[{"oa":1,"doi":"10.5061/DRYAD.R4XGXD29N","ddc":["570"],"date_published":"2020-09-22T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.r4xgxd29n"}],"status":"public","related_material":{"record":[{"status":"public","id":"8708","relation":"used_in_publication"}]},"citation":{"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. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>.","ieee":"A. Simon <i>et al.</i>, “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020.","short":"A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020).","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:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>","apa":"Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., &#38; Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">https://doi.org/10.5061/DRYAD.R4XGXD29N</a>","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, <a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>.","mla":"Simon, Alexis, et al. <i>How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels</i>. Dryad, 2020, doi:<a href=\"https://doi.org/10.5061/DRYAD.R4XGXD29N\">10.5061/DRYAD.R4XGXD29N</a>."},"author":[{"last_name":"Simon","first_name":"Alexis","full_name":"Simon, Alexis"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","full_name":"Fraisse, Christelle","last_name":"Fraisse","first_name":"Christelle"},{"first_name":"Tahani","last_name":"El Ayari","full_name":"El Ayari, Tahani"},{"full_name":"Liautard-Haag, Cathy","last_name":"Liautard-Haag","first_name":"Cathy"},{"first_name":"Petr","last_name":"Strelkov","full_name":"Strelkov, Petr"},{"full_name":"Welch, John","first_name":"John","last_name":"Welch"},{"last_name":"Bierne","first_name":"Nicolas","full_name":"Bierne, Nicolas"}],"month":"09","oa_version":"Published Version","type":"research_data_reference","day":"22","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_updated":"2023-08-04T11:04:11Z","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"}],"title":"How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels","date_created":"2023-05-23T16:48:27Z","publisher":"Dryad","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","department":[{"_id":"NiBa"}],"_id":"13073","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"},"article_processing_charge":"No"},{"year":"2020","_id":"14125","oa_version":"Published Version","type":"journal_article","month":"12","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","page":"i919-i927","date_created":"2023-08-21T12:28:20Z","volume":36,"status":"public","external_id":{"pmid":["33381818"]},"citation":{"ama":"Stark SG, Ficek J, Locatello F, et al. SCIM: Universal single-cell matching with unpaired feature sets. <i>Bioinformatics</i>. 2020;36(Supplement_2):i919-i927. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>","mla":"Stark, Stefan G., et al. “SCIM: Universal Single-Cell Matching with Unpaired Feature Sets.” <i>Bioinformatics</i>, vol. 36, no. Supplement_2, Oxford University Press, 2020, pp. i919–27, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">10.1093/bioinformatics/btaa843</a>.","ista":"Stark SG et al. 2020. SCIM: Universal single-cell matching with unpaired feature sets. Bioinformatics. 36(Supplement_2), i919–i927.","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. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>","ieee":"S. G. Stark <i>et al.</i>, “SCIM: Universal single-cell matching with unpaired feature sets,” <i>Bioinformatics</i>, 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.” <i>Bioinformatics</i>. Oxford University Press, 2020. <a href=\"https://doi.org/10.1093/bioinformatics/btaa843\">https://doi.org/10.1093/bioinformatics/btaa843</a>.","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."},"extern":"1","intvolume":"        36","related_material":{"link":[{"relation":"software","url":"https://github.com/ratschlab/scim"}]},"publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bioinformatics/btaa843"}],"date_published":"2020-12-01T00:00:00Z","department":[{"_id":"FrLo"}],"pmid":1,"publisher":"Oxford University Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","scopus_import":"1","article_processing_charge":"No","publication":"Bioinformatics","day":"01","author":[{"last_name":"Stark","first_name":"Stefan G","full_name":"Stark, Stefan G"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"full_name":"Locatello, Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","last_name":"Locatello","first_name":"Francesco"},{"first_name":"Ximena","last_name":"Bonilla","full_name":"Bonilla, Ximena"},{"full_name":"Chevrier, Stéphane","last_name":"Chevrier","first_name":"Stéphane"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"full_name":"Aebersold, Rudolf","first_name":"Rudolf","last_name":"Aebersold"},{"last_name":"Al-Quaddoomi","first_name":"Faisal S","full_name":"Al-Quaddoomi, Faisal S"},{"full_name":"Albinus, Jonas","last_name":"Albinus","first_name":"Jonas"},{"full_name":"Alborelli, Ilaria","last_name":"Alborelli","first_name":"Ilaria"},{"last_name":"Andani","first_name":"Sonali","full_name":"Andani, Sonali"},{"last_name":"Attinger","first_name":"Per-Olof","full_name":"Attinger, Per-Olof"},{"last_name":"Bacac","first_name":"Marina","full_name":"Bacac, Marina"},{"full_name":"Baumhoer, Daniel","last_name":"Baumhoer","first_name":"Daniel"},{"full_name":"Beck-Schimmer, Beatrice","last_name":"Beck-Schimmer","first_name":"Beatrice"},{"last_name":"Beerenwinkel","first_name":"Niko","full_name":"Beerenwinkel, Niko"},{"full_name":"Beisel, Christian","first_name":"Christian","last_name":"Beisel"},{"full_name":"Bernasconi, Lara","first_name":"Lara","last_name":"Bernasconi"},{"last_name":"Bertolini","first_name":"Anne","full_name":"Bertolini, Anne"},{"first_name":"Bernd","last_name":"Bodenmiller","full_name":"Bodenmiller, Bernd"},{"last_name":"Bonilla","first_name":"Ximena","full_name":"Bonilla, Ximena"},{"first_name":"Ruben","last_name":"Casanova","full_name":"Casanova, Ruben"},{"first_name":"Stéphane","last_name":"Chevrier","full_name":"Chevrier, Stéphane"},{"full_name":"Chicherova, Natalia","first_name":"Natalia","last_name":"Chicherova"},{"first_name":"Maya","last_name":"D'Costa","full_name":"D'Costa, Maya"},{"last_name":"Danenberg","first_name":"Esther","full_name":"Danenberg, Esther"},{"last_name":"Davidson","first_name":"Natalie","full_name":"Davidson, Natalie"},{"full_name":"gan, Monica-Andreea Dră","first_name":"Monica-Andreea Dră","last_name":"gan"},{"first_name":"Reinhard","last_name":"Dummer","full_name":"Dummer, Reinhard"},{"first_name":"Stefanie","last_name":"Engler","full_name":"Engler, Stefanie"},{"full_name":"Erkens, Martin","last_name":"Erkens","first_name":"Martin"},{"full_name":"Eschbach, Katja","last_name":"Eschbach","first_name":"Katja"},{"full_name":"Esposito, Cinzia","first_name":"Cinzia","last_name":"Esposito"},{"full_name":"Fedier, André","last_name":"Fedier","first_name":"André"},{"full_name":"Ferreira, Pedro","first_name":"Pedro","last_name":"Ferreira"},{"full_name":"Ficek, Joanna","last_name":"Ficek","first_name":"Joanna"},{"first_name":"Anja L","last_name":"Frei","full_name":"Frei, Anja L"},{"first_name":"Bruno","last_name":"Frey","full_name":"Frey, Bruno"},{"full_name":"Goetze, Sandra","first_name":"Sandra","last_name":"Goetze"},{"full_name":"Grob, Linda","first_name":"Linda","last_name":"Grob"},{"first_name":"Gabriele","last_name":"Gut","full_name":"Gut, Gabriele"},{"first_name":"Detlef","last_name":"Günther","full_name":"Günther, Detlef"},{"last_name":"Haberecker","first_name":"Martina","full_name":"Haberecker, Martina"},{"first_name":"Pirmin","last_name":"Haeuptle","full_name":"Haeuptle, Pirmin"},{"full_name":"Heinzelmann-Schwarz, Viola","first_name":"Viola","last_name":"Heinzelmann-Schwarz"},{"first_name":"Sylvia","last_name":"Herter","full_name":"Herter, Sylvia"},{"full_name":"Holtackers, Rene","last_name":"Holtackers","first_name":"Rene"},{"last_name":"Huesser","first_name":"Tamara","full_name":"Huesser, Tamara"},{"full_name":"Irmisch, Anja","last_name":"Irmisch","first_name":"Anja"},{"full_name":"Jacob, Francis","last_name":"Jacob","first_name":"Francis"},{"last_name":"Jacobs","first_name":"Andrea","full_name":"Jacobs, Andrea"},{"last_name":"Jaeger","first_name":"Tim M","full_name":"Jaeger, Tim M"},{"last_name":"Jahn","first_name":"Katharina","full_name":"Jahn, Katharina"},{"last_name":"James","first_name":"Alva R","full_name":"James, Alva R"},{"full_name":"Jermann, Philip M","last_name":"Jermann","first_name":"Philip M"},{"full_name":"Kahles, André","first_name":"André","last_name":"Kahles"},{"full_name":"Kahraman, Abdullah","last_name":"Kahraman","first_name":"Abdullah"},{"full_name":"Koelzer, Viktor H","first_name":"Viktor H","last_name":"Koelzer"},{"full_name":"Kuebler, Werner","first_name":"Werner","last_name":"Kuebler"},{"last_name":"Kuipers","first_name":"Jack","full_name":"Kuipers, Jack"},{"last_name":"Kunze","first_name":"Christian P","full_name":"Kunze, Christian P"},{"last_name":"Kurzeder","first_name":"Christian","full_name":"Kurzeder, Christian"},{"full_name":"Lehmann, Kjong-Van","first_name":"Kjong-Van","last_name":"Lehmann"},{"last_name":"Levesque","first_name":"Mitchell","full_name":"Levesque, Mitchell"},{"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"},{"full_name":"Markolin, Philipp","first_name":"Philipp","last_name":"Markolin"},{"first_name":"Julien","last_name":"Mena","full_name":"Mena, Julien"},{"full_name":"Menzel, Ulrike","last_name":"Menzel","first_name":"Ulrike"},{"full_name":"Metzler, Julian M","last_name":"Metzler","first_name":"Julian M"},{"last_name":"Miglino","first_name":"Nicola","full_name":"Miglino, Nicola"},{"last_name":"Milani","first_name":"Emanuela S","full_name":"Milani, Emanuela S"},{"last_name":"Moch","first_name":"Holger","full_name":"Moch, Holger"},{"first_name":"Simone","last_name":"Muenst","full_name":"Muenst, Simone"},{"full_name":"Murri, Riccardo","last_name":"Murri","first_name":"Riccardo"},{"first_name":"Charlotte KY","last_name":"Ng","full_name":"Ng, Charlotte KY"},{"full_name":"Nicolet, Stefan","last_name":"Nicolet","first_name":"Stefan"},{"full_name":"Nowak, Marta","last_name":"Nowak","first_name":"Marta"},{"first_name":"Patrick GA","last_name":"Pedrioli","full_name":"Pedrioli, Patrick GA"},{"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"},{"full_name":"Rommel, Christian","last_name":"Rommel","first_name":"Christian"},{"full_name":"Rosano-González, María L","last_name":"Rosano-González","first_name":"María