10.7554/elife.42530","status":"public","publisher":"eLife Sciences Publications","type":"journal_article","keyword":["General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","General Medicine","General Neuroscience"],"date_updated":"2025-01-14T14:31:41Z","intvolume":" 8","article_processing_charge":"No","volume":8,"month":"05","oa":1,"citation":{"ista":"He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530.","short":"S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).","ama":"He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530","chicago":"He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, 2019. https://doi.org/10.7554/elife.42530.","apa":"He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.42530","ieee":"S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, 2019.","mla":"He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, 2019, doi:10.7554/elife.42530."},"file_date_updated":"2023-02-07T09:42:46Z","date_published":"2019-05-28T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_identifier":{"issn":["2050-084X"]},"date_created":"2023-01-16T09:17:21Z"},{"citation":{"chicago":"Amberg, Nicole, Susanne Laukoter, and Simon Hippenmeyer. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14601.","ama":"Amberg N, Laukoter S, Hippenmeyer S. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 2019;149(1):12-26. doi:10.1111/jnc.14601","apa":"Amberg, N., Laukoter, S., & Hippenmeyer, S. (2019). Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14601","mla":"Amberg, Nicole, et al. “Epigenetic Cues Modulating the Generation of Cell Type Diversity in the Cerebral Cortex.” Journal of Neurochemistry, vol. 149, no. 1, Wiley, 2019, pp. 12–26, doi:10.1111/jnc.14601.","ieee":"N. Amberg, S. Laukoter, and S. Hippenmeyer, “Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex,” Journal of Neurochemistry, vol. 149, no. 1. Wiley, pp. 12–26, 2019.","ista":"Amberg N, Laukoter S, Hippenmeyer S. 2019. Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex. Journal of Neurochemistry. 149(1), 12–26.","short":"N. Amberg, S. Laukoter, S. Hippenmeyer, Journal of Neurochemistry 149 (2019) 12–26."},"oa":1,"month":"04","volume":149,"article_processing_charge":"Yes (via OA deal)","date_published":"2019-04-01T00:00:00Z","file_date_updated":"2020-07-14T12:45:45Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:44:14Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","isi":1,"article_type":"review","year":"2019","_id":"27","page":"12-26","doi":"10.1111/jnc.14601","acknowledgement":" This work was supported by IST Austria institutional funds; NÖ Forschung und Bildung \r\nn[f+b] (C13-002) to SH; a program grant from the Human Frontiers Science Program (RGP0053/2014) to SH; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No 618444 to SH, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro)to SH.\r\n","intvolume":" 149","date_updated":"2025-04-14T07:43:05Z","status":"public","publisher":"Wiley","type":"journal_article","department":[{"_id":"SiHi"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file":[{"file_name":"2019_Wiley_Amberg.pdf","date_updated":"2020-07-14T12:45:45Z","relation":"main_file","access_level":"open_access","date_created":"2020-01-07T13:35:52Z","checksum":"db027721a95d36f5de36aadcd0bdf7e6","creator":"kschuh","file_id":"7239","file_size":889709,"content_type":"application/pdf"}],"title":"Epigenetic cues modulating the generation of cell type diversity in the cerebral cortex","author":[{"orcid":"0000-0002-3183-8207","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","full_name":"Amberg, Nicole","first_name":"Nicole","last_name":"Amberg"},{"first_name":"Susanne","last_name":"Laukoter","full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7903-3010"},{"first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"external_id":{"isi":["000462680200002"]},"ddc":["570"],"day":"01","abstract":[{"lang":"eng","text":"The cerebral cortex is composed of a large variety of distinct cell-types including projection neurons, interneurons and glial cells which emerge from distinct neural stem cell (NSC) lineages. The vast majority of cortical projection neurons and certain classes of glial cells are generated by radial glial progenitor cells (RGPs) in a highly orchestrated manner. Recent studies employing single cell analysis and clonal lineage tracing suggest that NSC and RGP lineage progression are regulated in a profound deterministic manner. In this review we focus on recent advances based mainly on correlative phenotypic data emerging from functional genetic studies in mice. We establish hypotheses to test in future research and outline a conceptual framework how epigenetic cues modulate the generation of cell-type diversity during cortical development. This article is protected by copyright. All rights reserved."