[{"status":"public","abstract":[{"text":"This research is aimed to solve the tweet/user geolocation prediction task and provide a flexible methodology for the geo-tagging of textual big data. The suggested approach implements neural networks for natural language processing (NLP) to estimate the location as coordinate pairs (longitude, latitude) and two-dimensional Gaussian Mixture Models (GMMs). The scope of proposed models has been finetuned on a Twitter dataset using pretrained Bidirectional Encoder Representations from Transformers (BERT) as base models. Performance metrics show a median error of fewer than 30 km on a worldwide-level, and fewer than 15 km on the US-level datasets for the models trained and evaluated on text features of tweets' content and metadata context. Our source code and data are available at https://github.com/K4TEL/geo-twitter.git.","lang":"eng"}],"day":"26","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","doi":"10.5311/JOSIS.2024.29.295","file":[{"date_created":"2025-01-20T08:41:10Z","content_type":"application/pdf","date_updated":"2025-01-20T08:41:10Z","checksum":"b82413f00398ffb5168e8e747571a98d","file_name":"2024_JourSpatialInfoScience_Lutsai.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"18857","file_size":7250655,"success":1}],"article_type":"original","has_accepted_license":"1","department":[{"_id":"ChLa"}],"scopus_import":"1","publisher":"University of Maine","date_created":"2025-01-19T23:01:53Z","date_published":"2024-12-26T00:00:00Z","quality_controlled":"1","issue":"29","type":"journal_article","license":"https://creativecommons.org/licenses/by/3.0/","year":"2024","article_processing_charge":"Yes","corr_author":"1","oa_version":"Published Version","page":"69-99","author":[{"first_name":"Kateryna","last_name":"Lutsai","full_name":"Lutsai, Kateryna"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"DOAJ_listed":"1","file_date_updated":"2025-01-20T08:41:10Z","publication_identifier":{"eissn":["1948-660X"]},"language":[{"iso":"eng"}],"publication":"Journal of Spatial Information Science","citation":{"mla":"Lutsai, Kateryna, and Christoph Lampert. “Predicting the Geolocation of Tweets Using Transformer Models on Customized Data.” <i>Journal of Spatial Information Science</i>, no. 29, University of Maine, 2024, pp. 69–99, doi:<a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">10.5311/JOSIS.2024.29.295</a>.","chicago":"Lutsai, Kateryna, and Christoph Lampert. “Predicting the Geolocation of Tweets Using Transformer Models on Customized Data.” <i>Journal of Spatial Information Science</i>. University of Maine, 2024. <a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">https://doi.org/10.5311/JOSIS.2024.29.295</a>.","ama":"Lutsai K, Lampert C. Predicting the geolocation of tweets using transformer models on customized data. <i>Journal of Spatial Information Science</i>. 2024;(29):69-99. doi:<a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">10.5311/JOSIS.2024.29.295</a>","apa":"Lutsai, K., &#38; Lampert, C. (2024). Predicting the geolocation of tweets using transformer models on customized data. <i>Journal of Spatial Information Science</i>. University of Maine. <a href=\"https://doi.org/10.5311/JOSIS.2024.29.295\">https://doi.org/10.5311/JOSIS.2024.29.295</a>","ista":"Lutsai K, Lampert C. 2024. Predicting the geolocation of tweets using transformer models on customized data. Journal of Spatial Information Science. (29), 69–99.","short":"K. Lutsai, C. Lampert, Journal of Spatial Information Science (2024) 69–99.","ieee":"K. Lutsai and C. Lampert, “Predicting the geolocation of tweets using transformer models on customized data,” <i>Journal of Spatial Information Science</i>, no. 29. University of Maine, pp. 69–99, 2024."},"publication_status":"published","title":"Predicting the geolocation of tweets using transformer models on customized data","ddc":["500"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode","short":"CC BY (3.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)"},"month":"12","oa":1,"acknowledgement":"The authors acknowledge the Institute of Science and Technology (ISTA) for their material support and for granting access to the Twitter database archive, which was essential for the research.","OA_place":"publisher","OA_type":"gold","date_updated":"2025-06-05T13:47:12Z","related_material":{"link":[{"relation":"software","url":"https://github.com/K4TEL/geo-twitter.git"}]},"_id":"18856"},{"type":"journal_article","date_updated":"2025-01-27T10:52:16Z","_id":"18867","date_created":"2025-01-21T15:35:17Z","publisher":"Springer Nature","scopus_import":"1","OA_type":"closed access","quality_controlled":"1","date_published":"2024-08-01T00:00:00Z","doi":"10.1038/s41550-024-02295-8","extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":8,"month":"08","article_type":"original","title":"Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization","intvolume":"         8","publication":"Nature Astronomy","day":"01","publication_status":"published","citation":{"apa":"Heyl, J., Doroshenko, V., González-Caniulef, D., Caiazzo, I., Poutanen, J., Mushtukov, A., … Zane, S. (2024). Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization. <i>Nature Astronomy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41550-024-02295-8\">https://doi.org/10.1038/s41550-024-02295-8</a>","ista":"Heyl J et al. 2024. Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization. Nature Astronomy. 8, 1047–1053.","short":"J. Heyl, V. Doroshenko, D. González-Caniulef, I. Caiazzo, J. Poutanen, A. Mushtukov, S.S. Tsygankov, D. Kirmizibayrak, M. Bachetti, G.G. Pavlov, S.V. Forsblom, C. Malacaria, V.F. Suleimanov, I. Agudo, L.A. Antonelli, L. Baldini, W.H. Baumgartner, R. Bellazzini, S. Bianchi, S.D. Bongiorno, R. Bonino, A. Brez, N. Bucciantini, F. Capitanio, S. Castellano, E. Cavazzuti, C.-T. Chen, S. Ciprini, E. Costa, A. De Rosa, E. Del Monte, L. Di Gesu, N. Di Lalla, A. Di Marco, I. Donnarumma, M. Dovčiak, S.R. Ehlert, T. Enoto, Y. Evangelista, S. Fabiani, R. Ferrazzoli, J.A. Garcia, S. Gunji, K. Hayashida, W. Iwakiri, S.G. Jorstad, P. Kaaret, V. Karas, F. Kislat, T. Kitaguchi, J.J. Kolodziejczak, H. Krawczynski, F. La Monaca, L. Latronico, I. Liodakis, S. Maldera, A. Manfreda, F. Marin, A. Marinucci, A.P. Marscher, H.L. Marshall, F. Massaro, G. Matt, I. Mitsuishi, T. Mizuno, F. Muleri, M. Negro, C.-Y. Ng, S.L. O’Dell, N. Omodei, C. Oppedisano, A. Papitto, A.L. Peirson, M. Perri, M. Pesce-Rollins, P.-O. Petrucci, M. Pilia, A. Possenti, S. Puccetti, B.D. Ramsey, J. Rankin, A. Ratheesh, O.J. Roberts, R.W. Romani, C. Sgrò, P. Slane, P. Soffitta, G. Spandre, D.A. Swartz, T. Tamagawa, F. Tavecchio, R. Taverna, Y. Tawara, A.F. Tennant, N.E. Thomas, F. Tombesi, A. Trois, R. Turolla, J. Vink, M.C. Weisskopf, K. Wu, F. Xie, S. Zane, Nature Astronomy 8 (2024) 1047–1053.","ieee":"J. Heyl <i>et al.</i>, “Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization,” <i>Nature Astronomy</i>, vol. 8. Springer Nature, pp. 1047–1053, 2024.","mla":"Heyl, Jeremy, et al. “Complex Rotational Dynamics of the Neutron Star in Hercules X-1 Revealed by X-Ray Polarization.” <i>Nature Astronomy</i>, vol. 8, Springer Nature, 2024, pp. 1047–53, doi:<a href=\"https://doi.org/10.1038/s41550-024-02295-8\">10.1038/s41550-024-02295-8</a>.","chicago":"Heyl, Jeremy, Victor Doroshenko, Denis González-Caniulef, Ilaria Caiazzo, Juri Poutanen, Alexander Mushtukov, Sergey S. Tsygankov, et al. “Complex Rotational Dynamics of the Neutron Star in Hercules X-1 Revealed by X-Ray Polarization.” <i>Nature Astronomy</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41550-024-02295-8\">https://doi.org/10.1038/s41550-024-02295-8</a>.","ama":"Heyl J, Doroshenko V, González-Caniulef D, et al. Complex rotational dynamics of the neutron star in Hercules X-1 revealed by X-ray polarization. <i>Nature Astronomy</i>. 