L"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Santacroce","first_name":"Natascha","full_name":"Santacroce, Natascha"},{"full_name":"Castillo, Jacobo Sarabia del","last_name":"Castillo","first_name":"Jacobo Sarabia del"},{"last_name":"Schlenker","first_name":"Ramona","full_name":"Schlenker, Ramona"},{"first_name":"Petra C","last_name":"Schwalie","full_name":"Schwalie, Petra C"},{"full_name":"Schwan, Severin","last_name":"Schwan","first_name":"Severin"},{"full_name":"Schär, Tobias","last_name":"Schär","first_name":"Tobias"},{"full_name":"Senti, Gabriela","first_name":"Gabriela","last_name":"Senti"},{"first_name":"Franziska","last_name":"Singer","full_name":"Singer, Franziska"},{"first_name":"Sujana","last_name":"Sivapatham","full_name":"Sivapatham, Sujana"},{"full_name":"Snijder, Berend","first_name":"Berend","last_name":"Snijder"},{"first_name":"Bettina","last_name":"Sobottka","full_name":"Sobottka, Bettina"},{"full_name":"Sreedharan, Vipin T","last_name":"Sreedharan","first_name":"Vipin T"},{"first_name":"Stefan","last_name":"Stark","full_name":"Stark, Stefan"},{"full_name":"Stekhoven, Daniel J","last_name":"Stekhoven","first_name":"Daniel J"},{"last_name":"Theocharides","first_name":"Alexandre PA","full_name":"Theocharides, Alexandre PA"},{"full_name":"Thomas, Tinu M","first_name":"Tinu M","last_name":"Thomas"},{"full_name":"Tolnay, Markus","last_name":"Tolnay","first_name":"Markus"},{"last_name":"Tosevski","first_name":"Vinko","full_name":"Tosevski, Vinko"},{"last_name":"Toussaint","first_name":"Nora C","full_name":"Toussaint, Nora C"},{"full_name":"Tuncel, Mustafa A","last_name":"Tuncel","first_name":"Mustafa A"},{"last_name":"Tusup","first_name":"Marina","full_name":"Tusup, Marina"},{"last_name":"Drogen","first_name":"Audrey Van","full_name":"Drogen, Audrey Van"},{"full_name":"Vetter, Marcus","last_name":"Vetter","first_name":"Marcus"},{"full_name":"Vlajnic, Tatjana","last_name":"Vlajnic","first_name":"Tatjana"},{"last_name":"Weber","first_name":"Sandra","full_name":"Weber, Sandra"},{"last_name":"Weber","first_name":"Walter P","full_name":"Weber, Walter P"},{"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"},{"full_name":"Wey, Norbert","last_name":"Wey","first_name":"Norbert"},{"last_name":"Wicki","first_name":"Andreas","full_name":"Wicki, Andreas"},{"last_name":"Wollscheid","first_name":"Bernd","full_name":"Wollscheid, Bernd"},{"full_name":"Yu, Shuqing","last_name":"Yu","first_name":"Shuqing"},{"last_name":"Ziegler","first_name":"Johanna","full_name":"Ziegler, Johanna"},{"full_name":"Zimmermann, Marc","first_name":"Marc","last_name":"Zimmermann"},{"full_name":"Zoche, Martin","first_name":"Martin","last_name":"Zoche"},{"full_name":"Zuend, Gregor","last_name":"Zuend","first_name":"Gregor"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"last_name":"Lehmann","first_name":"Kjong-Van","full_name":"Lehmann, Kjong-Van"}],"title":"SCIM: Universal single-cell matching with unpaired feature sets","issue":"Supplement_2","language":[{"iso":"eng"}],"keyword":["Computational Mathematics","Computational Theory and Mathematics","Computer Science Applications","Molecular Biology","Biochemistry","Statistics and Probability"],"publication_identifier":{"eissn":["1367-4811"]},"quality_controlled":"1","doi":"10.1093/bioinformatics/btaa843"},{"year":"2020","_id":"14186","page":"13681-13684","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_updated":"2023-09-12T07:44:48Z","oa_version":"Preprint","month":"07","type":"conference","volume":34,"date_created":"2023-08-22T14:07:26Z","external_id":{"arxiv":["2007.14184"]},"status":"public","intvolume":"        34","extern":"1","citation":{"ama":"Locatello F, Bauer S, Lucic M, et al. A commentary on the unsupervised learning of disentangled representations. In: <i>The 34th AAAI Conference on Artificial Intelligence</i>. Vol 34. Association for the Advancement of Artificial Intelligence; 2020:13681-13684. doi:<a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">10.1609/aaai.v34i09.7120</a>","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2020). A commentary on the unsupervised learning of disentangled representations. In <i>The 34th AAAI Conference on Artificial Intelligence</i> (Vol. 34, pp. 13681–13684). New York, NY, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">https://doi.org/10.1609/aaai.v34i09.7120</a>","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.","mla":"Locatello, Francesco, et al. “A Commentary on the Unsupervised Learning of Disentangled Representations.” <i>The 34th AAAI Conference on Artificial Intelligence</i>, vol. 34, no. 9, Association for the Advancement of Artificial Intelligence, 2020, pp. 13681–84, doi:<a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">10.1609/aaai.v34i09.7120</a>.","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 <i>The 34th AAAI Conference on Artificial Intelligence</i>, 34:13681–84. Association for the Advancement of Artificial Intelligence, 2020. <a href=\"https://doi.org/10.1609/aaai.v34i09.7120\">https://doi.org/10.1609/aaai.v34i09.7120</a>.","ieee":"F. Locatello <i>et al.</i>, “A commentary on the unsupervised learning of disentangled representations,” in <i>The 34th AAAI Conference on Artificial Intelligence</i>, New York, NY, United States, 2020, vol. 34, no. 9, pp. 13681–13684.","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."},"oa":1,"publication_status":"published","date_published":"2020-07-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2007.14184"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for the Advancement of Artificial Intelligence","department":[{"_id":"FrLo"}],"publication":"The 34th AAAI Conference on Artificial Intelligence","scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Locatello","first_name":"Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco"},{"full_name":"Bauer, Stefan","first_name":"Stefan","last_name":"Bauer"},{"full_name":"Lucic, Mario","first_name":"Mario","last_name":"Lucic"},{"full_name":"Rätsch, Gunnar","last_name":"Rätsch","first_name":"Gunnar"},{"full_name":"Gelly, Sylvain","first_name":"Sylvain","last_name":"Gelly"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"},{"last_name":"Bachem","first_name":"Olivier","full_name":"Bachem, Olivier"}],"day":"28","title":"A commentary on the unsupervised learning of disentangled representations","arxiv":1,"conference":{"location":"New York, NY, United States","name":"AAAI: Conference on Artificial Intelligence","start_date":"2020-02-07","end_date":"2020-02-12"},"language":[{"iso":"eng"}],"issue":"9","publication_identifier":{"isbn":["9781577358350"],"eissn":["2374-3468"]},"doi":"10.1609/aaai.v34i09.7120","quality_controlled":"1"},{"external_id":{"arxiv":["2002.11860"]},"status":"public","alternative_title":["PMLR"],"citation":{"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 <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:7253–62, 2020.","ieee":"G. Négiar <i>et al.</i>, “Stochastic Frank-Wolfe for constrained finite-sum minimization,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Virtual, 2020, vol. 119, pp. 7253–7262.","apa":"Négiar, G., Dresdner, G., Tsai, A., Ghaoui, L. E., Locatello, F., Freund, R. M., &#38; Pedregosa, F. (2020). Stochastic Frank-Wolfe for constrained finite-sum minimization. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 7253–7262). Virtual.","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.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, 2020, pp. 7253–62.","ama":"Négiar G, Dresdner G, Tsai A, et al. Stochastic Frank-Wolfe for constrained finite-sum minimization. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ; 2020:7253-7262."},"extern":"1","intvolume":"       119","oa":1,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/2002.11860","open_access":"1"}],"date_published":"2020-07-27T00:00:00Z","year":"2020","_id":"14187","type":"conference","oa_version":"Preprint","month":"07","abstract":[{"lang":"eng","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."}],"date_updated":"2023-09-12T08:03:40Z","page":"7253-7262","date_created":"2023-08-22T14:07:52Z","volume":119,"language":[{"iso":"eng"}],"conference":{"name":"International Conference on Machine Learning","location":"Virtual","start_date":"2020-07-13","end_date":"2020-07-18"},"quality_controlled":"1","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication":"Proceedings of the 37th International Conference on Machine Learning","day":"27","author":[{"first_name":"Geoffrey","last_name":"Négiar","full_name":"Négiar, Geoffrey"},{"first_name":"Gideon","last_name":"Dresdner","full_name":"Dresdner, Gideon"},{"first_name":"Alicia","last_name":"Tsai","full_name":"Tsai, Alicia"},{"first_name":"Laurent El","last_name":"Ghaoui","full_name":"Ghaoui, Laurent El"},{"last_name":"Locatello","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","orcid":"0000-0002-4850-0683","full_name":"Locatello, Francesco"},{"full_name":"Freund, Robert M.","first_name":"Robert M.","last_name":"Freund"},{"last_name":"Pedregosa","first_name":"Fabian","full_name":"Pedregosa, Fabian"}],"title":"Stochastic Frank-Wolfe for constrained finite-sum minimization","arxiv":1},{"date_created":"2023-08-22T14:08:14Z","volume":119,"oa_version":"Preprint","type":"conference","month":"07","date_updated":"2023-09-12T07:59:29Z","abstract":[{"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.","lang":"eng"}],"page":"6348–6359","_id":"14188","year":"2020","main_file_link":[{"url":"https://arxiv.org/abs/2002.02886","open_access":"1"}],"date_published":"2020-07-07T00:00:00Z","oa":1,"publication_status":"published","citation":{"chicago":"Locatello, Francesco, Ben Poole, Gunnar Rätsch, Bernhard Schölkopf, Olivier Bachem, and Michael Tschannen. “Weakly-Supervised Disentanglement without Compromises.” In <i>Proceedings of the 37th International Conference on Machine Learning</i>, 119:6348–6359, 2020.","ieee":"F. Locatello, B. Poole, G. Rätsch, B. Schölkopf, O. Bachem, and M. Tschannen, “Weakly-supervised disentanglement without compromises,” in <i>Proceedings of the 37th International Conference on Machine Learning</i>, Virtual, 2020, vol. 119, pp. 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.","ama":"Locatello F, Poole B, Rätsch G, Schölkopf B, Bachem O, Tschannen M. Weakly-supervised disentanglement without compromises. In: <i>Proceedings of the 37th International Conference on Machine Learning</i>. Vol 119. ; 2020:6348–6359.","apa":"Locatello, F., Poole, B., Rätsch, G., Schölkopf, B., Bachem, O., &#38; Tschannen, M. (2020). Weakly-supervised disentanglement without compromises. In <i>Proceedings of the 37th International Conference on Machine Learning</i> (Vol. 119, pp. 6348–6359). Virtual.","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.” <i>Proceedings of the 37th International Conference on Machine Learning</i>, vol. 119, 2020, pp. 6348–6359."},"intvolume":"       119","extern":"1","external_id":{"arxiv":["2002.02886"]},"status":"public","alternative_title":["PMLR"],"title":"Weakly-supervised disentanglement without compromises","arxiv":1,"day":"07","author":[{"last_name":"Locatello","first_name":"Francesco","full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"full_name":"Poole, Ben","first_name":"Ben","last_name":"Poole"},{"full_name":"Rätsch, Gunnar","first_name":"Gunnar","last_name":"Rätsch"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"},{"last_name":"Tschannen","first_name":"Michael","full_name":"Tschannen, Michael"}],"scopus_import":"1","article_processing_charge":"No","publication":"Proceedings of the 37th International Conference on Machine Learning","department":[{"_id":"FrLo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","language":[{"iso":"eng"}],"conference":{"start_date":"2020-07-13","name":"International Conference on Machine Learning","location":"Virtual","end_date":"2020-07-18"}},{"year":"2020","_id":"14195","oa_version":"Published Version","type":"journal_article","month":"09","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":"2023-09-12T09:23:56Z","date_created":"2023-08-22T14:10:34Z","volume":21,"status":"public","external_id":{"arxiv":["2010.14766"]},"citation":{"ieee":"F. Locatello <i>et al.</i>, “A sober look at the unsupervised learning of disentangled representations and their evaluation,” <i>Journal of Machine Learning Research</i>, 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.” <i>Journal of Machine Learning Research</i>. MIT Press, 2020.","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. <i>Journal of Machine Learning Research</i>. 2020;21.","mla":"Locatello, Francesco, et al. “A Sober Look at the Unsupervised Learning of Disentangled Representations and Their Evaluation.” <i>Journal of Machine Learning Research</i>, vol. 21, 209, 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.","apa":"Locatello, F., Bauer, S., Lucic, M., Rätsch, G., Gelly, S., Schölkopf, B., &#38; Bachem, O. (2020). A sober look at the unsupervised learning of disentangled representations and their evaluation. <i>Journal of Machine Learning Research</i>. MIT Press."},"extern":"1","intvolume":"        21","has_accepted_license":"1","oa":1,"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://jmlr.csail.mit.edu/papers/v21/19-976.html"}],"date_published":"2020-09-01T00:00:00Z","ddc":["000"],"department":[{"_id":"FrLo"}],"publisher":"MIT Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication":"Journal of Machine Learning Research","day":"01","license":"https://creativecommons.org/licenses/by/4.0/","author":[{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","first_name":"Francesco"},{"first_name":"Stefan","last_name":"Bauer","full_name":"Bauer, Stefan"},{"first_name":"Mario","last_name":"Lucic","full_name":"Lucic, Mario"},{"first_name":"Gunnar","last_name":"Rätsch","full_name":"Rätsch, Gunnar"},{"last_name":"Gelly","first_name":"Sylvain","full_name":"Gelly, Sylvain"},{"full_name":"Schölkopf, Bernhard","last_name":"Schölkopf","first_name":"Bernhard"},{"first_name":"Olivier","last_name":"Bachem","full_name":"Bachem, Olivier"}],"article_number":"209","title":"A sober look at the unsupervised learning of disentangled representations and their evaluation","arxiv":1,"language":[{"iso":"eng"}],"quality_controlled":"1"},{"year":"2020","acknowledgement":"This work was supported by the Institute of Science and Technology Austria (IST Austria), the European Research Council under grant agreement number 758053 (ERC StG QUNNECT) and the EU’s Horizon 2020 research and innovation programme under grant agreement number 862644 (FET Open QUARTET). S.B. acknowledges support from the Marie Skłodowska Curie\r\nfellowship number 707438 (MSC-IF SUPEREOM), DV acknowledge support from EU’s Horizon 2020 research and innovation programme under grant agreement number 732894 (FET Proactive HOT) and the Project QuaSeRT funded by the QuantERA ERANET Cofund in Quantum Technologies, and J.M.F from the Austrian Science Fund (FWF) through BeyondC (F71), a NOMIS foundation research grant, and the EU’s Horizon 2020 research and\r\ninnovation programme under grant agreement number 732894 (FET Proactive\r\nHOT).","_id":"9001","abstract":[{"text":"Quantum illumination is a sensing technique that employs entangled signal-idler beams to improve the detection efficiency of low-reflectivity objects in environments with large thermal noise. The advantage over classical strategies is evident at low signal brightness, a feature which could make the protocol an ideal prototype for non-invasive scanning or low-power short-range radar. Here we experimentally investigate the concept of quantum illumination at microwave frequencies, by generating entangled fields using a Josephson parametric converter which are then amplified to illuminate a room-temperature object at a distance of 1 meter. Starting from experimental data, we simulate the case of perfect idler photon number detection, which results in a quantum advantage compared to the relative classical benchmark. Our results highlight the opportunities and challenges on the way towards a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"date_updated":"2024-09-10T12:23:52Z","month":"09","type":"conference","oa_version":"Preprint","date_created":"2021-01-10T23:01:17Z","volume":2020,"status":"public","external_id":{"isi":["000612224900089"],"arxiv":["1908.03058"]},"citation":{"short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, in:, IEEE National Radar Conference - Proceedings, IEEE, 2020.","chicago":"Barzanjeh, Shabir, Stefano Pirandola, David Vitali, and Johannes M Fink. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” In <i>IEEE National Radar Conference - Proceedings</i>, Vol. 2020. IEEE, 2020. <a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">https://doi.org/10.1109/RadarConf2043947.2020.9266397</a>.","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination with a digital phase-conjugated receiver,” in <i>IEEE National Radar Conference - Proceedings</i>, Florence, Italy, 2020, vol. 2020, no. 9.","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., &#38; Fink, J. M. (2020). Microwave quantum illumination with a digital phase-conjugated receiver. In <i>IEEE National Radar Conference - Proceedings</i> (Vol. 2020). Florence, Italy: IEEE. <a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">https://doi.org/10.1109/RadarConf2043947.2020.9266397</a>","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination with a Digital Phase-Conjugated Receiver.” <i>IEEE National Radar Conference - Proceedings</i>, vol. 2020, no. 9, 9266397, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">10.1109/RadarConf2043947.2020.9266397</a>.","ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination with a digital phase-conjugated receiver. IEEE National Radar Conference - Proceedings. RadarConf: National Conference on Radar vol. 2020, 9266397.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination with a digital phase-conjugated receiver. In: <i>IEEE National Radar Conference - Proceedings</i>. Vol 2020. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/RadarConf2043947.2020.9266397\">10.1109/RadarConf2043947.2020.9266397</a>"},"intvolume":"      2020","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"7910"}]},"oa":1,"publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1908.03058","open_access":"1"}],"date_published":"2020-09-21T00:00:00Z","department":[{"_id":"JoFi"}],"publisher":"IEEE","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","ec_funded":1,"scopus_import":"1","publication":"IEEE National Radar Conference - Proceedings","day":"21","author":[{"orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir","first_name":"Shabir","last_name":"Barzanjeh"},{"full_name":"Pirandola, Stefano","first_name":"Stefano","last_name":"Pirandola"},{"full_name":"Vitali, David","first_name":"David","last_name":"Vitali"},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"}],"title":"Microwave quantum illumination with a digital phase-conjugated receiver","arxiv":1,"article_number":"9266397","project":[{"name":"A Fiber Optic Transceiver for Superconducting Qubits","_id":"26336814-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"758053"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"},{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894"}],"language":[{"iso":"eng"}],"issue":"9","isi":1,"conference":{"end_date":"2020-09-25","name":"RadarConf: National Conference on Radar","location":"Florence, Italy","start_date":"2020-09-21"},"publication_identifier":{"issn":["1097-5659"],"isbn":["9781728189420"]},"quality_controlled":"1","doi":"10.1109/RadarConf2043947.2020.9266397"},{"intvolume":"        95","citation":{"ieee":"T. D. Browning and W. Sawin, “Free rational points on smooth hypersurfaces,” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4. European Mathematical Society, pp. 635–659, 2020.","chicago":"Browning, Timothy D, and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society, 2020. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>.","short":"T.D. Browning, W. Sawin, Commentarii Mathematici Helvetici 95 (2020) 635–659.","ama":"Browning TD, Sawin W. Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. 2020;95(4):635-659. doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>","ista":"Browning TD, Sawin W. 2020. Free rational points on smooth hypersurfaces. Commentarii Mathematici Helvetici. 95(4), 635–659.","mla":"Browning, Timothy D., and Will Sawin. “Free Rational Points on Smooth Hypersurfaces.” <i>Commentarii Mathematici Helvetici</i>, vol. 95, no. 4, European Mathematical Society, 2020, pp. 635–59, doi:<a href=\"https://doi.org/10.4171/CMH/499\">10.4171/CMH/499</a>.","apa":"Browning, T. D., &#38; Sawin, W. (2020). Free rational points on smooth hypersurfaces. <i>Commentarii Mathematici Helvetici</i>. European Mathematical Society. <a href=\"https://doi.org/10.4171/CMH/499\">https://doi.org/10.4171/CMH/499</a>"},"external_id":{"arxiv":["1906.08463"],"isi":["000596833300001"]},"status":"public","date_published":"2020-12-07T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.08463"}],"publication_status":"published","oa":1,"_id":"9007","year":"2020","volume":95,"date_created":"2021-01-17T23:01:11Z","page":"635-659","type":"journal_article","month":"12","oa_version":"Preprint","date_updated":"2023-08-24T11:11:36Z","abstract":[{"text":"Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.","lang":"eng"}],"isi":1,"issue":"4","language":[{"iso":"eng"}],"doi":"10.4171/CMH/499","quality_controlled":"1","publication_identifier":{"issn":["00102571"],"eissn":["14208946"]},"publication":"Commentarii Mathematici Helvetici","article_type":"original","scopus_import":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"European Mathematical Society","department":[{"_id":"TiBr"}],"title":"Free rational points on smooth hypersurfaces","arxiv":1,"author":[{"first_name":"Timothy D","last_name":"Browning","full_name":"Browning, Timothy D","id":"35827D50-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8314-0177"},{"first_name":"Will","last_name":"Sawin","full_name":"Sawin, Will"}],"day":"07"},{"isi":1,"issue":"4","language":[{"iso":"eng"}],"doi":"10.14778/3436905.3436917","quality_controlled":"1","publication_identifier":{"eissn":["2150-8097"]},"publication":"Proceedings of the VLDB Endowment","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","scopus_import":"1","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"title":"CALYPSO: Private data management for decentralized ledgers","author":[{"first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30"},{"full_name":"Alp, Enis Ceyhun","last_name":"Alp","first_name":"Enis Ceyhun"},{"first_name":"Linus","last_name":"Gasser","full_name":"Gasser, Linus"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"},{"full_name":"Syta, Ewa","first_name":"Ewa","last_name":"Syta"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}],"day":"01","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":"        14","citation":{"ama":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. 2020;14(4):586-599. doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>","ista":"Kokoris Kogias E, Alp EC, Gasser L, Jovanovic P, Syta E, Ford B. 2020. CALYPSO: Private data management for decentralized ledgers. Proceedings of the VLDB Endowment. 14(4), 586–599.","mla":"Kokoris Kogias, Eleftherios, et al. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4, Association for Computing Machinery, 2020, pp. 586–99, doi:<a href=\"https://doi.org/10.14778/3436905.3436917\">10.14778/3436905.3436917</a>.","apa":"Kokoris Kogias, E., Alp, E. C., Gasser, L., Jovanovic, P., Syta, E., &#38; Ford, B. (2020). CALYPSO: Private data management for decentralized ledgers. <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>","ieee":"E. Kokoris Kogias, E. C. Alp, L. Gasser, P. Jovanovic, E. Syta, and B. Ford, “CALYPSO: Private data management for decentralized ledgers,” <i>Proceedings of the VLDB Endowment</i>, vol. 14, no. 4. Association for Computing Machinery, pp. 586–599, 2020.","chicago":"Kokoris Kogias, Eleftherios, Enis Ceyhun Alp, Linus Gasser, Philipp Jovanovic, Ewa Syta, and Bryan Ford. “CALYPSO: Private Data Management for Decentralized Ledgers.” <i>Proceedings of the VLDB Endowment</i>. Association for Computing Machinery, 2020. <a href=\"https://doi.org/10.14778/3436905.3436917\">https://doi.org/10.14778/3436905.3436917</a>.","short":"E. Kokoris Kogias, E.C. Alp, L. Gasser, P. Jovanovic, E. Syta, B. Ford, Proceedings of the VLDB Endowment 14 (2020) 586–599."},"external_id":{"isi":["000658495400012"]},"status":"public","date_published":"2020-12-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://dl.acm.org/doi/10.14778/3436905.3436917"}],"publication_status":"published","oa":1,"_id":"9011","acknowledgement":"We thank Nicolas Gailly, Vincent Graf, Jean-Pierre Hubaux, Wouter Lueks, Massimo Marelli, Carmela Troncoso, Juan-Ramón Troncoso Pastoriza, Frédéric Pont, and Sandra Siby for their valuable feedback. This project was supported in part by the ETH domain under PHRT grant #2017−201, and by the AXA Research Fund, Byzgen, DFINITY, and the Swiss Data Science Center (SDSC).","year":"2020","volume":14,"date_created":"2021-01-17T23:01:13Z","page":"586-599","oa_version":"Published Version","type":"journal_article","month":"12","date_updated":"2023-08-24T13:57:13Z","abstract":[{"text":"Distributed ledgers provide high availability and integrity, making them a key enabler for practical and secure computation of distributed workloads among mutually distrustful parties. Many practical applications also require strong confidentiality, however. This work enhances permissioned and permissionless blockchains with the ability to manage confidential data without forfeiting availability or decentralization. The proposed Calypso architecture addresses two orthogonal challenges confronting modern distributed ledgers: (a) enabling the auditable management of secrets and (b) protecting distributed computations against arbitrage attacks when their results depend on the ordering and secrecy of inputs.\r\n\r\nCalypso introduces on-chain secrets, a novel abstraction that enforces atomic deposition of an auditable trace whenever users access confidential data. Calypso provides user-controlled consent management that ensures revocation atomicity and accountable anonymity. To enable permissionless deployment, we introduce an incentive scheme and provide users with the option to select their preferred trustees. We evaluated our Calypso prototype with a confidential document-sharing application and a decentralized lottery. Our benchmarks show that transaction-processing latency increases linearly in terms of security (number of trustees) and is in the range of 0.2 to 8 seconds for 16 to 128 trustees.","lang":"eng"}]},{"external_id":{"isi":["000600695200027"]},"status":"public","intvolume":"        52","citation":{"ama":"Fischer JL, Laux T, Simon TM. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. 2020;52(6):6222-6233. doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>","apa":"Fischer, J. L., Laux, T., &#38; Simon, T. M. (2020). Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>","mla":"Fischer, Julian L., et al. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6, Society for Industrial and Applied Mathematics, 2020, pp. 6222–33, doi:<a href=\"https://doi.org/10.1137/20M1322182\">10.1137/20M1322182</a>.","ista":"Fischer JL, Laux T, Simon TM. 2020. Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies. SIAM Journal on Mathematical Analysis. 52(6), 6222–6233.","chicago":"Fischer, Julian L, Tim Laux, and Theresa M. Simon. “Convergence Rates of the Allen-Cahn Equation to Mean Curvature Flow: A Short Proof Based on Relative Entropies.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2020. <a href=\"https://doi.org/10.1137/20M1322182\">https://doi.org/10.1137/20M1322182</a>.","ieee":"J. L. Fischer, T. Laux, and T. M. Simon, “Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 52, no. 6. Society for Industrial and Applied Mathematics, pp. 6222–6233, 2020.","short":"J.L. Fischer, T. Laux, T.M. Simon, SIAM Journal on Mathematical Analysis 52 (2020) 6222–6233."},"oa":1,"publication_status":"published","has_accepted_license":"1","date_published":"2020-12-15T00:00:00Z","ddc":["510"],"acknowledgement":"This work was supported by the European Union's Horizon 2020 Research and Innovation\r\nProgramme under Marie Sklodowska-Curie grant agreement 665385 and by the Deutsche\r\nForschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy, EXC-2047/1--390685813.","year":"2020","_id":"9039","page":"6222-6233","abstract":[{"lang":"eng","text":"We give a short and self-contained proof for rates of convergence of the Allen--Cahn equation towards mean curvature flow, assuming that a classical (smooth) solution to the latter exists and starting from well-prepared initial data. Our approach is based on a relative entropy technique. In particular, it does not require a stability analysis for the linearized Allen--Cahn operator. As our analysis also does not rely on the comparison principle, we expect it to be applicable to more complex equations and systems."}],"date_updated":"2023-08-24T11:15:16Z","month":"12","type":"journal_article","oa_version":"Published Version","volume":52,"date_created":"2021-01-24T23:01:09Z","file_date_updated":"2021-01-25T07:48:39Z","project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"isi":1,"language":[{"iso":"eng"}],"issue":"6","publication_identifier":{"issn":["00361410"],"eissn":["10957154"]},"doi":"10.1137/20M1322182","quality_controlled":"1","publisher":"Society for Industrial and Applied Mathematics","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JuFi"}],"publication":"SIAM Journal on Mathematical Analysis","article_processing_charge":"No","ec_funded":1,"scopus_import":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","author":[{"last_name":"Fischer","first_name":"Julian L","orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"last_name":"Laux","first_name":"Tim","full_name":"Laux, Tim"},{"full_name":"Simon, Theresa M.","first_name":"Theresa M.","last_name":"Simon"}],"file":[{"file_size":310655,"content_type":"application/pdf","relation":"main_file","creator":"dernst","file_name":"2020_SIAM_Fischer.pdf","success":1,"date_created":"2021-01-25T07:48:39Z","access_level":"open_access","file_id":"9041","date_updated":"2021-01-25T07:48:39Z","checksum":"21aa1cf4c30a86a00cae15a984819b5d"}],"day":"15","title":"Convergence rates of the Allen-Cahn equation to mean curvature flow: A short proof based on relative entropies"},{"file_date_updated":"2021-02-09T09:39:02Z","date_created":"2021-01-24T23:01:10Z","oa_version":"Published Version","type":"conference","month":"09","abstract":[{"text":"Machine learning and formal methods have complimentary benefits and drawbacks. In this work, we address the controller-design problem with a combination of techniques from both fields. The use of black-box neural networks in deep reinforcement learning (deep RL) poses a challenge for such a combination. Instead of reasoning formally about the output of deep RL, which we call the wizard, we extract from it a decision-tree based model, which we refer to as the magic book. Using the extracted model as an intermediary, we are able to handle problems that are infeasible for either deep RL or formal methods by themselves. First, we suggest, for the first time, a synthesis procedure that is based on a magic book. We synthesize a stand-alone correct-by-design controller that enjoys the favorable performance of RL. Second, we incorporate a magic book in a bounded model checking (BMC) procedure. BMC allows us to find numerous traces of the plant under the control of the wizard, which a user can use to increase the trustworthiness of the wizard and direct further training.","lang":"eng"}],"date_updated":"2021-02-09T09:39:59Z","page":"138-147","_id":"9040","year":"2020","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","ddc":["000"],"date_published":"2020-09-21T00:00:00Z","has_accepted_license":"1","publication_status":"published","oa":1,"citation":{"ama":"Alamdari PA, Avni G, Henzinger TA, Lukina A. Formal methods with a touch of magic. In: <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>. TU Wien Academic Press; 2020:138-147. doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>","apa":"Alamdari, P. A., Avni, G., Henzinger, T. A., &#38; Lukina, A. (2020). Formal methods with a touch of magic. In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i> (pp. 138–147). Online Conference: TU Wien Academic Press. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>","mla":"Alamdari, Par Alizadeh, et al. “Formal Methods with a Touch of Magic.” <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, TU Wien Academic Press, 2020, pp. 138–47, doi:<a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">10.34727/2020/isbn.978-3-85448-042-6_21</a>.","ista":"Alamdari PA, Avni G, Henzinger TA, Lukina A. 2020. Formal methods with a touch of magic. Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design.  FMCAD: Formal Methods in Computer-Aided Design, 138–147.","chicago":"Alamdari, Par Alizadeh, Guy Avni, Thomas A Henzinger, and Anna Lukina. “Formal Methods with a Touch of Magic.” In <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, 138–47. TU Wien Academic Press, 2020. <a href=\"https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21\">https://doi.org/10.34727/2020/isbn.978-3-85448-042-6_21</a>.","ieee":"P. A. Alamdari, G. Avni, T. A. Henzinger, and A. Lukina, “Formal methods with a touch of magic,” in <i>Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design</i>, Online Conference, 2020, pp. 138–147.","short":"P.A. Alamdari, G. Avni, T.A. Henzinger, A. Lukina, in:, Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2020, pp. 138–147."},"status":"public","title":"Formal methods with a touch of magic","day":"21","file":[{"access_level":"open_access","date_created":"2021-02-09T09:39:02Z","checksum":"d616d549a0ade78606b16f8a9540820f","date_updated":"2021-02-09T09:39:02Z","file_id":"9109","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":990999,"success":1,"file_name":"2020_FMCAD_Alamdari.pdf"}],"author":[{"first_name":"Par Alizadeh","last_name":"Alamdari","full_name":"Alamdari, Par Alizadeh"},{"last_name":"Avni","first_name":"Guy","orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","full_name":"Avni, Guy"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"},{"full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","last_name":"Lukina","first_name":"Anna"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","scopus_import":"1","publication":"Proceedings of the 20th Conference on Formal Methods in Computer-Aided Design","department":[{"_id":"ToHe"}],"publisher":"TU Wien Academic Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.34727/2020/isbn.978-3-85448-042-6_21","publication_identifier":{"eissn":["2708-7824"],"isbn":["9783854480426"]},"language":[{"iso":"eng"}],"conference":{"start_date":"2020-09-21","name":" FMCAD: Formal Methods in Computer-Aided Design","location":"Online Conference","end_date":"2020-09-24"},"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}]},{"editor":[{"full_name":"Starr, C","first_name":"C","last_name":"Starr"}],"status":"public","citation":{"chicago":"Schmid-Hempel, Paul, and Sylvia Cremer. “Parasites and Pathogens.” In <i>Encyclopedia of Social Insects</i>, edited by C Starr. Cham: Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">https://doi.org/10.1007/978-3-319-90306-4_94-1</a>.","ieee":"P. Schmid-Hempel and S. Cremer, “Parasites and Pathogens,” in <i>Encyclopedia of Social Insects</i>, C. Starr, Ed. Cham: Springer Nature, 2020.","short":"P. Schmid-Hempel, S. Cremer, in:, C. Starr (Ed.), Encyclopedia of Social Insects, Springer Nature, Cham, 2020.","ama":"Schmid-Hempel P, Cremer S. Parasites and Pathogens. In: Starr C, ed. <i>Encyclopedia of Social Insects</i>. Cham: Springer Nature; 2020. doi:<a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">10.1007/978-3-319-90306-4_94-1</a>","apa":"Schmid-Hempel, P., &#38; Cremer, S. (2020). Parasites and Pathogens. In C. Starr (Ed.), <i>Encyclopedia of Social Insects</i>. Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">https://doi.org/10.1007/978-3-319-90306-4_94-1</a>","ista":"Schmid-Hempel P, Cremer S. 2020.Parasites and Pathogens. In: Encyclopedia of Social Insects. .","mla":"Schmid-Hempel, Paul, and Sylvia Cremer. “Parasites and Pathogens.” <i>Encyclopedia of Social Insects</i>, edited by C Starr, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/978-3-319-90306-4_94-1\">10.1007/978-3-319-90306-4_94-1</a>."},"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9783319903064"]},"date_published":"2020-02-22T00:00:00Z","doi":"10.1007/978-3-319-90306-4_94-1","quality_controlled":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","place":"Cham","year":"2020","department":[{"_id":"SyCr"}],"publication":"Encyclopedia of Social Insects","_id":"9096","article_processing_charge":"No","author":[{"first_name":"Paul","last_name":"Schmid-Hempel","full_name":"Schmid-Hempel, Paul"},{"full_name":"Cremer, Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia M","last_name":"Cremer"}],"day":"22","date_updated":"2021-02-05T12:19:21Z","oa_version":"None","type":"book_chapter","month":"02","title":"Parasites and Pathogens","date_created":"2021-02-05T12:15:18Z"},{"date_created":"2021-02-07T23:01:14Z","volume":2020,"abstract":[{"lang":"eng","text":"We introduce LRT-NG, a set of techniques and an associated toolset that computes a reachtube (an over-approximation of the set of reachable states over a given time horizon) of a nonlinear dynamical system. LRT-NG significantly advances the state-of-the-art Langrangian Reachability and its associated tool LRT. From a theoretical perspective, LRT-NG is superior to LRT in three ways. First, it uses for the first time an analytically computed metric for the propagated ball which is proven to minimize the ball’s volume. We emphasize that the metric computation is the centerpiece of all bloating-based techniques. Secondly, it computes the next reachset as the intersection of two balls: one based on the Cartesian metric and the other on the new metric. While the two metrics were previously considered opposing approaches, their joint use considerably tightens the reachtubes. Thirdly, it avoids the \"wrapping effect\" associated with the validated integration of the center of the reachset, by optimally absorbing the interval approximation in the radius of the next ball. From a tool-development perspective, LRT-NG is superior to LRT in two ways. First, it is a standalone tool that no longer relies on CAPD. This required the implementation of the Lohner method and a Runge-Kutta time-propagation method. Secondly, it has an improved interface, allowing the input model and initial conditions to be provided as external input files. Our experiments on a comprehensive set of benchmarks, including two Neural ODEs, demonstrates LRT-NG’s superior performance compared to LRT, CAPD, and Flow*."}],"date_updated":"2021-02-09T09:20:58Z","type":"conference","month":"12","oa_version":"Preprint","page":"1556-1563","_id":"9103","year":"2020","acknowledgement":"The authors would like to thank Ramin Hasani and Guillaume Berger for intellectual discussions about the research which lead to the generation of new ideas. ML was supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). Smolka’s research was supported by NSF grants CPS-1446832 and CCF-1918225. Gruenbacher is funded by FWF project W1255-N23. JC was partially supported by NAWA Polish Returns grant\r\nPPN/PPO/2018/1/00029.\r\n","main_file_link":[{"url":"https://arxiv.org/abs/2012.07458","open_access":"1"}],"date_published":"2020-12-14T00:00:00Z","oa":1,"publication_status":"published","citation":{"chicago":"Gruenbacher, Sophie, Jacek Cyranka, Mathias Lechner, Md Ariful Islam, Scott A. Smolka, and Radu Grosu. “Lagrangian Reachtubes: The next Generation.” In <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>, 2020:1556–63. IEEE, 2020. <a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">https://doi.org/10.1109/CDC42340.2020.9304042</a>.","ieee":"S. Gruenbacher, J. Cyranka, M. Lechner, M. A. Islam, S. A. Smolka, and R. Grosu, “Lagrangian reachtubes: The next generation,” in <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>, Jeju Islang, Korea (South), 2020, vol. 2020, pp. 1556–1563.","short":"S. Gruenbacher, J. Cyranka, M. Lechner, M.A. Islam, S.A. Smolka, R. Grosu, in:, Proceedings of the 59th IEEE Conference on Decision and Control, IEEE, 2020, pp. 1556–1563.","ama":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. Lagrangian reachtubes: The next generation. In: <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>. Vol 2020. IEEE; 2020:1556-1563. doi:<a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">10.1109/CDC42340.2020.9304042</a>","apa":"Gruenbacher, S., Cyranka, J., Lechner, M., Islam, M. A., Smolka, S. A., &#38; Grosu, R. (2020). Lagrangian reachtubes: The next generation. In <i>Proceedings of the 59th IEEE Conference on Decision and Control</i> (Vol. 2020, pp. 1556–1563). Jeju Islang, Korea (South): IEEE. <a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">https://doi.org/10.1109/CDC42340.2020.9304042</a>","mla":"Gruenbacher, Sophie, et al. “Lagrangian Reachtubes: The next Generation.” <i>Proceedings of the 59th IEEE Conference on Decision and Control</i>, vol. 2020, IEEE, 2020, pp. 1556–63, doi:<a href=\"https://doi.org/10.1109/CDC42340.2020.9304042\">10.1109/CDC42340.2020.9304042</a>.","ista":"Gruenbacher S, Cyranka J, Lechner M, Islam MA, Smolka SA, Grosu R. 2020. Lagrangian reachtubes: The next generation. Proceedings of the 59th IEEE Conference on Decision and Control. CDC: Conference on Decision and Control vol. 2020, 1556–1563."