}],"project":[{"grant_number":"LS13-002","_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain"},{"name":"Quantitative Structure-Function Analysis of Cerebral Cortex Assembly at Clonal Level","_id":"25D7962E-B435-11E9-9278-68D0E5697425","grant_number":"RGP0053/2014"},{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Molecular Mechanisms of Cerebral Cortex Development","grant_number":"618444"},{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425"}],"publication":"Journal of Neurochemistry","issue":"1","oa_version":"Published Version","ec_funded":1,"has_accepted_license":"1","scopus_import":"1","corr_author":"1","publication_status":"published"},{"main_file_link":[{"url":"https://arxiv.org/abs/1611.04177","open_access":"1"}],"department":[{"_id":"JaMa"}],"title":"A Feynman–Kac formula for stochastic Dirichlet problems","author":[{"first_name":"Mate","last_name":"Gerencser","full_name":"Gerencser, Mate","id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gyöngy","first_name":"István","full_name":"Gyöngy, István"}],"external_id":{"arxiv":["1611.04177"],"isi":["000458945300012"]},"issue":"3","publication":"Stochastic Processes and their Applications","day":"01","abstract":[{"text":"A representation formula for solutions of stochastic partial differential equations with Dirichlet boundary conditions is proved. The scope of our setting is wide enough to cover the general situation when the backward characteristics that appear in the usual formulation are not even defined in the Itô sense.","lang":"eng"}],"oa_version":"Preprint","publication_status":"published","scopus_import":"1","oa":1,"volume":129,"month":"03","article_processing_charge":"No","citation":{"short":"M. Gerencser, I. Gyöngy, Stochastic Processes and Their Applications 129 (2019) 995–1012.","ista":"Gerencser M, Gyöngy I. 2019. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 129(3), 995–1012.","ama":"Gerencser M, Gyöngy I. A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and their Applications. 2019;129(3):995-1012. doi:10.1016/j.spa.2018.04.003","chicago":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications. Elsevier, 2019. https://doi.org/10.1016/j.spa.2018.04.003.","mla":"Gerencser, Mate, and István Gyöngy. “A Feynman–Kac Formula for Stochastic Dirichlet Problems.” Stochastic Processes and Their Applications, vol. 129, no. 3, Elsevier, 2019, pp. 995–1012, doi:10.1016/j.spa.2018.04.003.","ieee":"M. Gerencser and I. Gyöngy, “A Feynman–Kac formula for stochastic Dirichlet problems,” Stochastic Processes and their Applications, vol. 129, no. 3. Elsevier, pp. 995–1012, 2019.","apa":"Gerencser, M., & Gyöngy, I. (2019). A Feynman–Kac formula for stochastic Dirichlet problems. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2018.04.003"},"date_published":"2019-03-01T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"date_created":"2018-12-11T11:45:42Z","isi":1,"article_type":"original","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"301","page":"995-1012","year":"2019","doi":"10.1016/j.spa.2018.04.003","date_updated":"2023-08-24T14:20:49Z","publisher":"Elsevier","type":"journal_article","status":"public","intvolume":" 129"},{"language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2018-12-11T11:44:50Z","volume":65,"article_processing_charge":"Yes (via OA deal)","month":"02","oa":1,"citation":{"ista":"Nikolic N. 2019. Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system. Current Genetics. 65(1), 133–138.","short":"N. Nikolic, Current Genetics 65 (2019) 133–138.","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.","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","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.","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."},"file_date_updated":"2020-07-14T12:44:47Z","date_published":"2019-02-01T00:00:00Z","doi":"10.1007/s00294-018-0879-8","publist_id":"7785","status":"public","type":"journal_article","publisher":"Springer","date_updated":"2025-04-15T06:50:19Z","intvolume":" 65","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"133-138","_id":"138","year":"2019","author":[{"first_name":"Nela","full_name":"Nikolic, Nela","id":"42D9CABC-F248-11E8-B48F-1D18A9856A87","last_name":"Nikolic","orcid":"0000-0001-9068-6090"}],"external_id":{"isi":["000456958800017"]},"file":[{"file_size":776399,"content_type":"application/pdf","file_name":"2019_CurrentGenetics_Nikolic.pdf","relation":"main_file","date_updated":"2020-07-14T12:44:47Z","access_level":"open_access","date_created":"2019-02-06T07:50:58Z","file_id":"5930","creator":"dernst","checksum":"6779708b0b632a1a6ed28c56f5161142"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png"},"department":[{"_id":"CaGu"}],"title":"Autoregulation of bacterial gene expression: lessons from the MazEF toxin–antitoxin system","has_accepted_license":"1","publication_status":"published","scopus_import":"1","publication":"Current Genetics","issue":"1","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"abstract":[{"lang":"eng","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."