2024;8:1047-1053. doi:<a href=\"https://doi.org/10.1038/s41550-024-02295-8\">10.1038/s41550-024-02295-8</a>"},"author":[{"full_name":"Heyl, Jeremy","last_name":"Heyl","first_name":"Jeremy"},{"first_name":"Victor","full_name":"Doroshenko, Victor","last_name":"Doroshenko"},{"full_name":"González-Caniulef, Denis","last_name":"González-Caniulef","first_name":"Denis"},{"last_name":"Caiazzo","full_name":"Caiazzo, Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","first_name":"Ilaria","orcid":"0000-0002-4770-5388"},{"last_name":"Poutanen","full_name":"Poutanen, Juri","first_name":"Juri"},{"full_name":"Mushtukov, Alexander","last_name":"Mushtukov","first_name":"Alexander"},{"last_name":"Tsygankov","full_name":"Tsygankov, Sergey S.","first_name":"Sergey S."},{"full_name":"Kirmizibayrak, Demet","last_name":"Kirmizibayrak","first_name":"Demet"},{"first_name":"Matteo","last_name":"Bachetti","full_name":"Bachetti, Matteo"},{"full_name":"Pavlov, George G.","last_name":"Pavlov","first_name":"George G."},{"full_name":"Forsblom, Sofia V.","last_name":"Forsblom","first_name":"Sofia V."},{"first_name":"Christian","full_name":"Malacaria, Christian","last_name":"Malacaria"},{"last_name":"Suleimanov","full_name":"Suleimanov, Valery F.","first_name":"Valery F."},{"last_name":"Agudo","full_name":"Agudo, Iván","first_name":"Iván"},{"last_name":"Antonelli","full_name":"Antonelli, Lucio Angelo","first_name":"Lucio Angelo"},{"last_name":"Baldini","full_name":"Baldini, Luca","first_name":"Luca"},{"first_name":"Wayne H.","full_name":"Baumgartner, Wayne H.","last_name":"Baumgartner"},{"first_name":"Ronaldo","last_name":"Bellazzini","full_name":"Bellazzini, Ronaldo"},{"first_name":"Stefano","full_name":"Bianchi, Stefano","last_name":"Bianchi"},{"first_name":"Stephen D.","full_name":"Bongiorno, Stephen D.","last_name":"Bongiorno"},{"first_name":"Raffaella","last_name":"Bonino","full_name":"Bonino, Raffaella"},{"last_name":"Brez","full_name":"Brez, Alessandro","first_name":"Alessandro"},{"first_name":"Niccolò","full_name":"Bucciantini, Niccolò","last_name":"Bucciantini"},{"first_name":"Fiamma","last_name":"Capitanio","full_name":"Capitanio, Fiamma"},{"first_name":"Simone","last_name":"Castellano","full_name":"Castellano, Simone"},{"last_name":"Cavazzuti","full_name":"Cavazzuti, Elisabetta","first_name":"Elisabetta"},{"full_name":"Chen, Chien-Ting","last_name":"Chen","first_name":"Chien-Ting"},{"last_name":"Ciprini","full_name":"Ciprini, Stefano","first_name":"Stefano"},{"full_name":"Costa, Enrico","last_name":"Costa","first_name":"Enrico"},{"full_name":"De Rosa, Alessandra","last_name":"De Rosa","first_name":"Alessandra"},{"first_name":"Ettore","last_name":"Del Monte","full_name":"Del Monte, Ettore"},{"first_name":"Laura","full_name":"Di Gesu, Laura","last_name":"Di Gesu"},{"first_name":"Niccolò","full_name":"Di Lalla, Niccolò","last_name":"Di Lalla"},{"full_name":"Di Marco, Alessandro","last_name":"Di Marco","first_name":"Alessandro"},{"full_name":"Donnarumma, Immacolata","last_name":"Donnarumma","first_name":"Immacolata"},{"last_name":"Dovčiak","full_name":"Dovčiak, Michal","first_name":"Michal"},{"last_name":"Ehlert","full_name":"Ehlert, Steven R.","first_name":"Steven R."},{"first_name":"Teruaki","full_name":"Enoto, Teruaki","last_name":"Enoto"},{"first_name":"Yuri","last_name":"Evangelista","full_name":"Evangelista, Yuri"},{"last_name":"Fabiani","full_name":"Fabiani, Sergio","first_name":"Sergio"},{"last_name":"Ferrazzoli","full_name":"Ferrazzoli, Riccardo","first_name":"Riccardo"},{"first_name":"Javier A.","full_name":"Garcia, Javier A.","last_name":"Garcia"},{"first_name":"Shuichi","full_name":"Gunji, Shuichi","last_name":"Gunji"},{"first_name":"Kiyoshi","full_name":"Hayashida, Kiyoshi","last_name":"Hayashida"},{"full_name":"Iwakiri, Wataru","last_name":"Iwakiri","first_name":"Wataru"},{"full_name":"Jorstad, Svetlana G.","last_name":"Jorstad","first_name":"Svetlana G."},{"first_name":"Philip","last_name":"Kaaret","full_name":"Kaaret, Philip"},{"full_name":"Karas, Vladimir","last_name":"Karas","first_name":"Vladimir"},{"last_name":"Kislat","full_name":"Kislat, Fabian","first_name":"Fabian"},{"first_name":"Takao","last_name":"Kitaguchi","full_name":"Kitaguchi, Takao"},{"last_name":"Kolodziejczak","full_name":"Kolodziejczak, Jeffery J.","first_name":"Jeffery J."},{"first_name":"Henric","last_name":"Krawczynski","full_name":"Krawczynski, Henric"},{"full_name":"La Monaca, Fabio","last_name":"La Monaca","first_name":"Fabio"},{"full_name":"Latronico, Luca","last_name":"Latronico","first_name":"Luca"},{"full_name":"Liodakis, Ioannis","last_name":"Liodakis","first_name":"Ioannis"},{"first_name":"Simone","last_name":"Maldera","full_name":"Maldera, Simone"},{"last_name":"Manfreda","full_name":"Manfreda, Alberto","first_name":"Alberto"},{"first_name":"Frédéric","last_name":"Marin","full_name":"Marin, Frédéric"},{"last_name":"Marinucci","full_name":"Marinucci, Andrea","first_name":"Andrea"},{"full_name":"Marscher, Alan P.","last_name":"Marscher","first_name":"Alan P."},{"first_name":"Herman L.","full_name":"Marshall, Herman L.","last_name":"Marshall"},{"last_name":"Massaro","full_name":"Massaro, Francesco","first_name":"Francesco"},{"full_name":"Matt, Giorgio","last_name":"Matt","first_name":"Giorgio"},{"last_name":"Mitsuishi","full_name":"Mitsuishi, Ikuyuki","first_name":"Ikuyuki"},{"full_name":"Mizuno, Tsunefumi","last_name":"Mizuno","first_name":"Tsunefumi"},{"first_name":"Fabio","full_name":"Muleri, Fabio","last_name":"Muleri"},{"first_name":"Michela","full_name":"Negro, Michela","last_name":"Negro"},{"first_name":"C.-Y.","full_name":"Ng, C.-Y.","last_name":"Ng"},{"last_name":"O’Dell","full_name":"O’Dell, Stephen L.","first_name":"Stephen L."},{"first_name":"Nicola","full_name":"Omodei, Nicola","last_name":"Omodei"},{"full_name":"Oppedisano, Chiara","last_name":"Oppedisano","first_name":"Chiara"},{"first_name":"Alessandro","full_name":"Papitto, Alessandro","last_name":"Papitto"},{"last_name":"Peirson","full_name":"Peirson, Abel Lawrence","first_name":"Abel Lawrence"},{"first_name":"Matteo","last_name":"Perri","full_name":"Perri, Matteo"},{"first_name":"Melissa","last_name":"Pesce-Rollins","full_name":"Pesce-Rollins, Melissa"},{"full_name":"Petrucci, Pierre-Olivier","last_name":"Petrucci","first_name":"Pierre-Olivier"},{"last_name":"Pilia","full_name":"Pilia, Maura","first_name":"Maura"},{"first_name":"Andrea","last_name":"Possenti","full_name":"Possenti, Andrea"},{"last_name":"Puccetti","full_name":"Puccetti, Simonetta","first_name":"Simonetta"},{"full_name":"Ramsey, Brian D.","last_name":"Ramsey","first_name":"Brian D."},{"last_name":"Rankin","full_name":"Rankin, John","first_name":"John"},{"first_name":"Ajay","last_name":"Ratheesh","full_name":"Ratheesh, Ajay"},{"first_name":"Oliver J.","last_name":"Roberts","full_name":"Roberts, Oliver J."},{"last_name":"Romani","full_name":"Romani, Roger W.","first_name":"Roger W."