},"intvolume":"      2020","status":"public","external_id":{"arxiv":["2012.07458"]},"arxiv":1,"title":"Lagrangian reachtubes: The next generation","day":"14","author":[{"first_name":"Sophie","last_name":"Gruenbacher","full_name":"Gruenbacher, Sophie"},{"full_name":"Cyranka, Jacek","last_name":"Cyranka","first_name":"Jacek"},{"first_name":"Mathias","last_name":"Lechner","id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias"},{"full_name":"Islam, Md Ariful","first_name":"Md Ariful","last_name":"Islam"},{"last_name":"Smolka","first_name":"Scott A.","full_name":"Smolka, Scott A."},{"first_name":"Radu","last_name":"Grosu","full_name":"Grosu, Radu"}],"article_processing_charge":"No","scopus_import":"1","publication":"Proceedings of the 59th IEEE Conference on Decision and Control","department":[{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"IEEE","quality_controlled":"1","doi":"10.1109/CDC42340.2020.9304042","publication_identifier":{"issn":["07431546"],"isbn":["9781728174471"]},"language":[{"iso":"eng"}],"conference":{"location":"Jeju Islang, Korea (South)","name":"CDC: Conference on Decision and Control","start_date":"2020-12-14","end_date":"2020-12-18"},"project":[{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"}]},{"citation":{"ama":"Bao Z, Erdös L, Schnelli K. On the support of the free additive convolution. <i>Journal d’Analyse Mathematique</i>. 2020;142:323-348. doi:<a href=\"https://doi.org/10.1007/s11854-020-0135-2\">10.1007/s11854-020-0135-2</a>","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2020). On the support of the free additive convolution. <i>Journal d’Analyse Mathematique</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11854-020-0135-2\">https://doi.org/10.1007/s11854-020-0135-2</a>","ista":"Bao Z, Erdös L, Schnelli K. 2020. On the support of the free additive convolution. Journal d’Analyse Mathematique. 142, 323–348.","mla":"Bao, Zhigang, et al. “On the Support of the Free Additive Convolution.” <i>Journal d’Analyse Mathematique</i>, vol. 142, Springer Nature, 2020, pp. 323–48, doi:<a href=\"https://doi.org/10.1007/s11854-020-0135-2\">10.1007/s11854-020-0135-2</a>.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “On the Support of the Free Additive Convolution.” <i>Journal d’Analyse Mathematique</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s11854-020-0135-2\">https://doi.org/10.1007/s11854-020-0135-2</a>.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “On the support of the free additive convolution,” <i>Journal d’Analyse Mathematique</i>, vol. 142. Springer Nature, pp. 323–348, 2020.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal d’Analyse Mathematique 142 (2020) 323–348."},"intvolume":"       142","external_id":{"isi":["000611879400008"],"arxiv":["1804.11199"]},"status":"public","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.11199"}],"date_published":"2020-11-01T00:00:00Z","oa":1,"publication_status":"published","_id":"9104","year":"2020","acknowledgement":"Supported in part by Hong Kong RGC Grant ECS 26301517.\r\nSupported in part by ERC Advanced Grant RANMAT No. 338804.\r\nSupported in part by the Knut and Alice Wallenberg Foundation and the Swedish Research Council Grant VR-2017-05195.","date_created":"2021-02-07T23:01:15Z","volume":142,"type":"journal_article","month":"11","oa_version":"Preprint","date_updated":"2023-08-24T11:16:03Z","abstract":[{"lang":"eng","text":"We consider the free additive convolution of two probability measures μ and ν on the real line and show that μ ⊞ v is supported on a single interval if μ and ν each has single interval support. Moreover, the density of μ ⊞ ν is proven to vanish as a square root near the edges of its support if both μ and ν have power law behavior with exponents between −1 and 1 near their edges. In particular, these results show the ubiquity of the conditions in our recent work on optimal local law at the spectral edges for addition of random matrices [5]."}],"page":"323-348","language":[{"iso":"eng"}],"isi":1,"project":[{"call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804"}],"quality_controlled":"1","doi":"10.1007/s11854-020-0135-2","publication_identifier":{"issn":["00217670"],"eissn":["15658538"]},"article_type":"original","ec_funded":1,"scopus_import":"1","article_processing_charge":"No","publication":"Journal d'Analyse Mathematique","department":[{"_id":"LaEr"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","title":"On the support of the free additive convolution","arxiv":1,"day":"01","author":[{"first_name":"Zhigang","last_name":"Bao","full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3036-1475"},{"last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"first_name":"Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin"}]},{"day":"23","file":[{"success":1,"file_name":"2020_PRXQuantum_Hease.pdf","relation":"main_file","content_type":"application/pdf","file_size":2146924,"creator":"dernst","date_updated":"2021-02-12T11:16:16Z","file_id":"9115","checksum":"b70b12ded6d7660d4c9037eb09bfed0c","date_created":"2021-02-12T11:16:16Z","access_level":"open_access"}],"author":[{"full_name":"Hease, William J","id":"29705398-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9868-2166","last_name":"Hease","first_name":"William J"},{"full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"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","id":"45598606-F248-11E8-B48F-1D18A9856A87","last_name":"Wulf","first_name":"Matthias"},{"last_name":"Arnold","first_name":"Georg M","orcid":"0000-0003-1397-7876","id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."},{"first_name":"Johannes M","last_name":"Fink","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X"}],"article_number":"020315","title":"Bidirectional electro-optic wavelength conversion in the quantum ground state","department":[{"_id":"JoFi"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"American Physical Society","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","ec_funded":1,"article_processing_charge":"No","publication":"PRX Quantum","publication_identifier":{"issn":["2691-3399"]},"quality_controlled":"1","doi":"10.1103/prxquantum.1.020315","project":[{"grant_number":"758053","call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Quantum Local Area Networks with Superconducting Qubits","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","call_identifier":"H2020","grant_number":"899354"},{"grant_number":"F07105","name":"Integrating superconducting quantum circuits","_id":"26927A52-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"}],"issue":"2","language":[{"iso":"eng"}],"isi":1,"oa_version":"Published Version","month":"11","type":"journal_article","abstract":[{"lang":"eng","text":"Microwave photonics lends the advantages of fiber optics to electronic sensing and communication systems. In contrast to nonlinear optics, electro-optic devices so far require classical modulation fields whose variance is dominated by electronic or thermal noise rather than quantum fluctuations. Here we demonstrate bidirectional single-sideband conversion of X band microwave to C band telecom light with a microwave mode occupancy as low as 0.025 ± 0.005 and an added output noise of less than or equal to 0.074 photons. This is facilitated by radiative cooling and a triply resonant ultra-low-loss transducer operating at millikelvin temperatures. The high bandwidth of 10.7 MHz and total (internal) photon conversion\r\nefficiency of 0.03% (0.67%) combined with the extremely slow heating rate of 1.1 added output noise photons per second for the highest available pump power of 1.48 mW puts near-unity efficiency pulsed quantum transduction within reach. Together with the non-Gaussian resources of superconducting qubits this might provide the practical foundation to extend the range and scope of current quantum networks in analogy to electrical repeaters in classical fiber optic communication."}],"date_updated":"2024-10-29T09:11:05Z","file_date_updated":"2021-02-12T11:16:16Z","date_created":"2021-02-12T10:41:28Z","volume":1,"year":"2020","acknowledgement":"The authors acknowledge the support of T. Menner, A. Arslani, and T. Asenov from the Miba machine shop for machining the microwave cavity, and thank S. Barzanjeh, F. Sedlmeir, and C. Marquardt for fruitful discussions. This work is supported by IST Austria and the European Research Council under Grant No. 758053 (ERC StG QUNNECT). W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant No. 754411.\r\nG.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (F71) and the European Union’s Horizon 2020 research and innovation program under Grant No. 899354 (FET Open SuperQuLAN). H.G.L.S. acknowledges support from the Aotearoa/New Zealand’s MBIE Endeavour Smart Ideas Grant No UOOX1805.","_id":"9114","has_accepted_license":"1","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"M-Shop"}],"date_published":"2020-11-23T00:00:00Z","ddc":["530"],"status":"public","external_id":{"isi":["000674680100001"]},"citation":{"ama":"Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. <i>PRX Quantum</i>. 2020;1(2). doi:<a href=\"https://doi.org/10.1103/prxquantum.1.020315\">10.1103/prxquantum.1.020315</a>","ista":"Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel HGL, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state. PRX Quantum. 1(2), 020315.","mla":"Hease, William J., et al. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” <i>PRX Quantum</i>, vol. 1, no. 2, 020315, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/prxquantum.1.020315\">10.1103/prxquantum.1.020315</a>.","apa":"Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H. G. L., &#38; Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. <i>PRX Quantum</i>. American Physical Society. <a href=\"https://doi.org/10.1103/prxquantum.1.020315\">https://doi.org/10.1103/prxquantum.1.020315</a>","ieee":"W. J. Hease <i>et al.</i>, “Bidirectional electro-optic wavelength conversion in the quantum ground state,” <i>PRX Quantum</i>, vol. 1, no. 2. American Physical Society, 2020.","chicago":"Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald G.L. Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” <i>PRX Quantum</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/prxquantum.1.020315\">https://doi.org/10.1103/prxquantum.1.020315</a>.","short":"W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H.G.L. Schwefel, J.M. Fink, PRX Quantum 1 (2020)."},"intvolume":"         1","related_material":{"record":[{"status":"public","id":"13071","relation":"research_data"},{"id":"12900","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"13175","status":"public"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/how-to-transport-microwave-quantum-information-via-optical-fiber/","relation":"press_release"}]}},{"publication_identifier":{"isbn":["9780470016176","9780470015902"]},"publication_status":"published","quality_controlled":"1","date_published":"2020-05-16T00:00:00Z","doi":"10.1002/9780470015902.a0029007","status":"public","citation":{"ama":"Westram AM, Faria R, Butlin R, Johannesson K. Inversions and Evolution. In: <i>ELS</i>. Wiley; 2020. doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029007\">10.1002/9780470015902.a0029007</a>","mla":"Westram, Anja M., et al. “Inversions and Evolution.” <i>ELS</i>, Wiley, 2020, doi:<a href=\"https://doi.org/10.1002/9780470015902.a0029007\">10.1002/9780470015902.a0029007</a>.","ista":"Westram AM, Faria R, Butlin R, Johannesson K. 2020.Inversions and Evolution. In: eLS. .","apa":"Westram, A. M., Faria, R., Butlin, R., &#38; Johannesson, K. (2020). Inversions and Evolution. In <i>eLS</i>. Wiley. <a href=\"https://doi.org/10.1002/9780470015902.a0029007\">https://doi.org/10.1002/9780470015902.a0029007</a>","ieee":"A. M. Westram, R. Faria, R. Butlin, and K. Johannesson, “Inversions and Evolution,” in <i>eLS</i>, Wiley, 2020.","chicago":"Westram, Anja M, Rui Faria, Roger Butlin, and Kerstin Johannesson. “Inversions and Evolution.” In <i>ELS</i>. Wiley, 2020. <a href=\"https://doi.org/10.1002/9780470015902.a0029007\">https://doi.org/10.1002/9780470015902.a0029007</a>.","short":"A.M. Westram, R. Faria, R. Butlin, K. Johannesson, in:, ELS, Wiley, 2020."},"language":[{"iso":"eng"}],"oa_version":"None","type":"book_chapter","month":"05","day":"16","date_updated":"2021-02-15T13:18:16Z","abstract":[{"text":"Inversions are chromosomal rearrangements where the order of genes is reversed. Inversions originate by mutation and can be under positive, negative or balancing selection. Selective effects result from potential disruptive effects on meiosis, gene disruption at inversion breakpoints and, importantly, the effects of inversions as modifiers of recombination rate: Recombination is strongly reduced in individuals heterozygous for an inversion, allowing for alleles at different loci to be inherited as a ‘block’. This may lead to a selective advantage whenever it is favourable to keep certain combinations of alleles associated, for example under local adaptation with gene flow. Inversions can cover a considerable part of a chromosome and contain numerous loci under different selection pressures, so that the resulting overall effects may be complex. Empirical data from various systems show that inversions may have a prominent role in local adaptation, speciation, parallel evolution, the maintenance of polymorphism and sex chromosome evolution.","lang":"eng"}],"author":[{"first_name":"Anja M","last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"last_name":"Butlin","first_name":"Roger","full_name":"Butlin, Roger"},{"last_name":"Johannesson","first_name":"Kerstin","full_name":"Johannesson, Kerstin"}],"date_created":"2021-02-15T12:39:04Z","title":"Inversions and Evolution","year":"2020","department":[{"_id":"NiBa"}],"publisher":"Wiley","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","_id":"9123","publication":"eLS"},{"article_processing_charge":"No","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","publication":"Computational and Mathematical Biophysics","department":[{"_id":"HeEd"}],"publisher":"De Gruyter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"The weighted Gaussian curvature derivative of a space-filling diagram","arxiv":1,"file":[{"checksum":"ca43a7440834eab6bbea29c59b56ef3a","file_id":"9170","date_updated":"2021-02-19T13:33:19Z","access_level":"open_access","date_created":"2021-02-19T13:33:19Z","file_name":"2020_CompMathBiophysics_Akopyan.pdf","success":1,"creator":"dernst","file_size":707452,"content_type":"application/pdf","relation":"main_file"}],"day":"21","author":[{"last_name":"Akopyan","first_name":"Arseniy","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"issue":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"quality_controlled":"1","doi":"10.1515/cmb-2020-0101","publication_identifier":{"issn":["2544-7297"]},"_id":"9156","year":"2020","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of theweighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","file_date_updated":"2021-02-19T13:33:19Z","date_created":"2021-02-17T15:12:44Z","volume":8,"abstract":[{"text":"The morphometric approach [11, 14] writes the solvation free energy as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted Gaussian curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [4], and the weighted mean curvature in [1], this yields the derivative of the morphometric expression of solvation free energy.","lang":"eng"}],"date_updated":"2023-10-17T12:35:10Z","month":"07","oa_version":"Published Version","type":"journal_article","page":"74-88","citation":{"ieee":"A. Akopyan and H. Edelsbrunner, “The weighted Gaussian curvature derivative of a space-filling diagram,” <i>Computational and Mathematical Biophysics</i>, vol. 8, no. 1. De Gruyter, pp. 74–88, 2020.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” <i>Computational and Mathematical Biophysics</i>. De Gruyter, 2020. <a href=\"https://doi.org/10.1515/cmb-2020-0101\">https://doi.org/10.1515/cmb-2020-0101</a>.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 74–88.","ama":"Akopyan A, Edelsbrunner H. The weighted Gaussian curvature derivative of a space-filling diagram. <i>Computational and Mathematical Biophysics</i>. 2020;8(1):74-88. doi:<a href=\"https://doi.org/10.1515/cmb-2020-0101\">10.1515/cmb-2020-0101</a>","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Gaussian Curvature Derivative of a Space-Filling Diagram.” <i>Computational and Mathematical Biophysics</i>, vol. 8, no. 1, De Gruyter, 2020, pp. 74–88, doi:<a href=\"https://doi.org/10.1515/cmb-2020-0101\">10.1515/cmb-2020-0101</a>.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted Gaussian curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 74–88.","apa":"Akopyan, A., &#38; Edelsbrunner, H. (2020). The weighted Gaussian curvature derivative of a space-filling diagram. <i>Computational and Mathematical Biophysics</i>. De Gruyter. <a href=\"https://doi.org/10.1515/cmb-2020-0101\">https://doi.org/10.1515/cmb-2020-0101</a>"},"intvolume":"         8","external_id":{"arxiv":["1908.06777"]},"status":"public","ddc":["510"],"date_published":"2020-07-21T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published"},{"publisher":"De Gruyter","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"HeEd"}],"publication":"Computational and Mathematical Biophysics","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","ec_funded":1,"article_processing_charge":"No","author":[{"first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"}],"file":[{"content_type":"application/pdf","relation":"main_file","file_size":562359,"creator":"dernst","success":1,"file_name":"2020_CompMathBiophysics_Akopyan2.pdf","date_created":"2021-02-19T13:56:24Z","access_level":"open_access","date_updated":"2021-02-19T13:56:24Z","file_id":"9171","checksum":"cea41de9937d07a3b927d71ee8b4e432"}],"day":"20","title":"The weighted mean curvature derivative of a space-filling diagram","project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2544-7297"]},"doi":"10.1515/cmb-2020-0100","quality_controlled":"1","acknowledgement":"The authors of this paper thank Roland Roth for suggesting the analysis of the weighted\r\ncurvature derivatives for the purpose of improving molecular dynamics simulations and for his continued encouragement. They also thank Patrice Koehl for the implementation of the formulas and for his encouragement and advise along the road. Finally, they thank two anonymous reviewers for their constructive criticism.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","year":"2020","_id":"9157","page":"51-67","type":"journal_article","month":"06","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Representing an atom by a solid sphere in 3-dimensional Euclidean space, we get the space-filling diagram of a molecule by taking the union. Molecular dynamics simulates its motion subject to bonds and other forces, including the solvation free energy. The morphometric approach [12, 17] writes the latter as a linear combination of weighted versions of the volume, area, mean curvature, and Gaussian curvature of the space-filling diagram. We give a formula for the derivative of the weighted mean curvature. Together with the derivatives of the weighted volume in [7], the weighted area in [3], and the weighted Gaussian curvature [1], this yields the derivative of the morphometric expression of the solvation free energy."}],"date_updated":"2023-10-17T12:34:51Z","volume":8,"file_date_updated":"2021-02-19T13:56:24Z","date_created":"2021-02-17T15:13:01Z","status":"public","intvolume":"         8","citation":{"ama":"Akopyan A, Edelsbrunner H. The weighted mean curvature derivative of a space-filling diagram. <i>Computational and Mathematical Biophysics</i>. 2020;8(1):51-67. doi:<a href=\"https://doi.org/10.1515/cmb-2020-0100\">10.1515/cmb-2020-0100</a>","apa":"Akopyan, A., &#38; Edelsbrunner, H. (2020). The weighted mean curvature derivative of a space-filling diagram. <i>Computational and Mathematical Biophysics</i>. De Gruyter. <a href=\"https://doi.org/10.1515/cmb-2020-0100\">https://doi.org/10.1515/cmb-2020-0100</a>","mla":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” <i>Computational and Mathematical Biophysics</i>, vol. 8, no. 1, De Gruyter, 2020, pp. 51–67, doi:<a href=\"https://doi.org/10.1515/cmb-2020-0100\">10.1515/cmb-2020-0100</a>.","ista":"Akopyan A, Edelsbrunner H. 2020. The weighted mean curvature derivative of a space-filling diagram. Computational and Mathematical Biophysics. 8(1), 51–67.","chicago":"Akopyan, Arseniy, and Herbert Edelsbrunner. “The Weighted Mean Curvature Derivative of a Space-Filling Diagram.” <i>Computational and Mathematical Biophysics</i>. De Gruyter, 2020. <a href=\"https://doi.org/10.1515/cmb-2020-0100\">https://doi.org/10.1515/cmb-2020-0100</a>.","ieee":"A. Akopyan and H. Edelsbrunner, “The weighted mean curvature derivative of a space-filling diagram,” <i>Computational and Mathematical Biophysics</i>, vol. 8, no. 1. De Gruyter, pp. 51–67, 2020.","short":"A. Akopyan, H. Edelsbrunner, Computational and Mathematical Biophysics 8 (2020) 51–67."},"oa":1,"publication_status":"published","has_accepted_license":"1","ddc":["510"],"date_published":"2020-06-20T00:00:00Z"},{"department":[{"_id":"EvBe"}],"pmid":1,"publisher":"Elsevier","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"scopus_import":"1","article_processing_charge":"No","publication":"Plant Communications","day":"11","file":[{"access_level":"open_access","date_created":"2021-02-18T10:23:59Z","checksum":"785b266d82a94b007cf40dbbe7c4847e","date_updated":"2021-02-18T10:23:59Z","file_id":"9161","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":840289,"success":1,"file_name":"2020_PlantComm_Semeradova.pdf"}],"author":[{"last_name":"Semeradova","first_name":"Hana","id":"42FE702E-F248-11E8-B48F-1D18A9856A87","full_name":"Semeradova, Hana"},{"first_name":"Juan C","last_name":"Montesinos López","id":"310A8E3E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9179-6099","full_name":"Montesinos López, Juan C"},{"last_name":"Benková","first_name":"Eva","full_name":"Benková, Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"}],"article_number":"100048","title":"All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways","project":[{"_id":"261821BC-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of the cytokinin regulated endomembrane trafficking to coordinate plant organogenesis.","grant_number":"24746"},{"name":"Molecular mechanism of auxindriven formative divisions delineating lateral root organogenesis in plants","_id":"253E54C8-B435-11E9-9278-68D0E5697425","grant_number":"ALTF710-2016"}],"issue":"3","language":[{"iso":"eng"}],"isi":1,"publication_identifier":{"issn":["2590-3462"]},"quality_controlled":"1","doi":"10.1016/j.xplc.2020.100048","year":"2020","acknowledgement":"H.S. is the recipient of a DOC Fellowship of the Austrian Academy of Sciences at the Institute of Science and Technology, Austria. J.C.M. is the recipient of an EMBO Long-Term Fellowship (ALTF number 710-2016). We would like to thank Jiri Friml and Carina Baskett for critical reading of the manuscript and Shutang Tan and Maciek Adamowski for helpful discussions. No conflict of interest declared.","_id":"9160","oa_version":"Published Version","month":"05","type":"journal_article","date_updated":"2024-03-25T23:30:26Z","abstract":[{"lang":"eng","text":"Auxin is a key hormonal regulator, that governs plant growth and development in concert with other hormonal pathways. The unique feature of auxin is its polar, cell-to-cell transport that leads to the formation of local auxin maxima and gradients, which coordinate initiation and patterning of plant organs. The molecular machinery mediating polar auxin transport is one of the important points of interaction with other hormones. Multiple hormonal pathways converge at the regulation of auxin transport and form a regulatory network that integrates various developmental and environmental inputs to steer plant development. In this review, we discuss recent advances in understanding the mechanisms that underlie regulation of polar auxin transport by multiple hormonal pathways. Specifically, we focus on the post-translational mechanisms that contribute to fine-tuning of the abundance and polarity of auxin transporters at the plasma membrane and thereby enable rapid modification of the auxin flow to coordinate plant growth and development."}],"date_created":"2021-02-18T10:18:43Z","file_date_updated":"2021-02-18T10:23:59Z","volume":1,"external_id":{"isi":["000654052800010"],"pmid":["33367243"]},"status":"public","citation":{"apa":"Semerádová, H., Montesinos López, J. C., &#38; Benková, E. (2020). All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">https://doi.org/10.1016/j.xplc.2020.100048</a>","mla":"Semerádová, Hana, et al. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” <i>Plant Communications</i>, vol. 1, no. 3, 100048, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">10.1016/j.xplc.2020.100048</a>.","ista":"Semerádová H, Montesinos López JC, Benková E. 2020. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. Plant Communications. 1(3), 100048.","ama":"Semerádová H, Montesinos López JC, Benková E. All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways. <i>Plant Communications</i>. 2020;1(3). doi:<a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">10.1016/j.xplc.2020.100048</a>","short":"H. Semerádová, J.C. Montesinos López, E. Benková, Plant Communications 1 (2020).","chicago":"Semerádová, Hana, Juan C Montesinos López, and Eva Benková. “All Roads Lead to Auxin: Post-Translational Regulation of Auxin Transport by Multiple Hormonal Pathways.” <i>Plant Communications</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.xplc.2020.100048\">https://doi.org/10.1016/j.xplc.2020.100048</a>.","ieee":"H. Semerádová, J. C. Montesinos López, and E. Benková, “All roads lead to auxin: Post-translational regulation of auxin transport by multiple hormonal pathways,” <i>Plant Communications</i>, vol. 1, no. 3. Elsevier, 2020."},"related_material":{"record":[{"id":"10135","status":"public","relation":"dissertation_contains"}]},"intvolume":"         1","has_accepted_license":"1","publication_status":"published","oa":1,"date_published":"2020-05-11T00:00:00Z","ddc":["580"]},{"_id":"9194","year":"2020","acknowledgement":"During the writing of this article we became aware of another review of quantum transduction with somewhat different emphasis [99].\r\nWe would like to thank the participants of the transduction workshop at Caltech in September 2018 for helpful and stimulating discussions. We particularly thank John Bartholomew, Andrei Faraon, Johannes Fink, Jeff Holzgrafe, Linbo Shao, Marko Lončar, Daniel Oblak, and Oskar Painter.\r\nN L and N S acknowledge support from the Alliance for Quantum Technologies' (AQT) Intelligent Quantum Networks and Technologies (INQNET) research program and by DOE/HEP QuantISED program grant, QCCFP (Quantum Communication Channels for Fundamental Physics), award number DE-SC0019219. NS further acknowledges support by the Natural Sciences and Engineering Research Council of Canada (NSERC). SB acknowledges support from the Marie Skłodowska Curie fellowship number 707 438 (MSC-IF SUPEREOM). JPC acknowledges support from the Caltech PMA prize postdoctoral fellowship. MS acknowledges support from the ARL-CDQI and the National Science Foundation. CS acknowledges NSERC, Quantum Alberta, and the Alberta Major Innovation Fund.","date_created":"2021-02-25T08:32:29Z","file_date_updated":"2021-03-02T09:47:13Z","volume":5,"oa_version":"Published Version","type":"journal_article","month":"03","abstract":[{"text":"Quantum transduction, the process of converting quantum signals from one form of energy to another, is an important area of quantum science and technology. The present perspective article reviews quantum transduction between microwave and optical photons, an area that has recently seen a lot of activity and progress because of its relevance for connecting superconducting quantum processors over long distances, among other applications. Our review covers the leading approaches to achieving such transduction, with an emphasis on those based on atomic ensembles, opto-electro-mechanics, and electro-optics. We briefly discuss relevant metrics from the point of view of different applications, as well as challenges for the future.","lang":"eng"}],"date_updated":"2023-08-24T11:17:48Z","citation":{"short":"N. Lauk, N. Sinclair, S. Barzanjeh, J.P. Covey, M. Saffman, M. Spiropulu, C. Simon, Quantum Science and Technology 5 (2020).","ieee":"N. Lauk <i>et al.</i>, “Perspectives on quantum transduction,” <i>Quantum Science and Technology</i>, vol. 5, no. 2. IOP Publishing, 2020.","chicago":"Lauk, Nikolai, Neil Sinclair, Shabir Barzanjeh, Jacob P Covey, Mark Saffman, Maria Spiropulu, and Christoph Simon. “Perspectives on Quantum Transduction.” <i>Quantum Science and Technology</i>. IOP Publishing, 2020. <a href=\"https://doi.org/10.1088/2058-9565/ab788a\">https://doi.org/10.1088/2058-9565/ab788a</a>.","mla":"Lauk, Nikolai, et al. “Perspectives on Quantum Transduction.” <i>Quantum Science and Technology</i>, vol. 5, no. 2, 020501, IOP Publishing, 2020, doi:<a href=\"https://doi.org/10.1088/2058-9565/ab788a\">10.1088/2058-9565/ab788a</a>.","ista":"Lauk N, Sinclair N, Barzanjeh S, Covey JP, Saffman M, Spiropulu M, Simon C. 2020. Perspectives on quantum transduction. Quantum Science and Technology. 5(2), 020501.","apa":"Lauk, N., Sinclair, N., Barzanjeh, S., Covey, J. P., Saffman, M., Spiropulu, M., &#38; Simon, C. (2020). Perspectives on quantum transduction. <i>Quantum Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2058-9565/ab788a\">https://doi.org/10.1088/2058-9565/ab788a</a>","ama":"Lauk N, Sinclair N, Barzanjeh S, et al. Perspectives on quantum transduction. <i>Quantum Science and Technology</i>. 2020;5(2). doi:<a href=\"https://doi.org/10.1088/2058-9565/ab788a\">10.1088/2058-9565/ab788a</a>"},"intvolume":"         5","status":"public","external_id":{"isi":["000521449500001"]},"ddc":["530"],"date_published":"2020-03-01T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","ec_funded":1,"scopus_import":"1","publication":"Quantum Science and Technology","department":[{"_id":"JoFi"}],"publisher":"IOP Publishing","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"020501","title":"Perspectives on quantum transduction","day":"01","file":[{"access_level":"open_access","date_created":"2021-03-02T09:47:13Z","checksum":"a8562c42124a66b86836fe2489eb5f4f","file_id":"9215","date_updated":"2021-03-02T09:47:13Z","creator":"dernst","file_size":974399,"content_type":"application/pdf","relation":"main_file","file_name":"2020_QuantumScience_Lauk.pdf","success":1}],"author":[{"last_name":"Lauk","first_name":"Nikolai","full_name":"Lauk, Nikolai"},{"full_name":"Sinclair, Neil","last_name":"Sinclair","first_name":"Neil"},{"full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","first_name":"Shabir"},{"full_name":"Covey, Jacob P","first_name":"Jacob P","last_name":"Covey"},{"full_name":"Saffman, Mark","last_name":"Saffman","first_name":"Mark"},{"last_name":"Spiropulu","first_name":"Maria","full_name":"Spiropulu, Maria"},{"first_name":"Christoph","last_name":"Simon","full_name":"Simon, Christoph"}],"issue":"2","language":[{"iso":"eng"}],"isi":1,"project":[{"grant_number":"707438","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","doi":"10.1088/2058-9565/ab788a","publication_identifier":{"issn":["2058-9565"]}}]