}],"ddc":["570"],"day":"01","ec_funded":1,"oa_version":"Published Version"},{"extern":"1","publication_status":"published","status":"public","type":"conference","date_updated":"2023-09-12T07:01:34Z","scopus_import":"1","publication":"8th International Conference on Learning Representations","day":"20","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14184","year":"2019","oa_version":"Preprint","author":[{"orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Tschannen, Michael","first_name":"Michael","last_name":"Tschannen"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"}],"language":[{"iso":"eng"}],"quality_controlled":"1","date_created":"2023-08-22T14:06:37Z","arxiv":1,"external_id":{"arxiv":["1905.01258"]},"conference":{"location":"Virtual","start_date":"2020-04-26","name":"ICLR: International Conference on Learning Representations","end_date":"2020-05-01"},"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.01258"}],"month":"12","oa":1,"department":[{"_id":"FrLo"}],"citation":{"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.","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.","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.","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.","short":"F. Locatello, M. Tschannen, S. Bauer, G. Rätsch, B. Schölkopf, O. Bachem, in:, 8th International Conference on Learning Representations, 2019."},"date_published":"2019-12-20T00:00:00Z","title":"Disentangling factors of variation using few labels"},{"arxiv":1,"date_created":"2023-08-22T14:08:35Z","conference":{"end_date":"2019-07-25","name":"UAI: Uncertainty in Artificial Intelligence","location":"Tel Aviv, Israel","start_date":"2019-07-22"},"language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2019-05-16T00:00:00Z","oa":1,"month":"05","volume":115,"article_processing_charge":"No","citation":{"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.","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.","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.","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.","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.","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.","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."},"date_updated":"2023-09-12T08:07:38Z","status":"public","publisher":"ML Research Press","type":"conference","intvolume":" 115","_id":"14189","page":"217-227","year":"2019","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1905.06642"]},"author":[{"first_name":"Luigi","full_name":"Gresele, Luigi","last_name":"Gresele"},{"last_name":"Rubenstein","full_name":"Rubenstein, Paul K.","first_name":"Paul K."},{"full_name":"Mehrjou, Arash","first_name":"Arash","last_name":"Mehrjou"},{"last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Bernhard","last_name":"Schölkopf","full_name":"Schölkopf, Bernhard"}],"title":"The incomplete Rosetta Stone problem: Identifiability results for multi-view nonlinear ICA","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.06642"}],"department":[{"_id":"FrLo"}],"extern":"1","publication_status":"published","scopus_import":"1","alternative_title":["PMLR"],"oa_version":"Preprint","publication":"Proceedings of the 35th Conference on Uncertainty in Artificial Intelligence","abstract":[{"lang":"eng","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."}],"day":"16"},{"title":"On the transfer of inductive bias from simulation to the real world: a new disentanglement dataset","date_published":"2019-06-07T00:00:00Z","citation":{"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.","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.","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.","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.","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.","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."},"department":[{"_id":"FrLo"}],"oa":1,"month":"06","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.03292"}],"volume":32,"conference":{"name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14","start_date":"2019-12-08","location":"Vancouver, Canada"},"arxiv":1,"external_id":{"arxiv":["1906.03292"]},"date_created":"2023-08-22T14:09:13Z","quality_controlled":"1","publication_identifier":{"isbn":["9781713807933"]},"language":[{"iso":"eng"}],"author":[{"first_name":"Muhammad Waleed","full_name":"Gondal, Muhammad Waleed","last_name":"Gondal"},{"first_name":"Manuel","full_name":"Wüthrich, Manuel","last_name":"Wüthrich"},{"full_name":"Miladinović, Đorđe","last_name":"Miladinović","first_name":"Đorđe"},{"orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco"},{"full_name":"Breidt, Martin","last_name":"Breidt","first_name":"Martin"},{"first_name":"Valentin","last_name":"Volchkov","full_name":"Volchkov, Valentin"},{"last_name":"Akpo","full_name":"Akpo, Joel","first_name":"Joel"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"last_name":"Bauer","full_name":"Bauer, Stefan","first_name":"Stefan"}],"oa_version":"Preprint","year":"2019","_id":"14190","day":"07","abstract":[{"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.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication":"Advances in Neural Information Processing Systems","intvolume":" 32","date_updated":"2023-09-13T09:46:38Z","publication_status":"published","status":"public","extern":"1","type":"conference"},{"conference":{"start_date":"2019-12-08","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14"},"date_created":"2023-08-22T14:09:35Z","arxiv":1,"publication_identifier":{"isbn":["9781713807933"]},"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2019-12-29T00:00:00Z","citation":{"short":"F. Locatello, A. Yurtsever, O. Fercoq, V. Cevher, in:, Advances in Neural Information Processing Systems, 2019, pp. 14291–14301.","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.","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.","mla":"Locatello, Francesco, et al. “Stochastic Frank-Wolfe for Composite Convex Minimization.” Advances in Neural Information Processing Systems, vol. 32, 2019, pp. 