},{"first_name":"Carmelo","last_name":"Sgrò","full_name":"Sgrò, Carmelo"},{"full_name":"Slane, Patrick","last_name":"Slane","first_name":"Patrick"},{"first_name":"Paolo","last_name":"Soffitta","full_name":"Soffitta, Paolo"},{"first_name":"Gloria","last_name":"Spandre","full_name":"Spandre, Gloria"},{"first_name":"Douglas A.","full_name":"Swartz, Douglas A.","last_name":"Swartz"},{"first_name":"Toru","full_name":"Tamagawa, Toru","last_name":"Tamagawa"},{"full_name":"Tavecchio, Fabrizio","last_name":"Tavecchio","first_name":"Fabrizio"},{"last_name":"Taverna","full_name":"Taverna, Roberto","first_name":"Roberto"},{"last_name":"Tawara","full_name":"Tawara, Yuzuru","first_name":"Yuzuru"},{"last_name":"Tennant","full_name":"Tennant, Allyn F.","first_name":"Allyn F."},{"full_name":"Thomas, Nicholas E.","last_name":"Thomas","first_name":"Nicholas E."},{"full_name":"Tombesi, Francesco","last_name":"Tombesi","first_name":"Francesco"},{"first_name":"Alessio","last_name":"Trois","full_name":"Trois, Alessio"},{"first_name":"Roberto","last_name":"Turolla","full_name":"Turolla, Roberto"},{"full_name":"Vink, Jacco","last_name":"Vink","first_name":"Jacco"},{"full_name":"Weisskopf, Martin C.","last_name":"Weisskopf","first_name":"Martin C."},{"first_name":"Kinwah","last_name":"Wu","full_name":"Wu, Kinwah"},{"full_name":"Xie, Fei","last_name":"Xie","first_name":"Fei"},{"first_name":"Silvia","last_name":"Zane","full_name":"Zane, Silvia"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2397-3366"]},"status":"public","oa_version":"None","abstract":[{"text":"In an accreting X-ray pulsar, a neutron star accretes matter from a companion star through an accretion disk. The magnetic field of the rotating neutron star disrupts the inner edge of the disk, funnelling the gas to flow onto the poles on its surface. Hercules X-1 is a prototypical persistent X-ray pulsar about 7 kpc from Earth. Its emission varies on three distinct timescales: the neutron star rotates every 1.2 s, it is eclipsed by its companion each 1.7 d, and the system exhibits a superorbital period of 35 d, which has remained stable since its discovery. Several lines of evidence point to the source of this variation as the precession of the accretion disk or that of the neutron star. Despite the many hints over the past 50 yr, the precession of the neutron star itself has yet not been confirmed or refuted. X-ray polarization measurements (probing the spin geometry of Her X-1) with the Imaging X-ray Polarimetry Explorer suggest that free precession of the neutron star crust sets the 35 d period; this has the important implication that its crust is somewhat asymmetric by a few parts per ten million.","lang":"eng"}],"page":"1047-1053","year":"2024","article_processing_charge":"No"},{"OA_type":"gold","OA_place":"publisher","date_updated":"2025-01-27T10:48:19Z","_id":"18868","title":"Optimal summary statistics for X-ray polarization","intvolume":"         7","oa":1,"volume":7,"month":"05","external_id":{"arxiv":["2311.07805"]},"DOAJ_listed":"1","author":[{"first_name":"Jeremy","last_name":"Heyl","full_name":"Heyl, Jeremy"},{"last_name":"González-Caniulef","full_name":"González-Caniulef, Denis","first_name":"Denis"},{"last_name":"Caiazzo","full_name":"Caiazzo, Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","orcid":"0000-0002-4770-5388","first_name":"Ilaria"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2565-6120"]},"publication":"The Open Journal of Astrophysics","publication_status":"published","citation":{"chicago":"Heyl, Jeremy, Denis González-Caniulef, and Ilaria Caiazzo. “Optimal Summary Statistics for X-Ray Polarization.” <i>The Open Journal of Astrophysics</i>. Maynooth Academic Publishing, 2024. <a href=\"https://doi.org/10.33232/001c.117476\">https://doi.org/10.33232/001c.117476</a>.","ama":"Heyl J, González-Caniulef D, Caiazzo I. Optimal summary statistics for X-ray polarization. <i>The Open Journal of Astrophysics</i>. 2024;7. doi:<a href=\"https://doi.org/10.33232/001c.117476\">10.33232/001c.117476</a>","mla":"Heyl, Jeremy, et al. “Optimal Summary Statistics for X-Ray Polarization.” <i>The Open Journal of Astrophysics</i>, vol. 7, Maynooth Academic Publishing, 2024, doi:<a href=\"https://doi.org/10.33232/001c.117476\">10.33232/001c.117476</a>.","short":"J. Heyl, D. González-Caniulef, I. Caiazzo, The Open Journal of Astrophysics 7 (2024).","ieee":"J. Heyl, D. González-Caniulef, and I. Caiazzo, “Optimal summary statistics for X-ray polarization,” <i>The Open Journal of Astrophysics</i>, vol. 7. Maynooth Academic Publishing, 2024.","ista":"Heyl J, González-Caniulef D, Caiazzo I. 2024. Optimal summary statistics for X-ray polarization. The Open Journal of Astrophysics. 7.","apa":"Heyl, J., González-Caniulef, D., &#38; Caiazzo, I. (2024). Optimal summary statistics for X-ray polarization. <i>The Open Journal of Astrophysics</i>. Maynooth Academic Publishing. <a href=\"https://doi.org/10.33232/001c.117476\">https://doi.org/10.33232/001c.117476</a>"},"year":"2024","article_processing_charge":"No","arxiv":1,"oa_version":"Published Version","publisher":"Maynooth Academic Publishing","date_created":"2025-01-21T15:54:16Z","scopus_import":"1","quality_controlled":"1","date_published":"2024-05-01T00:00:00Z","type":"journal_article","doi":"10.33232/001c.117476","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","article_type":"original","day":"01","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.33232/001c.117476"}],"abstract":[{"lang":"eng","text":"We develop two new highly efficient estimators to measure the polarization (Stokes parameters) in experiments that constrain the position angle of individual photons such as scattering and gas-pixel-detector polarimeters, and analyse in detail a previously proposed estimator. All three of these estimators are at least fifty percent more efficient on typical datasets than the standard estimator used in the field. We present analytic estimates of the variance of these estimators and numerical experiments to verify these estimates. Two of the three estimators can be calculated quickly and directly through summations over the measurements of individual photons."}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"has_accepted_license":"1","file":[{"date_updated":"2025-01-27T09:52:15Z","content_type":"application/pdf","date_created":"2025-01-27T09:52:15Z","success":1,"file_size":1144656,"file_id":"18888","access_level":"open_access","relation":"main_file","creator":"dernst","file_name":"2024_NeurIPS_Nikita.pdf","checksum":"a216cab8eddc1fe7840aede0e2c0d41e"}],"type":"conference","publisher":"Neural Information Processing Systems Foundation","date_created":"2025-01-24T17:58:16Z","scopus_import":"1","quality_controlled":"1","date_published":"2024-12-01T00:00:00Z","status":"public","abstract":[{"lang":"eng","text":"Current state-of-the-art methods for differentially private model training are based on matrix factorization techniques. However, these methods suffer from high computational overhead because they require numerically solving a demanding optimization problem to determine an approximately optimal factorization prior to the actual model training. In this work, we present a new matrix factorization approach, BSR, which overcomes this computational bottleneck. By exploiting properties of the standard matrix square root, BSR allows to efficiently handle also large-scale problems. For the key scenario of stochastic gradient descent with momentum and weight decay, we even derive analytical expressions for BSR that render the computational overhead negligible. We prove bounds on the approximation quality that hold both in the centralized and in the federated learning setting. Our numerical experiments demonstrate that models trained using BSR perform on par with the best existing methods, while completely avoiding their computational overhead."}],"alternative_title":["Advances in Neural Information Processing Systems"],"day":"01","oa":1,"volume":37,"month":"12","external_id":{"arxiv":["2405.13763"]},"title":"Banded square root matrix factorization for differentially private model training","intvolume":"        37","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-05-14T11:34:20Z","_id":"18875","OA_place":"publisher","OA_type":"gold","arxiv":1,"oa_version":"Published Version","corr_author":"1","year":"2024","article_processing_charge":"No","conference":{"location":"Vancouver, Canada","end_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems","start_date":"2024-12-16"},"publication":"38th Annual Conference on Neural Information Processing Systems","publication_status":"published","citation":{"chicago":"Kalinin, Nikita, and Christoph Lampert. “Banded Square Root Matrix Factorization for Differentially Private Model Training.” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","ama":"Kalinin N, Lampert C. Banded square root matrix factorization for differentially private model training. In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","mla":"Kalinin, Nikita, and Christoph Lampert. “Banded Square Root Matrix Factorization for Differentially Private Model Training.” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","ieee":"N. Kalinin and C. Lampert, “Banded square root matrix factorization for differentially private model training,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","short":"N. Kalinin, C. Lampert, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","apa":"Kalinin, N., &#38; Lampert, C. (2024). Banded square root matrix factorization for differentially private model training. In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","ista":"Kalinin N, Lampert C. 2024. Banded square root matrix factorization for differentially private model training. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37."},"file_date_updated":"2025-01-27T09:52:15Z","author":[{"id":"4b14526e-14d2-11ed-ba64-c14c9553d137","first_name":"Nikita","last_name":"Kalinin","full_name":"Kalinin, Nikita"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1049-5258"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"},{"_id":"MaMo"}],"type":"conference","scopus_import":"1","date_created":"2025-01-27T11:11:40Z","publisher":"Neural Information Processing Systems Foundation","date_published":"2024-12-01T00:00:00Z","quality_controlled":"1","status":"public","abstract":[{"lang":"eng","text":"Deep Neural Collapse (DNC) refers to the surprisingly rigid structure of the data representations in the final layers of Deep Neural Networks (DNNs). Though the phenomenon has been measured in a variety of settings, its emergence is typically explained via data-agnostic approaches, such as the unconstrained features model. In this work, we introduce a data-dependent setting where DNC forms due to feature learning through the average gradient outer product (AGOP). The AGOP is defined with respect to a learned predictor and is equal to the uncentered covariance matrix of its input-output gradients averaged over the training dataset. The Deep Recursive Feature Machine (Deep RFM) is a method that constructs a neural network by iteratively mapping the data with the AGOP and applying an untrained random feature map. We demonstrate empirically that DNC occurs in Deep RFM across standard settings as a consequence of the projection with the AGOP matrix computed at each layer. Further, we theoretically explain DNC in Deep RFM in an asymptotic setting and as a result of kernel learning. We then provide evidence that this mechanism holds for neural networks more generally. In particular, we show that the right singular vectors and values of the weights can be responsible for the majority of within-class variability collapse for DNNs trained in the feature learning regime. As observed in recent work, this singular structure is highly correlated with that of the AGOP."}],"main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=lJ1jdl2K9k"}],"alternative_title":["Advances in Neural Information Processing Systems"],"day":"01","volume":37,"month":"12","oa":1,"external_id":{"arxiv":["2402.13728"]},"intvolume":"        37","title":"Average gradient outer product as a mechanism for deep neural collapse","date_updated":"2025-05-14T11:29:45Z","_id":"18890","acknowledgement":"We acknowledge support from the National Science Foundation (NSF) and the Simons Foundation for the Collaboration on the Theoretical Foundations of Deep Learning through awards DMS-2031883 and #814639 as well as the TILOS institute (NSF CCF-2112665). This work used the programs (1) XSEDE (Extreme science and engineering discovery environment) which is supported by NSF grant numbers ACI-1548562, and (2) ACCESS (Advanced cyberinfrastructure coordination ecosystem: services & support) which is supported by NSF grants numbers #2138259, #2138286, #2138307, #2137603, and #2138296. Specifically, we used the resources from SDSC Expanse GPU compute nodes, and NCSA Delta system, via allocations TG-CIS220009. Marco Mondelli is supported by the 2019 Lopez-Loreta prize. We also acknowledge useful feedback from anonymous reviewers. ","OA_type":"green","OA_place":"repository","arxiv":1,"corr_author":"1","oa_version":"Preprint","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"year":"2024","conference":{"location":"Vancouver, Canada","end_date":"2024-12-16","name":"NeurIPS: Neural Information Processing Systems","start_date":"2024-12-16"},"article_processing_charge":"No","publication":"38th Annual Conference on Neural Information Processing Systems","citation":{"ista":"Beaglehole D, Súkeník P, Mondelli M, Belkin M. 2024. Average gradient outer product as a mechanism for deep neural collapse. 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","apa":"Beaglehole, D., Súkeník, P., Mondelli, M., &#38; Belkin, M. (2024). Average gradient outer product as a mechanism for deep neural collapse. In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","short":"D. Beaglehole, P. Súkeník, M. Mondelli, M. Belkin, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ieee":"D. Beaglehole, P. Súkeník, M. Mondelli, and M. Belkin, “Average gradient outer product as a mechanism for deep neural collapse,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37.","mla":"Beaglehole, Daniel, et al. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","ama":"Beaglehole D, Súkeník P, Mondelli M, Belkin M. Average gradient outer product as a mechanism for deep neural collapse. In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","chicago":"Beaglehole, Daniel, Peter Súkeník, Marco Mondelli, and Mikhail Belkin. “Average Gradient Outer Product as a Mechanism for Deep Neural Collapse.” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024."},"publication_status":"published","author":[{"full_name":"Beaglehole, Daniel","last_name":"Beaglehole","first_name":"Daniel"},{"last_name":"Súkeník","full_name":"Súkeník, Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","first_name":"Peter"},{"first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","last_name":"Mondelli"},{"full_name":"Belkin, Mikhail","last_name":"Belkin","first_name":"Mikhail"}],"publication_identifier":{"eissn":["1049-5258"]},"language":[{"iso":"eng"}]},{"project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"arxiv":1,"oa_version":"Published Version","corr_author":"1","article_processing_charge":"No","conference":{"name":"NeurIPS: Neural Information Processing Systems","start_date":"2024-12-16","location":"Vancouver, Canada","end_date":"2024-12-16"},"year":"2024","citation":{"mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” <i>38th Annual Conference on Neural Information Processing Systems</i>, vol. 37, Neural Information Processing Systems Foundation, 2024.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: <i>38th Annual Conference on Neural Information Processing Systems</i>. Vol 37. Neural Information Processing Systems Foundation; 2024.","chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In <i>38th Annual Conference on Neural Information Processing Systems</i>, Vol. 37. Neural Information Processing Systems Foundation, 2024.","apa":"Súkeník, P., Lampert, C., &#38; Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In <i>38th Annual Conference on Neural Information Processing Systems</i> (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024.","ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in <i>38th Annual Conference on Neural Information Processing Systems</i>, Vancouver, Canada, 2024, vol. 37."},"publication_status":"published","publication":"38th Annual Conference on Neural Information Processing Systems","language":[{"iso":"eng"}],"author":[{"first_name":"Peter","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","full_name":"Súkeník, Peter","last_name":"Súkeník"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","last_name":"Lampert"},{"full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"}],"file_date_updated":"2025-02-04T08:11:25Z","external_id":{"arxiv":["2405.14468"]},"volume":37,"month":"12","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000"],"intvolume":"        37","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","_id":"18891","date_updated":"2025-06-04T07:19:21Z","OA_type":"gold","OA_place":"publisher","acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent."}],"status":"public","alternative_title":["Advances in Neural Information Processing Systems"],"day":"01","file":[{"success":1,"file_size":1784118,"file_id":"18989","access_level":"open_access","relation":"main_file","creator":"dernst","checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","file_name":"2024_NeurIPS_Sukenik.pdf","date_updated":"2025-02-04T08:11:25Z","content_type":"application/pdf","date_created":"2025-02-04T08:11:25Z"}],"has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","date_published":"2024-12-01T00:00:00Z","quality_controlled":"1","date_created":"2025-01-27T11:15:18Z","publisher":"Neural Information Processing Systems Foundation"},{"oa":1,"doi":"10.6084/M9.FIGSHARE.26484934.V2","month":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"title":"ISTAnt","ddc":["570"],"type":"research_data_reference","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"18847"}]},"date_updated":"2025-01-27T11:58:38Z","_id":"18895","date_created":"2025-01-27T11:45:43Z","publisher":"Institute of Science and Technology Austria","OA_place":"repository","OA_type":"gold","date_published":"2024-10-23T00:00:00Z","status":"public","oa_version":"Published Version","corr_author":"1","main_file_link":[{"open_access":"1","url":"https://10.6084/M9.FIGSHARE.26484934.V2"}],"abstract":[{"lang":"eng","text":"ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \\citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see 'annotations' folder). In one of the videos, one of the nestmates' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see 'video' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see 'experiments_settings.csv' file)."}],"year":"2024","article_processing_charge":"No","day":"23","citation":{"ama":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. ISTAnt. 2024. doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>","chicago":"Cadei, Riccardo, Francesco Locatello, Sylvia Cremer, Lukas Lindorfer, and Cordelia Schmid. “ISTAnt.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>.","mla":"Cadei, Riccardo, et al. <i>ISTAnt</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","ieee":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, and C. Schmid, “ISTAnt.” Institute of Science and Technology Austria, 2024.","short":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, C. Schmid, (2024).","ista":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. 2024. ISTAnt, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">10.6084/M9.FIGSHARE.26484934.V2</a>.","apa":"Cadei, R., Locatello, F., Cremer, S., Lindorfer, L., &#38; Schmid, C. (2024). ISTAnt. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.6084/M9.FIGSHARE.26484934.V2\">https://doi.org/10.6084/M9.FIGSHARE.26484934.V2</a>"},"author":[{"first_name":"Riccardo","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b","full_name":"Cadei, Riccardo","last_name":"Cadei"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","full_name":"Locatello, Francesco","last_name":"Locatello"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia M","last_name":"Cremer","full_name":"Cremer, Sylvia M"},{"first_name":"Lukas","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","full_name":"Lindorfer, Lukas","last_name":"Lindorfer"},{"last_name":"Schmid","full_name":"Schmid, Cordelia","first_name":"Cordelia"}]},{"ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Improved convergence of score-based diffusion models via prediction-correction","external_id":{"arxiv":["2305.14164"]},"oa":1,"month":"06","OA_type":"gold","OA_place":"publisher","acknowledgement":"Francesco Pedrotti and Jan Maas acknowledge support by the Austrian Science Fund (FWF) project 10.55776/F65. Marco Mondelli acknowledges support by the 2019 Lopez-Loreta prize.\r\n","_id":"18897","date_updated":"2025-04-15T08:31:35Z","related_material":{"record":[{"status":"public","id":"17350","relation":"earlier_version"}]},"article_processing_charge":"No","year":"2024","project":[{"name":"Taming Complexity in Partial Differential Systems","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504"},{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"arxiv":1,"oa_version":"Published Version","corr_author":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2835-8856"]},"file_date_updated":"2025-01-27T12:19:44Z","author":[{"last_name":"Pedrotti","full_name":"Pedrotti, Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","first_name":"Francesco"},{"last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","orcid":"0000-0002-0845-1338"},{"last_name":"Mondelli","full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020"}],"publication_status":"published","citation":{"chicago":"Pedrotti, Francesco, Jan Maas, and Marco Mondelli. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” In <i>Transactions on Machine Learning Research</i>, 2024.","ama":"Pedrotti F, Maas J, Mondelli M. Improved convergence of score-based diffusion models via prediction-correction. In: <i>Transactions on Machine Learning Research</i>. ; 2024.","mla":"Pedrotti, Francesco, et al. “Improved Convergence of Score-Based Diffusion Models via Prediction-Correction.” <i>Transactions on Machine Learning Research</i>, 2024.","ieee":"F. Pedrotti, J. Maas, and M. Mondelli, “Improved convergence of score-based diffusion models via prediction-correction,” in <i>Transactions on Machine Learning Research</i>, 2024.","short":"F. Pedrotti, J. Maas, M. Mondelli, in:, Transactions on Machine Learning Research, 2024.","ista":"Pedrotti F, Maas J, Mondelli M. 2024. Improved convergence of score-based diffusion models via prediction-correction. Transactions on Machine Learning Research. , TMLR, .","apa":"Pedrotti, F., Maas, J., &#38; Mondelli, M. (2024). Improved convergence of score-based diffusion models via prediction-correction. In <i>Transactions on Machine Learning Research</i>."},"publication":"Transactions on Machine Learning Research","department":[{"_id":"JaMa"},{"_id":"MaMo"}],"has_accepted_license":"1","file":[{"file_name":"2024_TMLR_Pedrotti.pdf","checksum":"76a1fd5afd8ee6f7ae0e5912d7dbf6b4","relation":"main_file","creator":"dernst","file_size":780315,"file_id":"18898","access_level":"open_access","success":1,"date_created":"2025-01-27T12:19:44Z","content_type":"application/pdf","date_updated":"2025-01-27T12:19:44Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_published":"2024-06-01T00:00:00Z","date_created":"2025-01-27T12:18:05Z","scopus_import":"1","type":"conference","alternative_title":["TMLR"],"abstract":[{"text":"Score-based generative models (SGMs) are powerful tools to sample from complex data distributions. Their underlying idea is to (i) run a forward process for time T1 by adding noise to the data, (ii) estimate its score function, and (iii) use such estimate to run a reverse process. As the reverse process is initialized with the stationary distribution of the forward one, the existing analysis paradigm requires T1→∞. This is however problematic: from a theoretical viewpoint, for a given precision of the score approximation, the convergence guarantee fails as T1 diverges; from a practical viewpoint, a large T1 increases computational costs and leads to error propagation. This paper addresses the issue by considering a version of the popular predictor-corrector scheme: after running the forward process, we first estimate the final distribution via an inexact Langevin dynamics and then revert the process. Our key technical contribution is to provide convergence guarantees which require to run the forward process only for a fixed finite time T1. Our bounds exhibit a mild logarithmic dependence on the input dimension and the subgaussian norm of the target distribution, have minimal assumptions on the data, and require only to control the L2 loss on the score approximation, which is the quantity minimized in practice.","lang":"eng"}],"status":"public","day":"01"},{"article_processing_charge":"No","alternative_title":["Bolyai Society Mathematical Studies"],"year":"2024","abstract":[{"text":"The flourishing theory of classical optimal transport concerns mass transportation at minimal cost. This book introduces the reader to optimal transport on quantum structures, i.e., optimal transportation between quantum states and related non-commutative concepts of mass transportation. It contains lecture notes on\r\n\r\nclassical optimal transport and Wasserstein gradient flows\r\ndynamics and quantum optimal transport\r\nquantum couplings and many-body problems\r\nquantum channels and qubits\r\n\r\nThese notes are based on lectures given by the authors at the \"Optimal Transport on Quantum Structures\" School held at the Erdös Center in Budapest in the fall of 2022. The lecture notes are complemented by two survey chapters presenting the state of the art in different research areas of non-commutative optimal transport.","lang":"eng"}],"oa_version":"None","status":"public","publication_identifier":{"eisbn":["9783031504662"],"isbn":["9783031504655"],"eissn":["2947-9460"],"issn":["1217-4696"]},"language":[{"iso":"eng"}],"citation":{"ieee":"J. Maas, S. A. E. Rademacher, T. Titkos, and D. Virosztek, Eds., <i>Optimal Transport on Quantum Structures</i>, vol. 29. Cham: Springer Nature, 2024.","short":"J. Maas, S.A.E. Rademacher, T. Titkos, D. Virosztek, eds., Optimal Transport on Quantum Structures, Springer Nature, Cham, 2024.","ista":"Maas J, Rademacher SAE, Titkos T, Virosztek D eds. 2024. Optimal Transport on Quantum Structures, Cham: Springer Nature,p.","apa":"Maas, J., Rademacher, S. A. E., Titkos, T., &#38; Virosztek, D. (Eds.). (2024). <i>Optimal Transport on Quantum Structures</i> (Vol. 29). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-50466-2\">https://doi.org/10.1007/978-3-031-50466-2</a>","chicago":"Maas, Jan, Simone Anna Elvira Rademacher, Tamás Titkos, and Daniel Virosztek, eds. <i>Optimal Transport on Quantum Structures</i>. Vol. 29. BSMS. Cham: Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-50466-2\">https://doi.org/10.1007/978-3-031-50466-2</a>.","ama":"Maas J, Rademacher SAE, Titkos T, Virosztek D, eds. <i>Optimal Transport on Quantum Structures</i>. Vol 29. Cham: Springer Nature; 2024. doi:<a href=\"https://doi.org/10.1007/978-3-031-50466-2\">10.1007/978-3-031-50466-2</a>","mla":"Maas, Jan, et al., editors. <i>Optimal Transport on Quantum Structures</i>. Vol. 29, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/978-3-031-50466-2\">10.1007/978-3-031-50466-2</a>."},"publication_status":"published","day":"19","intvolume":"        29","title":"Optimal Transport on Quantum Structures","department":[{"_id":"JaMa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","editor":[{"full_name":"Maas, Jan","last_name":"Maas","first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5059-4466","first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","full_name":"Rademacher, Simone Anna Elvira","last_name":"Rademacher"},{"first_name":"Tamás","last_name":"Titkos","full_name":"Titkos, Tamás"},{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1109-5511","first_name":"Daniel","last_name":"Virosztek","full_name":"Virosztek, Daniel"}],"volume":29,"month":"09","doi":"10.1007/978-3-031-50466-2","place":"Cham","quality_controlled":"1","date_published":"2024-09-19T00:00:00Z","scopus_import":"1","series_title":"BSMS","date_created":"2025-01-27T12:26:03Z","publisher":"Springer Nature","_id":"18899","date_updated":"2025-02-17T12:22:18Z","type":"book_editor"},{"day":"01","isi":1,"abstract":[{"lang":"eng","text":"We prove that certain closable derivations on the GNS Hilbert space associated with a non-tracial weight on a von Neumann algebra give rise to GNS-symmetric semigroups of contractive completely positive maps on the von Neumann algebra."}],"status":"public","type":"journal_article","issue":"14","quality_controlled":"1","date_published":"2024-07-01T00:00:00Z","publisher":"Oxford University Press","date_created":"2025-01-27T12:36:10Z","scopus_import":"1","department":[{"_id":"JaMa"}],"has_accepted_license":"1","file":[{"content_type":"application/pdf","date_updated":"2025-01-27T12:38:10Z","date_created":"2025-01-27T12:38:10Z","file_size":689984,"file_id":"18901","access_level":"open_access","success":1,"checksum":"3e1f80d58ada0c60a58f35df8080967e","file_name":"2024_IMRN_Wirth.pdf","creator":"dernst","relation":"main_file"}],"article_type":"original","doi":"10.1093/imrn/rnae092","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","citation":{"short":"M. Wirth, International Mathematics Research Notices 2024 (2024) 10597–10614.","ieee":"M. Wirth, “Modular completely Dirichlet forms as squares of derivations,” <i>International Mathematics Research Notices</i>, vol. 2024, no. 14. Oxford University Press, pp. 10597–10614, 2024.","apa":"Wirth, M. (2024). Modular completely Dirichlet forms as squares of derivations. <i>International Mathematics Research Notices</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/imrn/rnae092\">https://doi.org/10.1093/imrn/rnae092</a>","ista":"Wirth M. 2024. Modular completely Dirichlet forms as squares of derivations. International Mathematics Research Notices. 2024(14), 10597–10614.","ama":"Wirth M. Modular completely Dirichlet forms as squares of derivations. <i>International Mathematics Research Notices</i>. 2024;2024(14):10597-10614. doi:<a href=\"https://doi.org/10.1093/imrn/rnae092\">10.1093/imrn/rnae092</a>","chicago":"Wirth, Melchior. “Modular Completely Dirichlet Forms as Squares of Derivations.” <i>International Mathematics Research Notices</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/imrn/rnae092\">https://doi.org/10.1093/imrn/rnae092</a>.","mla":"Wirth, Melchior. “Modular Completely Dirichlet Forms as Squares of Derivations.” <i>International Mathematics Research Notices</i>, vol. 2024, no. 14, Oxford University Press, 2024, pp. 10597–614, doi:<a href=\"https://doi.org/10.1093/imrn/rnae092\">10.1093/imrn/rnae092</a>."},"publication":"International Mathematics Research Notices","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1073-7928"],"eissn":["1687-0247"]},"file_date_updated":"2025-01-27T12:38:10Z","author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","orcid":"0000-0002-0519-4241","first_name":"Melchior","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E"}],"page":"10597-10614","project":[{"grant_number":"ESP156_N","_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","name":"Gradient flow techniques for quantum Markov semigroups"}],"oa_version":"Published Version","corr_author":"1","article_processing_charge":"Yes (via OA deal)","year":"2024","_id":"18900","date_updated":"2025-09-09T12:02:46Z","OA_place":"publisher","OA_type":"hybrid","acknowledgement":"The author was funded by the Austrian Science Fund under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. ","external_id":{"isi":["001222279400001"]},"oa":1,"volume":2024,"month":"07","ddc":["510"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Modular completely Dirichlet forms as squares of derivations","intvolume":"      2024"},{"ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Assessing the precision of morphogen gradients in neural tube development","intvolume":"        15","external_id":{"pmid":["38302459"],"isi":["001156218500022"]},"oa":1,"month":"02","volume":15,"OA_type":"gold","OA_place":"publisher","pmid":1,"acknowledgement":"MZ is supported by National Science Center, Poland, 2021/42/E/NZ2/00188, the Polish National Agency for Academic Exchange, and by a grant from the Priority Research Area DigiWorld under the Strategic Programme Excellence Initiative at Jagiellonian University. Work in JB’s lab is supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK, the UK Medical Research Council and Wellcome Trust (all under CC001051). Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Neural Stem Cell Modulation).","_id":"18902","date_updated":"2025-12-30T10:57:08Z","article_processing_charge":"Yes","year":"2024","project":[{"name":"Mechanisms of tissue size regulation in spinal cord development","_id":"bd7e737f-d553-11ed-ba76-d69ffb5ee3aa","grant_number":"101044579"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P02-Morphogen control of growth and pattern in the spinal cord","_id":"059DF620-7A3F-11EA-A408-12923DDC885E","grant_number":"F7802"}],"corr_author":"1","oa_version":"Published Version","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2041-1723"]},"file_date_updated":"2025-01-27T13:04:03Z","DOAJ_listed":"1","author":[{"first_name":"Marcin","full_name":"Zagorski, Marcin","last_name":"Zagorski"},{"last_name":"Brandenberg","full_name":"Brandenberg, Nathalie","first_name":"Nathalie"},{"last_name":"Lutolf","full_name":"Lutolf, Matthias","first_name":"Matthias"},{"last_name":"Tkačik","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Bollenbach","full_name":"Bollenbach, Mark Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X","first_name":"Mark Tobias"},{"full_name":"Briscoe, James","last_name":"Briscoe","first_name":"James"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4509-4998","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna"}],"article_number":"929","publication_status":"published","citation":{"ama":"Zagorski M, Brandenberg N, Lutolf M, et al. Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>","chicago":"Zagorski, Marcin, Nathalie Brandenberg, Matthias Lutolf, Gašper Tkačik, Mark Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>.","mla":"Zagorski, Marcin, et al. “Assessing the Precision of Morphogen Gradients in Neural Tube Development.” <i>Nature Communications</i>, vol. 15, 929, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-45148-8\">10.1038/s41467-024-45148-8</a>.","ieee":"M. Zagorski <i>et al.</i>, “Assessing the precision of morphogen gradients in neural tube development,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","short":"M. Zagorski, N. Brandenberg, M. Lutolf, G. Tkačik, M.T. Bollenbach, J. Briscoe, A. Kicheva, Nature Communications 15 (2024).","apa":"Zagorski, M., Brandenberg, N., Lutolf, M., Tkačik, G., Bollenbach, M. T., Briscoe, J., &#38; Kicheva, A. (2024). Assessing the precision of morphogen gradients in neural tube development. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-45148-8\">https://doi.org/10.1038/s41467-024-45148-8</a>","ista":"Zagorski M, Brandenberg N, Lutolf M, Tkačik G, Bollenbach MT, Briscoe J, Kicheva A. 2024. Assessing the precision of morphogen gradients in neural tube development. Nature Communications. 15, 929."},"publication":"Nature Communications","has_accepted_license":"1","department":[{"_id":"GaTk"},{"_id":"AnKi"}],"file":[{"file_name":"2024_NatureComm_Zagorski.pdf","checksum":"acf75f2b6fa84a64d1f590dd4a53cbf7","relation":"main_file","creator":"dernst","file_id":"18903","file_size":4723831,"access_level":"open_access","success":1,"date_created":"2025-01-27T13:04:03Z","content_type":"application/pdf","date_updated":"2025-01-27T13:04:03Z"}],"article_type":"letter_note","doi":"10.1038/s41467-024-45148-8","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","date_published":"2024-02-01T00:00:00Z","date_created":"2025-01-27T13:01:01Z","publisher":"Springer Nature","scopus_import":"1","type":"journal_article","status":"public","isi":1,"day":"01"},{"type":"conference","publisher":"ACM","date_created":"2025-01-27T13:20:26Z","scopus_import":"1","date_published":"2024-09-01T00:00:00Z","quality_controlled":"1","doi":"10.1145/3637528.3671978","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MoHe"}],"has_accepted_license":"1","file":[{"content_type":"application/pdf","date_updated":"2025-01-27T13:25:23Z","date_created":"2025-01-27T13:25:23Z","access_level":"open_access","file_size":1450331,"file_id":"18907","success":1,"checksum":"1265d5cf6aa5f94157631651723c4a2b","file_name":"2024_ACMKDD_Hanauer.pdf","creator":"dernst","relation":"main_file"}],"day":"01","isi":1,"status":"public","abstract":[{"text":"Expander decompositions of graphs have significantly advanced the understanding of many classical graph problems and led to numerous fundamental theoretical results. However, their adoption in practice has been hindered due to their inherent intricacies and large hidden factors in their asymptotic running times. Here, we introduce the first practically efficient algorithm for computing expander decompositions and their hierarchies and demonstrate its effectiveness and utility by incorporating it as the core component in a novel solver for the normalized cut graph clustering objective.\r\nOur extensive experiments on a variety of large graphs show that our expander-based algorithm outperforms state-of-the-art solvers for normalized cut with respect to solution quality by a large margin on a variety of graph classes such as citation, e-mail, and social networks or web graphs while remaining competitive in running time.","lang":"eng"}],"date_updated":"2025-09-09T12:04:56Z","_id":"18906","acknowledgement":"Monika Henzinger: This project has received funding from the European Research\r\nCouncil (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI 10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nHarald Räcke, Robin Münk: This project has received funding from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – 498605858 and 470029389.","ec_funded":1,"OA_type":"hybrid","OA_place":"publisher","oa":1,"month":"09","external_id":{"isi":["001324524201013"]},"title":"Expander hierarchies for normalized cuts on graphs","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000"],"publication":"Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining","publication_status":"published","citation":{"mla":"Hanauer, Kathrin, et al. “Expander Hierarchies for Normalized Cuts on Graphs.” <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, ACM, 2024, pp. 1016–27, doi:<a href=\"https://doi.org/10.1145/3637528.3671978\">10.1145/3637528.3671978</a>.","chicago":"Hanauer, Kathrin, Monika Henzinger, Robin Münk, Harald Räcke, and Maximilian Vötsch. “Expander Hierarchies for Normalized Cuts on Graphs.” In <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, 1016–27. ACM, 2024. <a href=\"https://doi.org/10.1145/3637528.3671978\">https://doi.org/10.1145/3637528.3671978</a>.","ama":"Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. Expander hierarchies for normalized cuts on graphs. In: <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>. ACM; 2024:1016-1027. doi:<a href=\"https://doi.org/10.1145/3637528.3671978\">10.1145/3637528.3671978</a>","ista":"Hanauer K, Henzinger M, Münk R, Räcke H, Vötsch M. 2024. Expander hierarchies for normalized cuts on graphs. Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. KDD: Knowledge Discovery and Data Mining, 1016–1027.","apa":"Hanauer, K., Henzinger, M., Münk, R., Räcke, H., &#38; Vötsch, M. (2024). Expander hierarchies for normalized cuts on graphs. In <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i> (pp. 1016–1027). Barcelona, Spain: ACM. <a href=\"https://doi.org/10.1145/3637528.3671978\">https://doi.org/10.1145/3637528.3671978</a>","ieee":"K. Hanauer, M. Henzinger, R. Münk, H. Räcke, and M. Vötsch, “Expander hierarchies for normalized cuts on graphs,” in <i>Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining</i>, Barcelona, Spain, 2024, pp. 1016–1027.","short":"K. Hanauer, M. Henzinger, R. Münk, H. Räcke, M. Vötsch, in:, Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, ACM, 2024, pp. 1016–1027."},"file_date_updated":"2025-01-27T13:25:23Z","author":[{"last_name":"Hanauer","full_name":"Hanauer, Kathrin","first_name":"Kathrin"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger"},{"full_name":"Münk, Robin","last_name":"Münk","first_name":"Robin"},{"first_name":"Harald","full_name":"Räcke, Harald","last_name":"Räcke"},{"first_name":"Maximilian","full_name":"Vötsch, Maximilian","last_name":"Vötsch"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798400704901"]},"oa_version":"Published Version","project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"grant_number":"I05982","name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103"}],"page":"1016-1027","year":"2024","article_processing_charge":"Yes (in subscription journal)","conference":{"name":"KDD: Knowledge Discovery and Data Mining","start_date":"2024-08-05","location":"Barcelona, Spain","end_date":"2024-08-29"}},{"date_published":"2024-04-23T00:00:00Z","quality_controlled":"1","scopus_import":"1","date_created":"2025-01-27T13:30:27Z","publisher":"Oxford University Press","issue":"4","type":"journal_article","file":[{"creator":"dernst","relation":"main_file","file_name":"2024_EvolutionLetter_Moan.pdf","checksum":"2f7780b7b6b3489755f1815f476639c6","success":1,"access_level":"open_access","file_id":"18909","file_size":24356661,"date_created":"2025-01-27T13:33:14Z","date_updated":"2025-01-27T13:33:14Z","content_type":"application/pdf"}],"article_type":"letter_note","department":[{"_id":"NiBa"}],"has_accepted_license":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1093/evlett/qrae014","isi":1,"day":"23","abstract":[{"lang":"eng","text":"Chromosomal rearrangements can lead to the coupling of reproductive barriers, but whether and how they contribute to the completion of speciation remains unclear. Marine snails of the genus Littorina repeatedly form hybrid zones between populations segregating for multiple inversion arrangements, providing opportunities to study their barrier effects. Here, we analyzed 2 adjacent transects across hybrid zones between 2 ecotypes of Littorina fabalis (“large” and “dwarf”) adapted to different wave exposure conditions on a Swedish island. Applying whole-genome sequencing, we found 12 putative inversions on 9 of 17 chromosomes. Nine of the putative inversions reached near differential fixation between the 2 ecotypes, and all were in strong linkage disequilibrium. These inversions cover 20% of the genome and carry 93% of divergent single nucleotide polymorphisms (SNPs). Bimodal hybrid zones in both transects indicated that the 2 ecotypes of Littorina fabalis maintain their genetic and phenotypic integrity following contact. The bimodality reflects the strong coupling between inversion clines and the extension of the barrier effect across the whole genome. Demographic inference suggests that coupling arose during a period of allopatry and has been maintained for &amp;gt; 1,000 generations after secondary contact. Overall, this study shows that the coupling of multiple chromosomal inversions contributes to strong reproductive isolation. Notably, 2 of the putative inversions overlap with inverted genomic regions associated with ecotype differences in a closely related species (Littorina saxatilis), suggesting the same regions, with similar structural variants, repeatedly contribute to ecotype evolution in distinct species."}],"status":"public","OA_type":"gold","OA_place":"publisher","pmid":1,"acknowledgement":"The computations and data handling were enabled by resources provided by the Swedish National Infrastructure for Computing at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank all the member of the Littorina team for the stimulating discussions about the manuscripts, James Reeves for his help the implementation of Hsplit, and Thomas Broquet for his useful comments in the latter stage of manuscript revisions.","_id":"18908","date_updated":"2025-09-09T12:05:51Z","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"ddc":["570"],"intvolume":"         8","title":"Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes","external_id":{"isi":["001206532900001"],"pmid":["39479507"]},"month":"04","volume":8,"oa":1,"publication_identifier":{"issn":["2056-3744"]},"language":[{"iso":"eng"}],"author":[{"first_name":"Alan","last_name":"Le Moan","full_name":"Le Moan, