[{"year":"2021","publication_status":"published","file_date_updated":"2021-08-06T06:44:31Z","type":"journal_article","status":"public","quality_controlled":"1","article_number":"491","_id":"9760","publication_identifier":{"eissn":["2521-327X"]},"doi":"10.22331/Q-2021-07-01-491","article_type":"original","oa":1,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","scopus_import":"1","ec_funded":1,"date_created":"2021-08-01T22:01:21Z","acknowledgement":"We would like to thank D. Abanin and R. Medina for fruitful discussions and A. Smith and I. Kim for valuable feedback on the manuscript. We acknowledge support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 850899).","publication":"Quantum","title":"Quantum annealing initialization of the quantum approximate optimization algorithm","intvolume":" 5","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899","call_identifier":"H2020"}],"volume":5,"file":[{"checksum":"9706c2bb8e748e9b5b138381995a7f6f","date_created":"2021-08-06T06:44:31Z","creator":"cchlebak","file_id":"9774","relation":"main_file","access_level":"open_access","file_name":"2021_Quantum_Sack.pdf","content_type":"application/pdf","date_updated":"2021-08-06T06:44:31Z","file_size":2312482}],"article_processing_charge":"Yes","month":"07","arxiv":1,"date_published":"2021-07-01T00:00:00Z","related_material":{"record":[{"id":"14622","status":"public","relation":"dissertation_contains"}]},"publisher":"Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften","ddc":["530"],"isi":1,"external_id":{"arxiv":["2101.05742"],"isi":["000669830600001"]},"abstract":[{"text":"The quantum approximate optimization algorithm (QAOA) is a prospective near-term quantum algorithm due to its modest circuit depth and promising benchmarks. However, an external parameter optimization required in the QAOA could become a performance bottleneck. This motivates studies of the optimization landscape and search for heuristic ways of parameter initialization. In this work we visualize the optimization landscape of the QAOA applied to the MaxCut problem on random graphs, demonstrating that random initialization of the QAOA is prone to converging to local minima with suboptimal performance. We introduce the initialization of QAOA parameters based on the Trotterized quantum annealing (TQA) protocol, parameterized by the Trotter time step. We find that the TQA initialization allows to circumvent\r\nthe issue of false minima for a broad range of time steps, yielding the same performance as the best result out of an exponentially scaling number of random initializations. Moreover, we demonstrate that the optimal value of the time step coincides with the point of proliferation of Trotter errors in quantum annealing. Our results suggest practical ways of initializing QAOA protocols on near-term quantum devices and reveal new connections between QAOA and quantum annealing.","lang":"eng"}],"date_updated":"2026-08-16T22:31:06Z","department":[{"_id":"GradSch"},{"_id":"MaSe"}],"corr_author":"1","author":[{"orcid":"0000-0001-5400-8508","full_name":"Sack, Stefan","id":"dd622248-f6e0-11ea-865d-ce382a1c81a5","last_name":"Sack","first_name":"Stefan"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"ama":"Sack S, Serbyn M. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 2021;5. doi:10.22331/Q-2021-07-01-491","short":"S. Sack, M. Serbyn, Quantum 5 (2021).","apa":"Sack, S., & Serbyn, M. (2021). Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften. https://doi.org/10.22331/Q-2021-07-01-491","ieee":"S. Sack and M. Serbyn, “Quantum annealing initialization of the quantum approximate optimization algorithm,” Quantum, vol. 5. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021.","chicago":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum. Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021. https://doi.org/10.22331/Q-2021-07-01-491.","ista":"Sack S, Serbyn M. 2021. Quantum annealing initialization of the quantum approximate optimization algorithm. Quantum. 5, 491.","mla":"Sack, Stefan, and Maksym Serbyn. “Quantum Annealing Initialization of the Quantum Approximate Optimization Algorithm.” Quantum, vol. 5, 491, Verein zur Förderung des Open Access Publizierens in den Quantenwissenschaften, 2021, doi:10.22331/Q-2021-07-01-491."}},{"article_type":"original","publication_identifier":{"issn":["1433-2779"],"eissn":["1433-2787"]},"doi":"10.1007/s10009-020-00582-z","_id":"10861","status":"public","type":"journal_article","publication_status":"published","year":"2020","quality_controlled":"1","volume":22,"article_processing_charge":"No","month":"08","title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","page":"741-758","keyword":["Information Systems","Software"],"intvolume":" 22","publication":"International Journal on Software Tools for Technology Transfer","day":"03","date_created":"2022-03-18T10:10:53Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We introduce in this paper AMT2.0, a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended signal temporal logic, which integrates timed regular expressions within signal temporal logic. The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal. We demonstrate the tool functionality on several running examples and case studies, and evaluate its performance."}],"department":[{"_id":"ToHe"}],"date_updated":"2024-10-09T20:58:18Z","external_id":{"isi":["000555398600001"]},"isi":1,"related_material":{"record":[{"id":"299","relation":"earlier_version","status":"public"}]},"publisher":"Springer Nature","issue":"6","date_published":"2020-08-03T00:00:00Z","citation":{"chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer. Springer Nature, 2020. https://doi.org/10.1007/s10009-020-00582-z.","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6. Springer Nature, pp. 741–758, 2020.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2020. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 22(6), 741–758.","mla":"Nickovic, Dejan, et al. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” International Journal on Software Tools for Technology Transfer, vol. 22, no. 6, Springer Nature, 2020, pp. 741–58, doi:10.1007/s10009-020-00582-z.","apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2020). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-020-00582-z","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, International Journal on Software Tools for Technology Transfer 22 (2020) 741–758.","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. International Journal on Software Tools for Technology Transfer. 2020;22(6):741-758. doi:10.1007/s10009-020-00582-z"},"oa_version":"None","language":[{"iso":"eng"}],"author":[{"last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","full_name":"Nickovic, Dejan"},{"full_name":"Lebeltel, Olivier","last_name":"Lebeltel","first_name":"Olivier"},{"last_name":"Maler","first_name":"Oded","full_name":"Maler, Oded"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dogan","last_name":"Ulus","full_name":"Ulus, Dogan"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"author":[{"full_name":"Bao, Zhigang","orcid":"0000-0003-3036-1475","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös","orcid":"0000-0001-5366-9603","full_name":"Erdös, László"},{"first_name":"Kevin","last_name":"Schnelli","full_name":"Schnelli, Kevin"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","corr_author":"1","citation":{"apa":"Bao, Z., Erdös, L., & Schnelli, K. (2020). Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2020.108639","ama":"Bao Z, Erdös L, Schnelli K. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 2020;279(7). doi:10.1016/j.jfa.2020.108639","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 279 (2020).","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis. Elsevier, 2020. https://doi.org/10.1016/j.jfa.2020.108639.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Spectral rigidity for addition of random matrices at the regular edge,” Journal of Functional Analysis, vol. 279, no. 7. Elsevier, 2020.","ista":"Bao Z, Erdös L, Schnelli K. 2020. Spectral rigidity for addition of random matrices at the regular edge. Journal of Functional Analysis. 279(7), 108639.","mla":"Bao, Zhigang, et al. “Spectral Rigidity for Addition of Random Matrices at the Regular Edge.” Journal of Functional Analysis, vol. 279, no. 7, 108639, Elsevier, 2020, doi:10.1016/j.jfa.2020.108639."},"oa_version":"Preprint","language":[{"iso":"eng"}],"publisher":"Elsevier","issue":"7","arxiv":1,"date_published":"2020-10-15T00:00:00Z","abstract":[{"lang":"eng","text":"We consider the sum of two large Hermitian matrices A and B with a Haar unitary conjugation bringing them into a general relative position. We prove that the eigenvalue density on the scale slightly above the local eigenvalue spacing is asymptotically given by the free additive convolution of the laws of A and B as the dimension of the matrix increases. This implies optimal rigidity of the eigenvalues and optimal rate of convergence in Voiculescu's theorem. Our previous works [4], [5] established these results in the bulk spectrum, the current paper completely settles the problem at the spectral edges provided they have the typical square-root behavior. The key element of our proof is to compensate the deterioration of the stability of the subordination equations by sharp error estimates that properly account for the local density near the edge. Our results also hold if the Haar unitary matrix is replaced by the Haar orthogonal matrix."}],"department":[{"_id":"LaEr"}],"date_updated":"2025-04-15T08:05:01Z","external_id":{"arxiv":["1708.01597"],"isi":["000559623200009"]},"isi":1,"publication":"Journal of Functional Analysis","day":"15","acknowledgement":"Partially supported by ERC Advanced Grant RANMAT No. 338804.","date_created":"2022-03-18T10:18:59Z","ec_funded":1,"scopus_import":"1","volume":279,"article_processing_charge":"No","month":"10","title":"Spectral rigidity for addition of random matrices at the regular edge","keyword":["Analysis"],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"}],"intvolume":" 279","status":"public","type":"journal_article","year":"2020","publication_status":"published","quality_controlled":"1","oa":1,"article_type":"original","article_number":"108639","doi":"10.1016/j.jfa.2020.108639","publication_identifier":{"issn":["0022-1236"]},"_id":"10862","main_file_link":[{"url":"https://arxiv.org/abs/1708.01597","open_access":"1"}]},{"volume":2020,"article_processing_charge":"No","month":"02","page":"669-697","title":"Waist of balls in hyperbolic and spherical spaces","keyword":["General Mathematics"],"intvolume":" 2020","publication":"International Mathematics Research Notices","day":"01","date_created":"2022-03-18T11:39:30Z","acknowledgement":" Supported by the Russian Foundation for Basic Research grant 18-01-00036.","scopus_import":"1","oa":1,"article_type":"original","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"doi":"10.1093/imrn/rny037","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1702.07513"}],"_id":"10867","status":"public","type":"journal_article","year":"2020","publication_status":"published","quality_controlled":"1","citation":{"apa":"Akopyan, A., & Karasev, R. (2020). Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rny037","ama":"Akopyan A, Karasev R. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020;2020(3):669-697. doi:10.1093/imrn/rny037","short":"A. Akopyan, R. Karasev, International Mathematics Research Notices 2020 (2020) 669–697.","ista":"Akopyan A, Karasev R. 2020. Waist of balls in hyperbolic and spherical spaces. International Mathematics Research Notices. 2020(3), 669–697.","mla":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices, vol. 2020, no. 3, Oxford University Press, 2020, pp. 669–97, doi:10.1093/imrn/rny037.","chicago":"Akopyan, Arseniy, and Roman Karasev. “Waist of Balls in Hyperbolic and Spherical Spaces.” International Mathematics Research Notices. Oxford University Press, 2020. https://doi.org/10.1093/imrn/rny037.","ieee":"A. Akopyan and R. Karasev, “Waist of balls in hyperbolic and spherical spaces,” International Mathematics Research Notices, vol. 2020, no. 3. Oxford University Press, pp. 669–697, 2020."},"oa_version":"Preprint","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan"},{"full_name":"Karasev, Roman","first_name":"Roman","last_name":"Karasev"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"In this paper we find a tight estimate for Gromov’s waist of the balls in spaces of constant curvature, deduce the estimates for the balls in Riemannian manifolds with upper bounds on the curvature (CAT(ϰ)-spaces), and establish similar result for normed spaces.","lang":"eng"}],"department":[{"_id":"HeEd"}],"date_updated":"2023-08-24T14:19:55Z","external_id":{"isi":["000522852700002"],"arxiv":["1702.07513"]},"isi":1,"publisher":"Oxford University Press","issue":"3","arxiv":1,"date_published":"2020-02-01T00:00:00Z"},{"external_id":{"pmid":["32601198"]},"ddc":["580"],"department":[{"_id":"XiFe"}],"date_updated":"2023-05-08T10:53:55Z","abstract":[{"text":"Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site in FLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states at FLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.","lang":"eng"}],"date_published":"2020-05-22T00:00:00Z","issue":"28","publisher":"Proceedings of the National Academy of Sciences","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"ieee":"R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2,” Proceedings of the National Academy of Sciences, vol. 117, no. 28. Proceedings of the National Academy of Sciences, pp. 16660–16666, 2020.","chicago":"Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker, Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.","ista":"Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN, Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.","mla":"Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the National Academy of Sciences, vol. 117, no. 28, Proceedings of the National Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.","ama":"Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117","short":"R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N. Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings of the National Academy of Sciences 117 (2020) 16660–16666.","apa":"Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera, P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117"},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bloomer, Rebecca H.","first_name":"Rebecca H.","last_name":"Bloomer"},{"last_name":"Hutchison","first_name":"Claire E.","full_name":"Hutchison, Claire E."},{"full_name":"Bäurle, Isabel","last_name":"Bäurle","first_name":"Isabel"},{"full_name":"Walker, James","first_name":"James","last_name":"Walker"},{"full_name":"Fang, Xiaofeng","first_name":"Xiaofeng","last_name":"Fang"},{"last_name":"Perera","first_name":"Pumi","full_name":"Perera, Pumi"},{"first_name":"Christos N.","last_name":"Velanis","full_name":"Velanis, Christos N."},{"full_name":"Gümüs, Serin","first_name":"Serin","last_name":"Gümüs"},{"full_name":"Spanos, Christos","last_name":"Spanos","first_name":"Christos"},{"last_name":"Rappsilber","first_name":"Juri","full_name":"Rappsilber, Juri"},{"last_name":"Feng","first_name":"Xiaoqi","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","orcid":"0000-0002-4008-1234"},{"full_name":"Goodrich, Justin","last_name":"Goodrich","first_name":"Justin"},{"full_name":"Dean, Caroline","last_name":"Dean","first_name":"Caroline"}],"publication_identifier":{"issn":["0027-8424","1091-6490"]},"doi":"10.1073/pnas.1920621117","_id":"12188","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/"}],"has_accepted_license":"1","oa":1,"article_type":"original","quality_controlled":"1","type":"journal_article","status":"public","publication_status":"published","file_date_updated":"2023-02-07T11:29:55Z","year":"2020","keyword":["Multidisciplinary"],"intvolume":" 117","page":"16660-16666","title":"The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex 2","article_processing_charge":"No","month":"05","file":[{"date_created":"2023-02-07T11:29:55Z","checksum":"cedee184cb12f454f2fba4158ff47db9","relation":"main_file","creator":"alisjak","file_id":"12526","success":1,"access_level":"open_access","file_name":"2020_PNAS_Bloomer.pdf","date_updated":"2023-02-07T11:29:55Z","content_type":"application/pdf","file_size":1105414}],"volume":117,"acknowledgement":"We would like to thank Scott Berry for help with ICU-GFP nuclear localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation analysis, Donna Gibson for graphic design assistance, and members of the C.D. and Howard laboratories for helpful discussions. This work was funded by the European Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1), and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and \"WISDOM\" (to X. Fang). Additional funding via the Wellcome Trust through a Senior Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504). The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149).","date_created":"2023-01-16T09:15:44Z","scopus_import":"1","day":"22","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"publication":"Proceedings of the National Academy of Sciences"},{"citation":{"apa":"Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., … Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. Public Library of Science (PLoS). https://doi.org/10.1371/journal.pgen.1008894","ama":"Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 2020;16(6). doi:10.1371/journal.pgen.1008894","short":"N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns, A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS Genetics 16 (2020).","mla":"Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics, vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894.","ista":"Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization. PLOS Genetics. 16(6), e1008894.","chicago":"Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894.","ieee":"N. Christophorou et al., “AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization,” PLOS Genetics, vol. 16, no. 6. Public Library of Science (PLoS), 2020."},"language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Christophorou, Nicolas","last_name":"Christophorou","first_name":"Nicolas"},{"last_name":"She","first_name":"Wenjing","full_name":"She, Wenjing"},{"first_name":"Jincheng","last_name":"Long","full_name":"Long, Jincheng"},{"last_name":"Hurel","first_name":"Aurélie","full_name":"Hurel, Aurélie"},{"full_name":"Beaubiat, Sébastien","last_name":"Beaubiat","first_name":"Sébastien"},{"last_name":"Idir","first_name":"Yassir","full_name":"Idir, Yassir"},{"full_name":"Tagliaro-Jahns, Marina","first_name":"Marina","last_name":"Tagliaro-Jahns"},{"last_name":"Chambon","first_name":"Aurélie","full_name":"Chambon, Aurélie"},{"last_name":"Solier","first_name":"Victor","full_name":"Solier, Victor"},{"full_name":"Vezon, Daniel","first_name":"Daniel","last_name":"Vezon"},{"full_name":"Grelon, Mathilde","first_name":"Mathilde","last_name":"Grelon"},{"orcid":"0000-0002-4008-1234","full_name":"Feng, Xiaoqi","first_name":"Xiaoqi","last_name":"Feng","id":"e0164712-22ee-11ed-b12a-d80fcdf35958"},{"first_name":"Nicolas","last_name":"Bouché","full_name":"Bouché, Nicolas"},{"full_name":"Mézard, Christine","first_name":"Christine","last_name":"Mézard"}],"extern":"1","date_updated":"2023-05-08T10:54:39Z","department":[{"_id":"XiFe"}],"abstract":[{"text":"Meiotic crossovers (COs) are important for reshuffling genetic information between homologous chromosomes and they are essential for their correct segregation. COs are unevenly distributed along chromosomes and the underlying mechanisms controlling CO localization are not well understood. We previously showed that meiotic COs are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation protein modification pathway in Arabidopsis thaliana. Here, we report that in axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the formation of the telomere bouquet is not affected. COs are also redistributed towards subtelomeric chromosomal ends where they frequently form clusters, in contrast to large central regions depleted in recombination. The CO suppressed regions correlate with DNA hypermethylation of transposable elements (TEs) in the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we found axr1-/- affects DNA methylation in a plant, causing hypermethylation in all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic cells but does not restore regular chromosome segregation during meiosis. Collectively, our findings reveal that the neddylation pathway not only regulates hormonal perception and CO distribution but is also, directly or indirectly, a major limiting pathway of TE DNA methylation in somatic cells.","lang":"eng"}],"external_id":{"pmid":["32598340"]},"issue":"6","publisher":"Public Library of Science (PLoS)","date_published":"2020-06-29T00:00:00Z","month":"06","article_processing_charge":"No","volume":16,"intvolume":" 16","keyword":["Cancer Research","Genetics (clinical)","Genetics","Molecular Biology","Ecology","Evolution","Behavior and Systematics"],"title":"AXR1 affects DNA methylation independently of its role in regulating meiotic crossover localization","publication":"PLOS Genetics","scopus_import":"1","date_created":"2023-01-16T09:16:10Z","acknowledgement":"The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.","pmid":1,"day":"29","article_type":"original","oa":1,"_id":"12189","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/","open_access":"1"}],"publication_identifier":{"issn":["1553-7404"]},"doi":"10.1371/journal.pgen.1008894","article_number":"e1008894","quality_controlled":"1","year":"2020","publication_status":"published","status":"public","type":"journal_article"},{"citation":{"chicago":"Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561.","ieee":"G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020.","mla":"Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561.","ista":"Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561.","apa":"Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561","ama":"Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561","short":"G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020)."},"month":"07","article_processing_charge":"No","title":"Converting microwave and telecom photons with a silicon photonic nanomechanical interface","oa_version":"Published Version","author":[{"last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M"},{"first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6613-1378","full_name":"Wulf, Matthias"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"first_name":"Elena","last_name":"Redchenko","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87","full_name":"Redchenko, Elena"},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"full_name":"Hease, William J","orcid":"0000-0001-9868-2166","last_name":"Hease","first_name":"William J","id":"29705398-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6937-5773","full_name":"Hassani, Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"27","corr_author":"1","date_created":"2023-05-23T13:37:41Z","abstract":[{"lang":"eng","text":"This datasets comprises all data shown in plots of the submitted article \"Converting microwave and telecom photons with a silicon photonic nanomechanical interface\". Additional raw data are available from the corresponding author on reasonable request."}],"oa":1,"date_updated":"2025-06-12T07:03:01Z","department":[{"_id":"JoFi"}],"ddc":["530"],"_id":"13056","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3961562","open_access":"1"}],"doi":"10.5281/ZENODO.3961561","publisher":"Zenodo","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8529"}]},"year":"2020","type":"research_data_reference","status":"public","date_published":"2020-07-27T00:00:00Z"},{"citation":{"short":"B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020).","ama":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318","apa":"Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318","ieee":"B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020.","chicago":"Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318.","mla":"Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318.","ista":"Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318."},"month":"12","article_processing_charge":"No","title":"Social immunity modulates competition between coinfecting pathogens","oa_version":"Published Version","author":[{"last_name":"Milutinovic","first_name":"Barbara","id":"2CDC32B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8214-4758","full_name":"Milutinovic, Barbara"},{"first_name":"Miriam","last_name":"Stock","id":"42462816-F248-11E8-B48F-1D18A9856A87","full_name":"Stock, Miriam"},{"full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elisabeth","last_name":"Naderlinger","id":"31757262-F248-11E8-B48F-1D18A9856A87","full_name":"Naderlinger, Elisabeth"},{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hilbe","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"day":"19","corr_author":"1","date_created":"2023-05-23T16:11:22Z","abstract":[{"text":"Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity – influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level.","lang":"eng"}],"oa":1,"date_updated":"2025-06-12T07:32:35Z","department":[{"_id":"SyCr"},{"_id":"KrCh"}],"ddc":["570"],"_id":"13060","main_file_link":[{"url":"https://doi.org/10.5061/dryad.crjdfn318","open_access":"1"}],"doi":"10.5061/DRYAD.CRJDFN318","publisher":"Dryad","related_material":{"record":[{"id":"7343","relation":"used_in_publication","status":"public"}]},"license":"https://creativecommons.org/publicdomain/zero/1.0/","year":"2020","type":"research_data_reference","status":"public","date_published":"2020-12-19T00:00:00Z"},{"publisher":"Dryad","related_material":{"link":[{"url":"https://github.com/starnoux/arnoux_et_al_2019","relation":"software"}],"record":[{"id":"8928","relation":"used_in_publication","status":"public"}]},"date_published":"2020-10-19T00:00:00Z","year":"2020","type":"research_data_reference","status":"public","date_updated":"2026-06-18T19:37:16Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available.","lang":"eng"}],"oa":1,"_id":"13065","main_file_link":[{"url":"https://doi.org/10.5061/dryad.q2bvq83hd","open_access":"1"}],"doi":"10.5061/DRYAD.Q2BVQ83HD","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Arnoux","first_name":"Stephanie","full_name":"Arnoux, Stephanie"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Sauvage","first_name":"Christopher","full_name":"Sauvage, Christopher"}],"date_created":"2023-05-23T16:30:20Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"day":"19","month":"10","article_processing_charge":"No","citation":{"chicago":"Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.","ieee":"S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.","ista":"Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.","mla":"Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.","apa":"Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD","short":"S. Arnoux, C. Fraisse, C. Sauvage, (2020).","ama":"Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD"},"title":"VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species","oa_version":"Published Version"},{"title":"Surpassing the resistance quantum with a geometric superinductor","oa_version":"Published Version","article_processing_charge":"No","month":"09","citation":{"apa":"Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882","ama":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882","short":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020).","chicago":"Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882.","ieee":"M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020.","mla":"Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882.","ista":"Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882."},"corr_author":"1","date_created":"2023-05-23T16:42:30Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Peruzzo","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3415-4628","full_name":"Peruzzo, Matilda"},{"id":"42F71B44-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea","last_name":"Trioni","full_name":"Trioni, Andrea"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","first_name":"Farid","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.4052883"}],"_id":"13070","doi":"10.5281/ZENODO.4052882","ddc":["530"],"date_updated":"2026-04-15T06:43:02Z","department":[{"_id":"JoFi"}],"abstract":[{"lang":"eng","text":"This dataset comprises all data shown in the figures of the submitted article \"Surpassing the resistance quantum with a geometric superinductor\". Additional raw data are available from the corresponding author on reasonable request."}],"oa":1,"date_published":"2020-09-27T00:00:00Z","year":"2020","type":"research_data_reference","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"8755"}]},"publisher":"Zenodo"},{"author":[{"orcid":"0000-0001-9868-2166","full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Hease"},{"first_name":"Alfredo R","last_name":"Rueda Sanchez","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R"},{"full_name":"Sahu, Rishabh","orcid":"0000-0001-6264-2162","id":"47D26E34-F248-11E8-B48F-1D18A9856A87","last_name":"Sahu","first_name":"Rishabh"},{"full_name":"Wulf, Matthias","orcid":"0000-0001-6613-1378","first_name":"Matthias","last_name":"Wulf","id":"45598606-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1397-7876","full_name":"Arnold, Georg M","last_name":"Arnold","first_name":"Georg M","id":"3770C838-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schwefel, Harald","first_name":"Harald","last_name":"Schwefel"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","last_name":"Fink","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"10","corr_author":"1","date_created":"2023-05-23T16:44:11Z","citation":{"ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, 10.5281/ZENODO.4266025.","mla":"Hease, William J., et al. Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State. Zenodo, 2020, doi:10.5281/ZENODO.4266025.","ieee":"W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020).","ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:10.5281/ZENODO.4266025","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. https://doi.org/10.5281/ZENODO.4266025"},"article_processing_charge":"No","month":"11","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","oa_version":"Published Version","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"9114"}]},"publisher":"Zenodo","year":"2020","status":"public","type":"research_data_reference","date_published":"2020-11-10T00:00:00Z","abstract":[{"text":"This dataset comprises all data shown in the plots of the main part of the submitted article \"Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State\". Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa":1,"date_updated":"2026-04-15T06:43:26Z","department":[{"_id":"JoFi"}],"ddc":["530"],"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.4266026","open_access":"1"}],"_id":"13071","doi":"10.5281/ZENODO.4266025"},{"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","oa_version":"Published Version","article_processing_charge":"No","month":"09","citation":{"ieee":"A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","chicago":"Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N.","ista":"Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N.","mla":"Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N.","ama":"Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N"},"date_created":"2023-05-23T16:48:27Z","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"},"day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Simon, Alexis","last_name":"Simon","first_name":"Alexis"},{"orcid":"0000-0001-8441-5075","full_name":"Fraisse, Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","last_name":"Fraisse","first_name":"Christelle"},{"last_name":"El Ayari","first_name":"Tahani","full_name":"El Ayari, Tahani"},{"full_name":"Liautard-Haag, Cathy","first_name":"Cathy","last_name":"Liautard-Haag"},{"last_name":"Strelkov","first_name":"Petr","full_name":"Strelkov, Petr"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"first_name":"Nicolas","last_name":"Bierne","full_name":"Bierne, Nicolas"}],"_id":"13073","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"doi":"10.5061/DRYAD.R4XGXD29N","ddc":["570"],"date_updated":"2025-07-10T12:01:22Z","department":[{"_id":"NiBa"}],"abstract":[{"text":"The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study \"replicated\" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact.","lang":"eng"}],"oa":1,"date_published":"2020-09-22T00:00:00Z","year":"2020","type":"research_data_reference","status":"public","publisher":"Dryad","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8708"}]}},{"external_id":{"pmid":["33381818"]},"abstract":[{"text":"Motivation: Recent technological advances have led to an increase in the production and availability of single-cell data. The ability to integrate a set of multi-technology measurements would allow the identification of biologically or clinically meaningful observations through the unification of the perspectives afforded by each technology. In most cases, however, profiling technologies consume the used cells and thus pairwise correspondences between datasets are lost. Due to the sheer size single-cell datasets can acquire, scalable algorithms that are able to universally match single-cell measurements carried out in one cell to its corresponding sibling in another technology are needed.\r\nResults: We propose Single-Cell data Integration via Matching (SCIM), a scalable approach to recover such correspondences in two or more technologies. SCIM assumes that cells share a common (low-dimensional) underlying structure and that the underlying cell distribution is approximately constant across technologies. It constructs a technology-invariant latent space using an autoencoder framework with an adversarial objective. Multi-modal datasets are integrated by pairing cells across technologies using a bipartite matching scheme that operates on the low-dimensional latent representations. We evaluate SCIM on a simulated cellular branching process and show that the cell-to-cell matches derived by SCIM reflect the same pseudotime on the simulated dataset. Moreover, we apply our method to two real-world scenarios, a melanoma tumor sample and a human bone marrow sample, where we pair cells from a scRNA dataset to their sibling cells in a CyTOF dataset achieving 90% and 78% cell-matching accuracy for each one of the samples, respectively.","lang":"eng"}],"date_updated":"2023-09-11T10:21:00Z","department":[{"_id":"FrLo"}],"date_published":"2020-12-01T00:00:00Z","related_material":{"link":[{"url":"https://github.com/ratschlab/scim","relation":"software"}]},"publisher":"Oxford University Press","issue":"Supplement_2","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:10.1093/bioinformatics/btaa843.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","ieee":"S. G. Stark et al., “SCIM: Universal single-cell matching with unpaired feature sets,” Bioinformatics, vol. 36, no. Supplement_2. Oxford University Press, pp. i919–i927, 2020.","chicago":"Stark, Stefan G, Joanna Ficek, Francesco Locatello, Ximena Bonilla, Stéphane Chevrier, Franziska Singer, Rudolf Aebersold, et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” Bioinformatics. Oxford University Press, 2020. https://doi.org/10.1093/bioinformatics/btaa843.","short":"S.G. Stark, J. Ficek, F. Locatello, X. Bonilla, S. Chevrier, F. Singer, R. Aebersold, F.S. Al-Quaddoomi, J. Albinus, I. Alborelli, S. Andani, P.-O. Attinger, M. Bacac, D. Baumhoer, B. Beck-Schimmer, N. Beerenwinkel, C. Beisel, L. Bernasconi, A. Bertolini, B. Bodenmiller, X. Bonilla, R. Casanova, S. Chevrier, N. Chicherova, M. D’Costa, E. Danenberg, N. Davidson, M.-A.D. gan, R. Dummer, S. Engler, M. Erkens, K. Eschbach, C. Esposito, A. Fedier, P. Ferreira, J. Ficek, A.L. Frei, B. Frey, S. Goetze, L. Grob, G. Gut, D. Günther, M. Haberecker, P. Haeuptle, V. Heinzelmann-Schwarz, S. Herter, R. Holtackers, T. Huesser, A. Irmisch, F. Jacob, A. Jacobs, T.M. Jaeger, K. Jahn, A.R. James, P.M. Jermann, A. Kahles, A. Kahraman, V.H. Koelzer, W. Kuebler, J. Kuipers, C.P. Kunze, C. Kurzeder, K.-V. Lehmann, M. Levesque, S. Lugert, G. Maass, M. Manz, P. Markolin, J. Mena, U. Menzel, J.M. Metzler, N. Miglino, E.S. Milani, H. Moch, S. Muenst, R. Murri, C.K. Ng, S. Nicolet, M. Nowak, P.G. Pedrioli, L. Pelkmans, S. Piscuoglio, M. Prummer, M. Ritter, C. Rommel, M.L. Rosano-González, G. Rätsch, N. Santacroce, J.S. del Castillo, R. Schlenker, P.C. Schwalie, S. Schwan, T. Schär, G. Senti, F. Singer, S. Sivapatham, B. Snijder, B. Sobottka, V.T. Sreedharan, S. Stark, D.J. Stekhoven, A.P. Theocharides, T.M. Thomas, M. Tolnay, V. Tosevski, N.C. Toussaint, M.A. Tuncel, M. Tusup, A.V. Drogen, M. Vetter, T. Vlajnic, S. Weber, W.P. Weber, R. Wegmann, M. Weller, F. Wendt, N. Wey, A. Wicki, B. Wollscheid, S. Yu, J. Ziegler, M. Zimmermann, M. Zoche, G. Zuend, G. Rätsch, K.-V. Lehmann, Bioinformatics 36 (2020) i919–i927.","ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 2020;36(Supplement_2):i919-i927. doi:10.1093/bioinformatics/btaa843","apa":"Stark, S. G., Ficek, J., Locatello, F., Bonilla, X., Chevrier, S., Singer, F., … Lehmann, K.-V. (2020). SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. Oxford University Press. https://doi.org/10.1093/bioinformatics/btaa843"},"extern":"1","author":[{"full_name":"Stark, Stefan G","last_name":"Stark","first_name":"Stefan G"},{"last_name":"Ficek","first_name":"Joanna","full_name":"Ficek, Joanna"},{"id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Bonilla, Ximena","last_name":"Bonilla","first_name":"Ximena"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"last_name":"Singer","first_name":"Franziska","full_name":"Singer, Franziska"},{"full_name":"Aebersold, Rudolf","first_name":"Rudolf","last_name":"Aebersold"},{"full_name":"Al-Quaddoomi, Faisal S","first_name":"Faisal S","last_name":"Al-Quaddoomi"},{"last_name":"Albinus","first_name":"Jonas","full_name":"Albinus, Jonas"},{"full_name":"Alborelli, Ilaria","last_name":"Alborelli","first_name":"Ilaria"},{"full_name":"Andani, Sonali","first_name":"Sonali","last_name":"Andani"},{"first_name":"Per-Olof","last_name":"Attinger","full_name":"Attinger, Per-Olof"},{"first_name":"Marina","last_name":"Bacac","full_name":"Bacac, Marina"},{"full_name":"Baumhoer, Daniel","first_name":"Daniel","last_name":"Baumhoer"},{"full_name":"Beck-Schimmer, Beatrice","last_name":"Beck-Schimmer","first_name":"Beatrice"},{"last_name":"Beerenwinkel","first_name":"Niko","full_name":"Beerenwinkel, Niko"},{"first_name":"Christian","last_name":"Beisel","full_name":"Beisel, Christian"},{"full_name":"Bernasconi, Lara","last_name":"Bernasconi","first_name":"Lara"},{"full_name":"Bertolini, Anne","first_name":"Anne","last_name":"Bertolini"},{"full_name":"Bodenmiller, Bernd","last_name":"Bodenmiller","first_name":"Bernd"},{"full_name":"Bonilla, Ximena","first_name":"Ximena","last_name":"Bonilla"},{"first_name":"Ruben","last_name":"Casanova","full_name":"Casanova, Ruben"},{"first_name":"Stéphane","last_name":"Chevrier","full_name":"Chevrier, Stéphane"},{"last_name":"Chicherova","first_name":"Natalia","full_name":"Chicherova, Natalia"},{"first_name":"Maya","last_name":"D'Costa","full_name":"D'Costa, Maya"},{"first_name":"Esther","last_name":"Danenberg","full_name":"Danenberg, Esther"},{"full_name":"Davidson, Natalie","first_name":"Natalie","last_name":"Davidson"},{"last_name":"gan","first_name":"Monica-Andreea Dră","full_name":"gan, Monica-Andreea Dră"},{"full_name":"Dummer, Reinhard","first_name":"Reinhard","last_name":"Dummer"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"full_name":"Erkens, Martin","first_name":"Martin","last_name":"Erkens"},{"full_name":"Eschbach, Katja","first_name":"Katja","last_name":"Eschbach"},{"full_name":"Esposito, Cinzia","first_name":"Cinzia","last_name":"Esposito"},{"full_name":"Fedier, André","last_name":"Fedier","first_name":"André"},{"first_name":"Pedro","last_name":"Ferreira","full_name":"Ferreira, Pedro"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"last_name":"Frei","first_name":"Anja L","full_name":"Frei, Anja L"},{"first_name":"Bruno","last_name":"Frey","full_name":"Frey, Bruno"},{"first_name":"Sandra","last_name":"Goetze","full_name":"Goetze, Sandra"},{"full_name":"Grob, Linda","last_name":"Grob","first_name":"Linda"},{"full_name":"Gut, Gabriele","first_name":"Gabriele","last_name":"Gut"},{"last_name":"Günther","first_name":"Detlef","full_name":"Günther, Detlef"},{"first_name":"Martina","last_name":"Haberecker","full_name":"Haberecker, Martina"},{"first_name":"Pirmin","last_name":"Haeuptle","full_name":"Haeuptle, Pirmin"},{"first_name":"Viola","last_name":"Heinzelmann-Schwarz","full_name":"Heinzelmann-Schwarz, Viola"},{"last_name":"Herter","first_name":"Sylvia","full_name":"Herter, Sylvia"},{"full_name":"Holtackers, Rene","last_name":"Holtackers","first_name":"Rene"},{"full_name":"Huesser, Tamara","last_name":"Huesser","first_name":"Tamara"},{"last_name":"Irmisch","first_name":"Anja","full_name":"Irmisch, Anja"},{"full_name":"Jacob, Francis","first_name":"Francis","last_name":"Jacob"},{"full_name":"Jacobs, Andrea","first_name":"Andrea","last_name":"Jacobs"},{"full_name":"Jaeger, Tim M","last_name":"Jaeger","first_name":"Tim M"},{"last_name":"Jahn","first_name":"Katharina","full_name":"Jahn, Katharina"},{"last_name":"James","first_name":"Alva R","full_name":"James, Alva R"},{"last_name":"Jermann","first_name":"Philip M","full_name":"Jermann, Philip M"},{"first_name":"André","last_name":"Kahles","full_name":"Kahles, André"},{"first_name":"Abdullah","last_name":"Kahraman","full_name":"Kahraman, Abdullah"},{"first_name":"Viktor H","last_name":"Koelzer","full_name":"Koelzer, Viktor H"},{"first_name":"Werner","last_name":"Kuebler","full_name":"Kuebler, Werner"},{"first_name":"Jack","last_name":"Kuipers","full_name":"Kuipers, Jack"},{"last_name":"Kunze","first_name":"Christian P","full_name":"Kunze, Christian P"},{"first_name":"Christian","last_name":"Kurzeder","full_name":"Kurzeder, Christian"},{"full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van","last_name":"Lehmann"},{"full_name":"Levesque, Mitchell","first_name":"Mitchell","last_name":"Levesque"},{"full_name":"Lugert, Sebastian","first_name":"Sebastian","last_name":"Lugert"},{"full_name":"Maass, Gerd","last_name":"Maass","first_name":"Gerd"},{"full_name":"Manz, Markus","last_name":"Manz","first_name":"Markus"},{"last_name":"Markolin","first_name":"Philipp","full_name":"Markolin, Philipp"},{"full_name":"Mena, Julien","last_name":"Mena","first_name":"Julien"},{"last_name":"Menzel","first_name":"Ulrike","full_name":"Menzel, Ulrike"},{"full_name":"Metzler, Julian M","first_name":"Julian M","last_name":"Metzler"},{"full_name":"Miglino, Nicola","first_name":"Nicola","last_name":"Miglino"},{"first_name":"Emanuela S","last_name":"Milani","full_name":"Milani, Emanuela S"},{"last_name":"Moch","first_name":"Holger","full_name":"Moch, Holger"},{"full_name":"Muenst, Simone","first_name":"Simone","last_name":"Muenst"},{"last_name":"Murri","first_name":"Riccardo","full_name":"Murri, Riccardo"},{"last_name":"Ng","first_name":"Charlotte KY","full_name":"Ng, Charlotte KY"},{"first_name":"Stefan","last_name":"Nicolet","full_name":"Nicolet, Stefan"},{"first_name":"Marta","last_name":"Nowak","full_name":"Nowak, Marta"},{"full_name":"Pedrioli, Patrick GA","first_name":"Patrick GA","last_name":"Pedrioli"},{"full_name":"Pelkmans, Lucas","first_name":"Lucas","last_name":"Pelkmans"},{"first_name":"Salvatore","last_name":"Piscuoglio","full_name":"Piscuoglio, Salvatore"},{"full_name":"Prummer, Michael","last_name":"Prummer","first_name":"Michael"},{"full_name":"Ritter, Mathilde","first_name":"Mathilde","last_name":"Ritter"},{"first_name":"Christian","last_name":"Rommel","full_name":"Rommel, Christian"},{"first_name":"María L","last_name":"Rosano-González","full_name":"Rosano-González, María L"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"full_name":"Santacroce, Natascha","first_name":"Natascha","last_name":"Santacroce"},{"full_name":"Castillo, Jacobo Sarabia del","last_name":"Castillo","first_name":"Jacobo Sarabia del"},{"first_name":"Ramona","last_name":"Schlenker","full_name":"Schlenker, Ramona"},{"full_name":"Schwalie, Petra C","last_name":"Schwalie","first_name":"Petra C"},{"full_name":"Schwan, Severin","first_name":"Severin","last_name":"Schwan"},{"full_name":"Schär, Tobias","first_name":"Tobias","last_name":"Schär"},{"full_name":"Senti, Gabriela","first_name":"Gabriela","last_name":"Senti"},{"last_name":"Singer","first_name":"Franziska","full_name":"Singer, Franziska"},{"full_name":"Sivapatham, Sujana","first_name":"Sujana","last_name":"Sivapatham"},{"full_name":"Snijder, Berend","last_name":"Snijder","first_name":"Berend"},{"last_name":"Sobottka","first_name":"Bettina","full_name":"Sobottka, Bettina"},{"first_name":"Vipin T","last_name":"Sreedharan","full_name":"Sreedharan, Vipin T"},{"last_name":"Stark","first_name":"Stefan","full_name":"Stark, Stefan"},{"full_name":"Stekhoven, Daniel J","first_name":"Daniel J","last_name":"Stekhoven"},{"first_name":"Alexandre PA","last_name":"Theocharides","full_name":"Theocharides, Alexandre PA"},{"full_name":"Thomas, Tinu M","first_name":"Tinu M","last_name":"Thomas"},{"first_name":"Markus","last_name":"Tolnay","full_name":"Tolnay, Markus"},{"full_name":"Tosevski, Vinko","last_name":"Tosevski","first_name":"Vinko"},{"full_name":"Toussaint, Nora C","first_name":"Nora C","last_name":"Toussaint"},{"first_name":"Mustafa A","last_name":"Tuncel","full_name":"Tuncel, Mustafa A"},{"full_name":"Tusup, Marina","last_name":"Tusup","first_name":"Marina"},{"first_name":"Audrey Van","last_name":"Drogen","full_name":"Drogen, Audrey Van"},{"first_name":"Marcus","last_name":"Vetter","full_name":"Vetter, Marcus"},{"full_name":"Vlajnic, Tatjana","first_name":"Tatjana","last_name":"Vlajnic"},{"full_name":"Weber, Sandra","first_name":"Sandra","last_name":"Weber"},{"full_name":"Weber, Walter P","first_name":"Walter P","last_name":"Weber"},{"full_name":"Wegmann, Rebekka","first_name":"Rebekka","last_name":"Wegmann"},{"last_name":"Weller","first_name":"Michael","full_name":"Weller, Michael"},{"first_name":"Fabian","last_name":"Wendt","full_name":"Wendt, Fabian"},{"last_name":"Wey","first_name":"Norbert","full_name":"Wey, Norbert"},{"full_name":"Wicki, Andreas","last_name":"Wicki","first_name":"Andreas"},{"full_name":"Wollscheid, Bernd","first_name":"Bernd","last_name":"Wollscheid"},{"first_name":"Shuqing","last_name":"Yu","full_name":"Yu, Shuqing"},{"full_name":"Ziegler, Johanna","first_name":"Johanna","last_name":"Ziegler"},{"first_name":"Marc","last_name":"Zimmermann","full_name":"Zimmermann, Marc"},{"first_name":"Martin","last_name":"Zoche","full_name":"Zoche, Martin"},{"full_name":"Zuend, Gregor","last_name":"Zuend","first_name":"Gregor"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"full_name":"Lehmann, Kjong-Van","last_name":"Lehmann","first_name":"Kjong-Van"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"_id":"14125","doi":"10.1093/bioinformatics/btaa843","publication_identifier":{"eissn":["1367-4811"]},"article_type":"original","oa":1,"publication_status":"published","year":"2020","status":"public","type":"journal_article","quality_controlled":"1","page":"i919-i927","title":"SCIM: Universal single-cell matching with unpaired feature sets","intvolume":" 36","keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"volume":36,"article_processing_charge":"No","month":"12","pmid":1,"day":"01","scopus_import":"1","date_created":"2023-08-21T12:28:20Z","publication":"Bioinformatics"},{"doi":"10.1609/aaai.v34i09.7120","publication_identifier":{"isbn":["9781577358350"],"eissn":["2374-3468"]},"_id":"14186","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14184"}],"oa":1,"quality_controlled":"1","type":"conference","status":"public","year":"2020","publication_status":"published","intvolume":" 34","title":"A commentary on the unsupervised learning of disentangled representations","page":"13681-13684","article_processing_charge":"No","month":"07","volume":34,"date_created":"2023-08-22T14:07:26Z","scopus_import":"1","day":"28","publication":"The 34th AAAI Conference on Artificial Intelligence","external_id":{"arxiv":["2007.14184"]},"department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T07:44:48Z","abstract":[{"lang":"eng","text":"The goal of the unsupervised learning of disentangled representations is to\r\nseparate the independent explanatory factors of variation in the data without\r\naccess to supervision. In this paper, we summarize the results of Locatello et\r\nal., 2019, and focus on their implications for practitioners. We discuss the\r\ntheoretical result showing that the unsupervised learning of disentangled\r\nrepresentations is fundamentally impossible without inductive biases and the\r\npractical challenges it entails. Finally, we comment on our experimental\r\nfindings, highlighting the limitations of state-of-the-art approaches and\r\ndirections for future research."}],"date_published":"2020-07-28T00:00:00Z","arxiv":1,"issue":"9","conference":{"location":"New York, NY, United States","start_date":"2020-02-07","end_date":"2020-02-12","name":"AAAI: Conference on Artificial Intelligence"},"publisher":"Association for the Advancement of Artificial Intelligence","oa_version":"Preprint","language":[{"iso":"eng"}],"citation":{"apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In The 34th AAAI Conference on Artificial Intelligence (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. https://doi.org/10.1609/aaai.v34i09.7120","ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: The 34th AAAI Conference on Artificial Intelligence. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:10.1609/aaai.v34i09.7120","short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, in:, The 34th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–13684.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Commentary on the Unsupervised Learning of Disentangled Representations.” In The 34th AAAI Conference on Artificial Intelligence, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. https://doi.org/10.1609/aaai.v34i09.7120.","ieee":"F. Locatello et al., “A commentary on the unsupervised learning of disentangled representations,” in The 34th AAAI Conference on Artificial Intelligence, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” The 34th AAAI Conference on Artificial Intelligence, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:10.1609/aaai.v34i09.7120.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A commentary on the unsupervised learning of disentangled representations. The 34th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 34, 13681–13684."},"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}]},{"publication":"Proceedings of the 37th International Conference on Machine Learning","date_created":"2023-08-22T14:07:52Z","day":"27","article_processing_charge":"No","month":"07","volume":119,"intvolume":" 119","page":"7253-7262","title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","alternative_title":["PMLR"],"quality_controlled":"1","type":"conference","status":"public","publication_status":"published","year":"2020","oa":1,"_id":"14187","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.11860"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Négiar, Geoffrey","first_name":"Geoffrey","last_name":"Négiar"},{"last_name":"Dresdner","first_name":"Gideon","full_name":"Dresdner, Gideon"},{"first_name":"Alicia","last_name":"Tsai","full_name":"Tsai, Alicia"},{"full_name":"Ghaoui, Laurent El","first_name":"Laurent El","last_name":"Ghaoui"},{"last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"last_name":"Freund","first_name":"Robert M.","full_name":"Freund, Robert M."},{"full_name":"Pedregosa, Fabian","last_name":"Pedregosa","first_name":"Fabian"}],"extern":"1","citation":{"apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., & Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 7253–7262). Virtual.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:7253-7262.","short":"G. Négiar, G. Dresdner, A. Tsai, L.E. Ghaoui, F. Locatello, R.M. Freund, F. Pedregosa, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 7253–7262.","chicago":"Négiar, Geoffrey, Gideon Dresdner, Alicia Tsai, Laurent El Ghaoui, Francesco Locatello, Robert M. Freund, and Fabian Pedregosa. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” In Proceedings of the 37th International Conference on Machine Learning, 119:7253–62, 2020.","ieee":"G. Négiar et al., “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 7253–7262.","ista":"Négiar G, Dresdner G, Tsai A, Ghaoui LE, Locatello F, Freund RM, Pedregosa F. 2020. Stochastic Frank-Wolfe for constrained finite-sum minimization. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 7253–7262.","mla":"Négiar, Geoffrey, et al. “Stochastic Frank-Wolfe for Constrained Finite-Sum Minimization.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 7253–62."},"oa_version":"Preprint","language":[{"iso":"eng"}],"conference":{"name":"International Conference on Machine Learning","end_date":"2020-07-18","location":"Virtual","start_date":"2020-07-13"},"date_published":"2020-07-27T00:00:00Z","arxiv":1,"department":[{"_id":"FrLo"}],"date_updated":"2023-09-12T08:03:40Z","abstract":[{"text":"We propose a novel Stochastic Frank-Wolfe (a.k.a. conditional gradient)\r\nalgorithm for constrained smooth finite-sum minimization with a generalized\r\nlinear prediction/structure. This class of problems includes empirical risk\r\nminimization with sparse, low-rank, or other structured constraints. The\r\nproposed method is simple to implement, does not require step-size tuning, and\r\nhas a constant per-iteration cost that is independent of the dataset size.\r\nFurthermore, as a byproduct of the method we obtain a stochastic estimator of\r\nthe Frank-Wolfe gap that can be used as a stopping criterion. Depending on the\r\nsetting, the proposed method matches or improves on the best computational\r\nguarantees for Stochastic Frank-Wolfe algorithms. Benchmarks on several\r\ndatasets highlight different regimes in which the proposed method exhibits a\r\nfaster empirical convergence than related methods. Finally, we provide an\r\nimplementation of all considered methods in an open-source package.","lang":"eng"}],"external_id":{"arxiv":["2002.11860"]}},{"quality_controlled":"1","year":"2020","publication_status":"published","type":"conference","status":"public","alternative_title":["PMLR"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2002.02886"}],"_id":"14188","oa":1,"scopus_import":"1","date_created":"2023-08-22T14:08:14Z","day":"07","publication":"Proceedings of the 37th International Conference on Machine Learning","intvolume":" 119","title":"Weakly-supervised disentanglement without compromises","page":"6348–6359","article_processing_charge":"No","month":"07","volume":119,"date_published":"2020-07-07T00:00:00Z","arxiv":1,"conference":{"end_date":"2020-07-18","name":"International Conference on Machine Learning","location":"Virtual","start_date":"2020-07-13"},"external_id":{"arxiv":["2002.02886"]},"date_updated":"2024-10-14T12:28:02Z","department":[{"_id":"FrLo"}],"abstract":[{"lang":"eng","text":"Intelligent agents should be able to learn useful representations by\r\nobserving changes in their environment. We model such observations as pairs of\r\nnon-i.i.d. images sharing at least one of the underlying factors of variation.\r\nFirst, we theoretically show that only knowing how many factors have changed,\r\nbut not which ones, is sufficient to learn disentangled representations.\r\nSecond, we provide practical algorithms that learn disentangled representations\r\nfrom pairs of images without requiring annotation of groups, individual\r\nfactors, or the number of factors that have changed. Third, we perform a\r\nlarge-scale empirical study and show that such pairs of observations are\r\nsufficient to reliably learn disentangled representations on several benchmark\r\ndata sets. Finally, we evaluate our learned representations and find that they\r\nare simultaneously useful on a diverse suite of tasks, including generalization\r\nunder covariate shifts, fairness, and abstract reasoning. Overall, our results\r\ndemonstrate that weak supervision enables learning of useful disentangled\r\nrepresentations in realistic scenarios."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","first_name":"Francesco","last_name":"Locatello"},{"full_name":"Poole, Ben","first_name":"Ben","last_name":"Poole"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"full_name":"Schölkopf, Bernhard","first_name":"Bernhard","last_name":"Schölkopf"},{"full_name":"Bachem, Olivier","first_name":"Olivier","last_name":"Bachem"},{"full_name":"Tschannen, Michael","first_name":"Michael","last_name":"Tschannen"}],"language":[{"iso":"eng"}],"oa_version":"Preprint","citation":{"ista":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. 2020. Weakly-supervised disentanglement without compromises. Proceedings of the 37th International Conference on Machine Learning. International Conference on Machine Learning, PMLR, vol. 119, 6348–6359.","mla":"Locatello, Francesco, et al. “Weakly-Supervised Disentanglement without Compromises.” Proceedings of the 37th International Conference on Machine Learning, vol. 119, 2020, pp. 6348–6359.","chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In Proceedings of the 37th International Conference on Machine Learning, 119:6348–6359, 2020.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in Proceedings of the 37th International Conference on Machine Learning, Virtual, 2020, vol. 119, pp. 6348–6359.","apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., & Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In Proceedings of the 37th International Conference on Machine Learning (Vol. 119, pp. 6348–6359). Virtual.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: Proceedings of the 37th International Conference on Machine Learning. Vol 119. ; 2020:6348–6359.","short":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, M. Tschannen, in:, Proceedings of the 37th International Conference on Machine Learning, 2020, pp. 6348–6359."}},{"title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","intvolume":" 21","volume":21,"month":"09","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","scopus_import":"1","date_created":"2023-08-22T14:10:34Z","publication":"Journal of Machine Learning Research","article_number":"209","_id":"14195","main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}],"article_type":"original","oa":1,"has_accepted_license":"1","year":"2020","publication_status":"published","status":"public","type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","citation":{"short":"F. Locatello, S. Bauer, M. Lucic, G. Rätsch, S. Gelly, B. Schölkopf, O. Bachem, Journal of Machine Learning Research 21 (2020).","ama":"Locatello F, Bauer S, Lucic M, et al. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 2020;21.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., & Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. MIT Press.","ieee":"F. Locatello et al., “A sober look at the unsupervised learning of disentangled representations and their evaluation,” Journal of Machine Learning Research, vol. 21. MIT Press, 2020.","chicago":"Locatello, Francesco, Stefan Bauer, Mario Lucic, Gunnar Rätsch, Sylvain Gelly, Bernhard Schölkopf, and Olivier Bachem. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research. MIT Press, 2020.","ista":"Locatello F, Bauer S, Lucic M, Rätsch G, Gelly S, Schölkopf B, Bachem O. 2020. A sober look at the unsupervised learning of disentangled representations and their evaluation. Journal of Machine Learning Research. 21, 209.","mla":"Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” Journal of Machine Learning Research, vol. 21, 209, MIT Press, 2020."},"extern":"1","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"full_name":"Bauer, Stefan","last_name":"Bauer","first_name":"Stefan"},{"full_name":"Lucic, Mario","last_name":"Lucic","first_name":"Mario"},{"last_name":"Rätsch","first_name":"Gunnar","full_name":"Rätsch, Gunnar"},{"first_name":"Sylvain","last_name":"Gelly","full_name":"Gelly, Sylvain"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"external_id":{"arxiv":["2010.14766"]},"abstract":[{"lang":"eng","text":"The idea behind the unsupervised learning of disentangled representations is that real-world data is generated by a few explanatory factors of variation which can be recovered by unsupervised learning algorithms. In this paper, we provide a sober look at recent progress in the field and challenge some common assumptions. We first theoretically show that the unsupervised learning of disentangled representations is fundamentally impossible without inductive biases on both the models and the data. Then, we train over 14000\r\n models covering most prominent methods and evaluation metrics in a reproducible large-scale experimental study on eight data sets. We observe that while the different methods successfully enforce properties “encouraged” by the corresponding losses, well-disentangled models seemingly cannot be identified without supervision. Furthermore, different evaluation metrics do not always agree on what should be considered “disentangled” and exhibit systematic differences in the estimation. Finally, increased disentanglement does not seem to necessarily lead to a decreased sample complexity of learning for downstream tasks. Our results suggest that future work on disentanglement learning should be explicit about the role of inductive biases and (implicit) supervision, investigate concrete benefits of enforcing disentanglement of the learned representations, and consider a reproducible experimental setup covering several data sets."}],"date_updated":"2024-10-14T12:28:26Z","department":[{"_id":"FrLo"}],"arxiv":1,"date_published":"2020-09-01T00:00:00Z","publisher":"MIT Press"},{"oa_version":"Preprint","language":[{"iso":"eng"}],"citation":{"apa":"Locatello, F., Weissenborn, D., Unterthiner, T., Mahendran, A., Heigold, G., Uszkoreit, J., … Kipf, T. (2020). Object-centric learning with slot attention. In 34th International Conference on Neural Information Processing Systems (Vol. 33, pp. 11525–11538). Virtual: Neural Information Processing Systems Foundation.","short":"F. Locatello, D. Weissenborn, T. Unterthiner, A. Mahendran, G. Heigold, J. Uszkoreit, A. Dosovitskiy, T. Kipf, in:, 34th International Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2020, pp. 11525–11538.","ama":"Locatello F, Weissenborn D, Unterthiner T, et al. Object-centric learning with slot attention. In: 34th International Conference on Neural Information Processing Systems. Vol 33. Neural Information Processing Systems Foundation; 2020:11525-11538.","chicago":"Locatello, Francesco, Dirk Weissenborn, Thomas Unterthiner, Aravindh Mahendran, Georg Heigold, Jakob Uszkoreit, Alexey Dosovitskiy, and Thomas Kipf. “Object-Centric Learning with Slot Attention.” In 34th International Conference on Neural Information Processing Systems, 33:11525–38. Neural Information Processing Systems Foundation, 2020.","ieee":"F. Locatello et al., “Object-centric learning with slot attention,” in 34th International Conference on Neural Information Processing Systems, Virtual, 2020, vol. 33, pp. 11525–11538.","ista":"Locatello F, Weissenborn D, Unterthiner T, Mahendran A, Heigold G, Uszkoreit J, Dosovitskiy A, Kipf T. 2020. Object-centric learning with slot attention. 34th International Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 33, 11525–11538.","mla":"Locatello, Francesco, et al. “Object-Centric Learning with Slot Attention.” 34th International Conference on Neural Information Processing Systems, vol. 33, Neural Information Processing Systems Foundation, 2020, pp. 11525–38."},"extern":"1","author":[{"first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683"},{"full_name":"Weissenborn, Dirk","last_name":"Weissenborn","first_name":"Dirk"},{"last_name":"Unterthiner","first_name":"Thomas","full_name":"Unterthiner, Thomas"},{"first_name":"Aravindh","last_name":"Mahendran","full_name":"Mahendran, Aravindh"},{"first_name":"Georg","last_name":"Heigold","full_name":"Heigold, Georg"},{"first_name":"Jakob","last_name":"Uszkoreit","full_name":"Uszkoreit, Jakob"},{"last_name":"Dosovitskiy","first_name":"Alexey","full_name":"Dosovitskiy, Alexey"},{"full_name":"Kipf, Thomas","first_name":"Thomas","last_name":"Kipf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2006.15055"]},"abstract":[{"text":"Learning object-centric representations of complex scenes is a promising step towards enabling efficient abstract reasoning from low-level perceptual features. Yet, most deep learning approaches learn distributed representations that do not capture the compositional properties of natural scenes. In this paper, we present the Slot Attention module, an architectural component that interfaces with perceptual representations such as the output of a convolutional neural network and produces a set of task-dependent abstract representations which we call slots. These slots are exchangeable and can bind to any object in the input by specializing through a competitive procedure over multiple rounds of attention. We empirically demonstrate that Slot Attention can extract object-centric representations that enable generalization to unseen compositions when trained on unsupervised object discovery and supervised property prediction tasks.\r\n\r\n","lang":"eng"}],"department":[{"_id":"FrLo"}],"date_updated":"2025-07-10T11:50:47Z","arxiv":1,"date_published":"2020-12-20T00:00:00Z","publisher":"Neural Information Processing Systems Foundation","conference":{"start_date":"2020-12-06","location":"Virtual","name":"NeurIPS: Neural Information Processing Systems","end_date":"2020-12-12"},"title":"Object-centric learning with slot attention","page":"11525-11538","intvolume":" 33","volume":33,"article_processing_charge":"No","month":"12","day":"20","date_created":"2023-09-13T12:03:46Z","publication":"34th International Conference on Neural Information Processing Systems","publication_identifier":{"eissn":["1049-5258"],"isbn":["9781713829546"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2006.15055"}],"_id":"14326","oa":1,"type":"conference","status":"public","year":"2020","publication_status":"published","quality_controlled":"1","alternative_title":["Advances in Neural Information Processing Systems"]},{"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"day":"01","corr_author":"1","date_created":"2023-11-22T15:00:57Z","author":[{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy","oa_version":"Published Version","project":[{"_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex"}],"contributor":[{"contributor_type":"researcher","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian"},{"contributor_type":"researcher","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","last_name":"Zens","first_name":"Bettina"},{"contributor_type":"researcher","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"contributor_type":"researcher","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"file":[{"file_name":"3Dprint-files_download_v2.zip","file_size":49297,"date_updated":"2023-11-22T14:58:44Z","content_type":"application/zip","file_id":"14593","creator":"fschur","relation":"main_file","date_created":"2023-11-22T14:58:44Z","checksum":"0108616e2a59e51879ea51299a29b091","access_level":"open_access","success":1},{"access_level":"open_access","success":1,"file_id":"14637","creator":"cchlebak","relation":"main_file","checksum":"4c66ddedee4d01c1c4a7978208350cfc","date_created":"2023-12-01T10:39:59Z","file_size":641,"content_type":"text/plain","date_updated":"2023-12-01T10:39:59Z","file_name":"readme.txt"}],"citation":{"ista":"Schur FK. 2020. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592.","mla":"Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592.","chicago":"Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592.","ieee":"F. K. Schur, “STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020.","apa":"Schur, F. K. (2020). STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592","short":"F.K. Schur, (2020).","ama":"Schur FK. STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592"},"article_processing_charge":"No","month":"12","file_date_updated":"2023-12-01T10:39:59Z","year":"2020","type":"research_data","status":"public","date_published":"2020-12-01T00:00:00Z","related_material":{"record":[{"id":"8586","status":"public","relation":"research_data"}]},"publisher":"Institute of Science and Technology Austria","ddc":["570"],"_id":"14592","doi":"10.15479/AT:ISTA:14592","abstract":[{"text":"Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications.","lang":"eng"}],"oa":1,"has_accepted_license":"1","date_updated":"2025-06-12T07:35:28Z","department":[{"_id":"FlSc"}]},{"has_accepted_license":"1","article_type":"original","oa":1,"_id":"14694","doi":"10.4171/dm/780","publication_identifier":{"issn":["1431-0635"],"eissn":["1431-0643"]},"quality_controlled":"1","publication_status":"published","file_date_updated":"2023-12-18T10:42:32Z","year":"2020","type":"journal_article","status":"public","month":"09","article_processing_charge":"Yes","volume":25,"file":[{"file_size":1374708,"date_updated":"2023-12-18T10:42:32Z","content_type":"application/pdf","file_name":"2020_DocumentaMathematica_Alt.pdf","access_level":"open_access","success":1,"creator":"dernst","file_id":"14695","relation":"main_file","checksum":"12aacc1d63b852ff9a51c1f6b218d4a6","date_created":"2023-12-18T10:42:32Z"}],"intvolume":" 25","keyword":["General Mathematics"],"page":"1421-1539","title":"The Dyson equation with linear self-energy: Spectral bands, edges and cusps","publication":"Documenta Mathematica","date_created":"2023-12-18T10:37:43Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","date_updated":"2025-04-15T08:05:00Z","department":[{"_id":"LaEr"}],"abstract":[{"lang":"eng","text":"We study the unique solution m of the Dyson equation \\( -m(z)^{-1} = z\\1 - a + S[m(z)] \\) on a von Neumann algebra A with the constraint Imm≥0. Here, z lies in the complex upper half-plane, a is a self-adjoint element of A and S is a positivity-preserving linear operator on A. We show that m is the Stieltjes transform of a compactly supported A-valued measure on R. Under suitable assumptions, we establish that this measure has a uniformly 1/3-Hölder continuous density with respect to the Lebesgue measure, which is supported on finitely many intervals, called bands. In fact, the density is analytic inside the bands with a square-root growth at the edges and internal cubic root cusps whenever the gap between two bands vanishes. The shape of these singularities is universal and no other singularity may occur. We give a precise asymptotic description of m near the singular points. These asymptotics generalize the analysis at the regular edges given in the companion paper on the Tracy-Widom universality for the edge eigenvalue statistics for correlated random matrices [the first author et al., Ann. Probab. 48, No. 2, 963--1001 (2020; Zbl 1434.60017)] and they play a key role in the proof of the Pearcey universality at the cusp for Wigner-type matrices [G. Cipolloni et al., Pure Appl. Anal. 1, No. 4, 615--707 (2019; Zbl 07142203); the second author et al., Commun. Math. Phys. 378, No. 2, 1203--1278 (2020; Zbl 07236118)]. We also extend the finite dimensional band mass formula from [the first author et al., loc. cit.] to the von Neumann algebra setting by showing that the spectral mass of the bands is topologically rigid under deformations and we conclude that these masses are quantized in some important cases."}],"ddc":["510"],"external_id":{"arxiv":["1804.07752"]},"publisher":"EMS Press","related_material":{"record":[{"id":"6183","status":"public","relation":"earlier_version"}]},"date_published":"2020-09-01T00:00:00Z","arxiv":1,"citation":{"apa":"Alt, J., Erdös, L., & Krüger, T. H. (2020). The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. EMS Press. https://doi.org/10.4171/dm/780","short":"J. Alt, L. Erdös, T.H. Krüger, Documenta Mathematica 25 (2020) 1421–1539.","ama":"Alt J, Erdös L, Krüger TH. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 2020;25:1421-1539. doi:10.4171/dm/780","chicago":"Alt, Johannes, László Erdös, and Torben H Krüger. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica. EMS Press, 2020. https://doi.org/10.4171/dm/780.","ieee":"J. Alt, L. Erdös, and T. H. Krüger, “The Dyson equation with linear self-energy: Spectral bands, edges and cusps,” Documenta Mathematica, vol. 25. EMS Press, pp. 1421–1539, 2020.","mla":"Alt, Johannes, et al. “The Dyson Equation with Linear Self-Energy: Spectral Bands, Edges and Cusps.” Documenta Mathematica, vol. 25, EMS Press, 2020, pp. 1421–539, doi:10.4171/dm/780.","ista":"Alt J, Erdös L, Krüger TH. 2020. The Dyson equation with linear self-energy: Spectral bands, edges and cusps. Documenta Mathematica. 25, 1421–1539."},"language":[{"iso":"eng"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Alt, Johannes","last_name":"Alt","first_name":"Johannes","id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Torben H","last_name":"Krüger","id":"3020C786-F248-11E8-B48F-1D18A9856A87","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"}],"corr_author":"1"}]