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.","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.","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."},"volume":32,"month":"12","article_processing_charge":"No","oa":1,"intvolume":" 32","status":"public","type":"conference","date_updated":"2023-09-12T08:48:45Z","year":"2019","page":"14291–14301","_id":"14191","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1901.10348"]},"author":[{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco"},{"full_name":"Yurtsever, Alp","last_name":"Yurtsever","first_name":"Alp"},{"first_name":"Olivier","full_name":"Fercoq, Olivier","last_name":"Fercoq"},{"first_name":"Volkan","last_name":"Cevher","full_name":"Cevher, Volkan"}],"title":"Stochastic Frank-Wolfe for composite convex minimization","department":[{"_id":"FrLo"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1901.10348"}],"scopus_import":"1","publication_status":"published","extern":"1","oa_version":"Preprint","day":"29","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"}],"publication":"Advances in Neural Information Processing Systems"},{"language":[{"iso":"eng"}],"author":[{"last_name":"Steenkiste","full_name":"Steenkiste, Sjoerd van","first_name":"Sjoerd van"},{"full_name":"Locatello, Francesco","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683"},{"first_name":"Jürgen","last_name":"Schmidhuber","full_name":"Schmidhuber, Jürgen"},{"last_name":"Bachem","full_name":"Bachem, Olivier","first_name":"Olivier"}],"quality_controlled":"1","publication_identifier":{"isbn":["9781713807933"]},"date_created":"2023-08-22T14:09:53Z","external_id":{"arxiv":["1905.12506"]},"arxiv":1,"conference":{"start_date":"2019-12-08","location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14"},"volume":32,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1905.12506","open_access":"1"}],"month":"05","article_processing_charge":"No","oa":1,"department":[{"_id":"FrLo"}],"citation":{"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.","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.","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.","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.","short":"S. van Steenkiste, F. Locatello, J. Schmidhuber, O. Bachem, in:, Advances in Neural Information Processing Systems, 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."},"date_published":"2019-05-29T00:00:00Z","title":"Are disentangled representations helpful for abstract visual reasoning?","status":"public","type":"conference","publication_status":"published","extern":"1","date_updated":"2024-10-14T12:28:15Z","intvolume":" 32","publication":"Advances in Neural Information Processing Systems","day":"29","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"_id":"14193","year":"2019","oa_version":"Preprint"},{"title":"On the fairness of disentangled representations","department":[{"_id":"FrLo"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1905.13662"}],"external_id":{"arxiv":["1905.13662"]},"author":[{"orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"first_name":"Gabriele","full_name":"Abbati, Gabriele","last_name":"Abbati"},{"last_name":"Rainforth","full_name":"Rainforth, Tom","first_name":"Tom"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"}],"oa_version":"Preprint","day":"08","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":"Advances in Neural Information Processing Systems","scopus_import":"1","publication_status":"published","extern":"1","date_published":"2019-12-08T00:00:00Z","citation":{"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.","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.","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.","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.","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.","short":"F. Locatello, G. Abbati, T. Rainforth, S. Bauer, B. Schölkopf, O. Bachem, in:, Advances in Neural Information Processing Systems, 2019, pp. 14611–14624."},"oa":1,"volume":32,"article_processing_charge":"No","month":"12","conference":{"location":"Vancouver, Canada","start_date":"2019-12-08","name":"NeurIPS: Neural Information Processing Systems","end_date":"2019-12-14"},"arxiv":1,"date_created":"2023-08-22T14:12:28Z","publication_identifier":{"isbn":["9781713807933"]},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2019","_id":"14197","page":"14611–14624","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 32","date_updated":"2024-10-14T12:29:05Z","type":"conference","status":"public"},{"publication":"Proceedings of the 36th International Conference on Machine Learning","day":"09","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."}],"oa_version":"Preprint","extern":"1","publication_status":"published","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.12359"}],"department":[{"_id":"FrLo"}],"title":"Challenging common assumptions in the unsupervised learning of disentangled representations","author":[{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683"},{"first_name":"Stefan","full_name":"Bauer, Stefan","last_name":"Bauer"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"first_name":"Gunnar","full_name":"Rätsch, Gunnar","last_name":"Rätsch"},{"last_name":"Gelly","first_name":"Sylvain","full_name":"Gelly, Sylvain"},{"first_name":"Bernhard","full_name":"Schölkopf, Bernhard","last_name":"Schölkopf"},{"first_name":"Olivier","full_name":"Bachem, Olivier","last_name":"Bachem"}],"external_id":{"arxiv":["1811.12359"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14200","page":"4114-4124","year":"2019","date_updated":"2024-10-14T12:29:16Z","status":"public","publisher":"ML Research Press","type":"conference","intvolume":" 97","oa":1,"month":"06","article_processing_charge":"No","volume":97,"citation":{"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.","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.","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.","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.","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.","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."},"date_published":"2019-06-09T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","arxiv":1,"date_created":"2023-08-22T14:13:08Z","conference":{"location":"Long Beach, CA, United States","start_date":"2019-06-10","end_date":"2019-06-15","name":"International Conference on Machine Learning"}},{"date_updated":"2024-10-09T21:05:24Z","publisher":"Institut für Mathematik und wissenschaftliches Rechnen der Universität Graz","publication_status":"published","status":"public","corr_author":"1","type":"conference_abstract","has_accepted_license":"1","oa_version":"Published Version","year":"2019","_id":"12901","page":"25","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"27","ddc":["000"],"publication":"AHPC19 - Austrian HPC Meeting 2019 ","conference":{"name":"AHPC: Austrian HPC Meeting","end_date":"2019-02-27","start_date":"2019-02-25","location":"Grundlsee, Austria"},"date_created":"2023-05-05T12:48:48Z","author":[{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","last_name":"Schlögl","first_name":"Alois","orcid":"0000-0002-5621-8100"},{"first_name":"Janos","full_name":"Kiss, Janos","last_name":"Kiss","id":"3D3A06F8-F248-11E8-B48F-1D18A9856A87"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","last_name":"Elefante","first_name":"Stefano","full_name":"Elefante, Stefano"}],"language":[{"iso":"eng"}],"title":"Is Debian suitable for running an HPC Cluster?","date_published":"2019-02-27T00:00:00Z","file_date_updated":"2023-05-16T07:27:09Z","citation":{"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.","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.","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.","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.","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.","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."},"department":[{"_id":"ScienComp"}],"oa":1,"file":[{"success":1,"file_name":"2019_AHPC_Schloegl.pdf","date_updated":"2023-05-16T07:27:09Z","access_level":"open_access","relation":"main_file","date_created":"2023-05-16T07:27:09Z","creator":"dernst","file_id":"12970","checksum":"acc8272027faaf30709c51ac5c58ffa4","file_size":1097603,"content_type":"application/pdf"}],"main_file_link":[{"url":"https://vsc.ac.at/fileadmin/user_upload/vsc/conferences/ahpc19/BOOKLET_AHPC19.pdf","open_access":"1"}],"article_processing_charge":"No","month":"02"},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"7205"}]},"doi":"10.5061/DRYAD.TB2RBNZWK","date_updated":"2025-07-10T11:54:22Z","publisher":"Dryad","type":"research_data_reference","status":"public","day":"02","ddc":["570"],"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","year":"2019","_id":"13067","license":"https://creativecommons.org/publicdomain/zero/1.0/","author":[{"full_name":"Johannesson, Kerstin","last_name":"Johannesson","first_name":"Kerstin"},{"first_name":"Zuzanna","last_name":"Zagrodzka","full_name":"Zagrodzka, Zuzanna"},{"first_name":"Rui","full_name":"Faria, Rui","last_name":"Faria"},{"last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969"},{"first_name":"Roger","full_name":"Butlin, Roger","last_name":"Butlin"}],"date_created":"2023-05-23T16:36:27Z","citation":{"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","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.","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.","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","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.","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.","short":"K. Johannesson, Z. Zagrodzka, R. Faria, A.M. Westram, R. Butlin, (2019)."},"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"},"department":[{"_id":"NiBa"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.tb2rbnzwk","open_access":"1"}],"article_processing_charge":"No","month":"12","title":"Data from: Is embryo abortion a postzygotic barrier to gene flow between Littorina ecotypes?","date_published":"2019-12-02T00:00:00Z"},{"year":"2019","_id":"19987","page":"675-691","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","series_title":"MXBS","OA_type":"green","intvolume":" 2","date_updated":"2025-09-23T11:59:52Z","publisher":"Springer International Publishing","status":"public","type":"book_chapter","acknowledgement":"Y.Y. would like to thank the organizers of the MATRIX program Geometric R-Matrices: from Geometry to Probability for their kind invitation, and many participants of the program for useful discussions, including Vassily Gorbounov, Andrei Okounkov, Allen Knutson, Hitoshi Konno, Paul Zinn-Justin. Proposition 1 and Sect. 3.3 are new, for which we thank Hitoshi Konno for interesting discussions and communications. These notes were written when both authors were visiting the Perimeter Institute for Theoretical Physics (PI). We are grateful to PI for the hospitality.","doi":"10.1007/978-3-030-04161-8_54","date_published":"2019-03-25T00:00:00Z","citation":{"ista":"Yang Y, Zhao G. 2019.How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. MATRIX Book Series, vol. 2, 675–691.","short":"Y. Yang, G. Zhao, in:, 2017 MATRIX Annals, Springer International Publishing, Cham, 2019, pp. 675–691.","chicago":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” In 2017 MATRIX Annals, 2:675–91. MXBS. Cham: Springer International Publishing, 2019. https://doi.org/10.1007/978-3-030-04161-8_54.","ama":"Yang Y, Zhao G. How to Sheafify an Elliptic Quantum Group. In: 2017 MATRIX Annals. Vol 2. MXBS. Cham: Springer International Publishing; 2019:675-691. doi:10.1007/978-3-030-04161-8_54","apa":"Yang, Y., & Zhao, G. (2019). How to Sheafify an Elliptic Quantum Group. In 2017 MATRIX Annals (Vol. 2, pp. 675–691). Cham: Springer International Publishing. https://doi.org/10.1007/978-3-030-04161-8_54","mla":"Yang, Yaping, and Gufang Zhao. “How to Sheafify an Elliptic Quantum Group.” 2017 MATRIX Annals, vol. 2, Springer International Publishing, 2019, pp. 675–91, doi:10.1007/978-3-030-04161-8_54.","ieee":"Y. Yang and G. Zhao, “How to Sheafify an Elliptic Quantum Group,” in 2017 MATRIX Annals, vol. 2, Cham: Springer International Publishing, 2019, pp. 675–691."},"oa":1,"month":"03","volume":2,"article_processing_charge":"No","arxiv":1,"date_created":"2025-07-10T13:31:38Z","quality_controlled":"1","publication_identifier":{"eisbn":["9783030041618"],"issn":["2523-3041"],"eissn":["2523-305X"],"isbn":["9783030041601"]},"language":[{"iso":"eng"}],"oa_version":"Preprint","day":"25","abstract":[{"text":"These lecture notes are based on Yang’s talk at the MATRIX program Geometric R-Matrices: from Geometry to Probability, at the University of Melbourne, Dec. 18–22, 2017, and Zhao’s talk at Perimeter Institute for Theoretical Physics in January 2018. We give an introductory survey of the results in Yang and Zhao (Quiver varieties and elliptic quantum groups, 2017. arxiv1708.01418). We discuss a sheafified elliptic quantum group associated to any symmetric Kac-Moody Lie algebra. The sheafification is obtained by applying the equivariant elliptic cohomological theory to the moduli space of representations of a preprojective algebra. By construction, the elliptic quantum group naturally acts on the equivariant elliptic cohomology of Nakajima quiver varieties. As an application, we obtain a relation between the sheafified elliptic quantum group and the global affine Grassmannian over an elliptic curve.","lang":"eng"}],"publication":"2017 MATRIX Annals","publication_status":"published","OA_place":"repository","alternative_title":["MATRIX Book Series"],"title":"How to Sheafify an Elliptic Quantum Group","department":[{"_id":"TaHa"}],"place":"Cham","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1803.06627"}],"external_id":{"arxiv":["1803.06627"]},"author":[{"first_name":"Yaping","full_name":"Yang, Yaping","id":"360D8648-F248-11E8-B48F-1D18A9856A87","last_name":"Yang"},{"last_name":"Zhao","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","first_name":"Gufang","full_name":"Zhao, Gufang"}]},{"citation":{"ieee":"A. De Martino, D. De Martino, and E. Marinari, “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges,” in Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–471.","mla":"De Martino, A., et al. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–71, doi:10.1142/9781786347015_0018.","apa":"De Martino, A., De Martino, D., & Marinari, E. (2019). The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In Chemical Kinetics (pp. 455–471). World Scientific Publishing. https://doi.org/10.1142/9781786347015_0018","ama":"De Martino A, De Martino D, Marinari E. The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: Chemical Kinetics. World Scientific Publishing; 2019:455-471. doi:10.1142/9781786347015_0018","chicago":"De Martino, A, Daniele De Martino, and E Marinari. “The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges.” In Chemical Kinetics, 455–71. World Scientific Publishing, 2019. https://doi.org/10.1142/9781786347015_0018.","short":"A. De Martino, D. De Martino, E. Marinari, in:, Chemical Kinetics, World Scientific Publishing, 2019, pp. 455–471.","ista":"De Martino A, De Martino D, Marinari E. 2019.The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges. In: Chemical Kinetics. , 455–471."},"oa":1,"article_processing_charge":"No","month":"09","date_published":"2019-09-01T00:00:00Z","publication_identifier":{"isbn":["9781786347008"],"eisbn":["9781786347022"]},"quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"date_created":"2025-07-10T13:34:01Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_type":"green","year":"2019","_id":"19988","page":"455-471","doi":"10.1142/9781786347015_0018","date_updated":"2025-09-23T11:53:34Z","type":"book_chapter","status":"public","publisher":"World Scientific Publishing","department":[{"_id":"GaTk"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1902.07129"}],"title":"The Essential Role of Thermodynamics in Metabolic Network Modeling: Physical Insights and Computational Challenges","author":[{"last_name":"De Martino","first_name":"A","full_name":"De Martino, A"},{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino","full_name":"De Martino, Daniele"},{"full_name":"Marinari, E","first_name":"E","last_name":"Marinari"}],"external_id":{"arxiv":["1902.07129"]},"day":"01","abstract":[{"text":"Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady-state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental knowledge on kinetic laws and parameters, but it should be supported by a correct implementation of thermodynamic constraints. In this chapter, we review the latter aspect, highlighting its computational challenges and physical insights. The simple introduction of Gibbs inequalities avoids the presence of unfeasible loops allowing for correct timescale analysis, but leads to possibly non-convex feasible flux spaces whose exploration needs efficient algorithms. We briefly review the implementation of thermodynamics through variational principles in constraint-based models of metabolic networks.","lang":"eng"}],"publication":"Chemical Kinetics","oa_version":"Preprint","OA_place":"repository","publication_status":"published"},{"date_updated":"2025-09-23T11:44:57Z","publication_status":"published","publisher":"Springer Nature","status":"public","corr_author":"1","type":"book_chapter","doi":"10.1007/978-3-662-56468-4_7","_id":"19989","page":"72-82","oa_version":"None","year":"2019","publication":"Physiologie des Menschen","OA_type":"closed access","day":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"ger","text":"Neurone empfangen Eingangssignale, konvertieren diese in Aktionspotenziale und generieren schließlich Ausgangssignale auf ihren Zielzellen. Dabei sind die zu überwindenden räumlichen Distanzen oft groß. Daher ist entscheidend, dass elektrische Signale in Nervenzellen schnell von einem zum anderen Ort geleitet werden können. Diese wichtige Aufgabe erfüllt das Axon, der „Ausgangsfortsatz“ der Nervenzelle. Für die schnelle Leitung des Aktionspotenzials sind sowohl die passiven Eigenschaften des axonalen Kabels als auch die aktiven Eigenschaften der Zellmembran von entscheidender Bedeutung. Die Evolution bedient sich zweier Tricks, um die Leitungsgeschwindigkeit des Aktionspotenzials zu maximieren. Der eine Trick ist die Zunahme des Axondurchmessers. Der andere Trick ist die Ausbildung von Markscheiden. Dies führt bei nahezu gleichem Platzbedarf zu einer Zunahme der Leistungsgeschwindigkeit um fast zwei Größenordnungen. Die Aktionspotenzialleitung an myelinisierten Axonen erfolgt „saltatorisch“."}],"series_title":"Springer-Lehrbuch","date_created":"2025-07-10T13:36:36Z","edition":"32","author":[{"last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M","full_name":"Jonas, Peter M","orcid":"0000-0001-5001-4804"}],"language":[{"iso":"ger"}],"publication_identifier":{"eissn":["2512-5214"],"isbn":["9783662564677"],"issn":["0937-7433"],"eisbn":["9783662564684"]},"quality_controlled":"1","title":"Aktionspotenzial: Fortleitung im Axon","date_published":"2019-04-02T00:00:00Z","place":"Berlin, Heidelberg","month":"04","article_processing_charge":"No","citation":{"apa":"Jonas, P. M. (2019). Aktionspotenzial: Fortleitung im Axon. In Physiologie des Menschen (32nd ed., pp. 72–82). Berlin, Heidelberg: Springer Nature. https://doi.org/10.1007/978-3-662-56468-4_7","ieee":"P. M. Jonas, “Aktionspotenzial: Fortleitung im Axon,” in Physiologie des Menschen, 32nd ed., Berlin, Heidelberg: Springer Nature, 2019, pp. 72–82.","mla":"Jonas, Peter M. “Aktionspotenzial: Fortleitung im Axon.” Physiologie des Menschen, 32nd ed., Springer Nature, 2019, pp. 72–82, doi:10.1007/978-3-662-56468-4_7.","ama":"Jonas PM. Aktionspotenzial: Fortleitung im Axon. In: Physiologie des Menschen. 32nd ed. Springer-Lehrbuch. Berlin, Heidelberg: Springer Nature; 2019:72-82. doi:10.1007/978-3-662-56468-4_7","chicago":"Jonas, Peter M. “Aktionspotenzial: Fortleitung im Axon.” In Physiologie des Menschen, 32nd ed., 72–82. Springer-Lehrbuch. Berlin, Heidelberg: Springer Nature, 2019. https://doi.org/10.1007/978-3-662-56468-4_7.","ista":"Jonas PM. 2019.Aktionspotenzial: Fortleitung im Axon. In: Physiologie des Menschen. , 72–82.","short":"P.M. Jonas, in:, Physiologie des Menschen, 32nd ed., Springer Nature, Berlin, Heidelberg, 2019, pp. 72–82."},"department":[{"_id":"PeJo"}]},{"department":[{"_id":"CaGu"},{"_id":"GaTk"},{"_id":"TaHa"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1812015116","open_access":"1"}],"title":"Harmonic dynamics of the Abelian sandpile","author":[{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz","first_name":"Moritz","last_name":"Lang"},{"last_name":"Shkolnikov","full_name":"Shkolnikov, Mikhail","first_name":"Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X"}],"external_id":{"arxiv":["1806.10823"],"pmid":[" 30728300"],"isi":["000459074400013"]},"day":"19","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"}],"issue":"8","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa_version":"Published Version","related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/famous-sandpile-model-shown-to-move-like-a-traveling-sand-dune/","description":"News on IST Webpage"}]},"scopus_import":"1","corr_author":"1","publication_status":"published","citation":{"short":"M. Lang, M. Shkolnikov, Proceedings of the National Academy of Sciences of the United States of America 116 (2019) 2821–2830.","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.","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","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.","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"},"oa":1,"volume":116,"article_processing_charge":"No","month":"02","date_published":"2019-02-19T00:00:00Z","publication_identifier":{"eissn":["1091-6490"]},"quality_controlled":"1","language":[{"iso":"eng"}],"arxiv":1,"date_created":"2018-12-11T11:45:08Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","isi":1,"article_type":"original","year":"2019","pmid":1,"_id":"196","page":"2821-2830","doi":"10.1073/pnas.1812015116","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","date_updated":"2025-06-03T11:18:16Z","type":"journal_article","publisher":"National Academy of Sciences","status":"public"},{"external_id":{"isi":["000449108500010"],"arxiv":["1408.1587"]},"author":[{"orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"full_name":"Kneuss, Olivier","first_name":"Olivier","last_name":"Kneuss"}],"title":"Bi-Sobolev solutions to the prescribed Jacobian inequality in the plane with L p data and applications to nonlinear elasticity","main_file_link":[{"url":"https://arxiv.org/abs/1408.1587","open_access":"1"}],"department":[{"_id":"JuFi"}],"publication_status":"published","scopus_import":"1","oa_version":"Preprint","publication":"Journal of Differential Equations","issue":"1","day":"05","abstract":[{"lang":"eng","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."}],"date_created":"2018-12-11T11:44:54Z","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2019-01-05T00:00:00Z","month":"01","volume":266,"article_processing_charge":"No","oa":1,"citation":{"short":"J.L. Fischer, O. Kneuss, Journal of Differential Equations 266 (2019) 257–311.","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.","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","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.","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"},"status":"public","type":"journal_article","publisher":"Elsevier","date_updated":"2023-09-08T13:25:35Z","intvolume":" 266","doi":"10.1016/j.jde.2018.07.045","publist_id":"7770","page":"257 - 311","_id":"151","year":"2019","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_published":"2019-01-02T00:00:00Z","citation":{"mla":"Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6.","ieee":"S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019.","apa":"Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6","ama":"Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6","chicago":"Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6.","short":"S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019).","ista":"Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9."},"oa":1,"volume":5,"month":"01","article_processing_charge":"No","arxiv":1,"date_created":"2022-03-18T12:09:48Z","publication_identifier":{"issn":["2522-0160"],"eissn":["2363-9555"]},"quality_controlled":"1","language":[{"iso":"eng"}],"year":"2019","_id":"10874","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_type":"original","intvolume":" 5","date_updated":"2023-09-05T15:39:31Z","status":"public","type":"journal_article","keyword":["Algebra and Number Theory"],"publisher":"Springer Nature","acknowledgement":"The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. ","doi":"10.1007/s40993-018-0146-6","title":"Modular invariants for genus 3 hyperelliptic curves","department":[{"_id":"TiBr"}],"main_file_link":[{"url":"https://arxiv.org/abs/1807.08986","open_access":"1"}],"external_id":{"arxiv":["1807.08986"]},"author":[{"full_name":"Ionica, Sorina","first_name":"Sorina","last_name":"Ionica"},{"first_name":"Pınar","full_name":"Kılıçer, Pınar","last_name":"Kılıçer"},{"full_name":"Lauter, Kristin","first_name":"Kristin","last_name":"Lauter"},{"full_name":"Lorenzo García, Elisa","last_name":"Lorenzo García","first_name":"Elisa"},{"last_name":"Manzateanu","full_name":"Manzateanu, Maria-Adelina","first_name":"Maria-Adelina","id":"be8d652e-a908-11ec-82a4-e2867729459c"},{"first_name":"Maike","full_name":"Massierer, Maike","last_name":"Massierer"},{"first_name":"Christelle","full_name":"Vincent, Christelle","last_name":"Vincent"}],"oa_version":"Preprint","day":"02","abstract":[{"lang":"eng","text":"In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM."}],"publication":"Research in Number Theory","scopus_import":"1","publication_status":"published","article_number":"9"}]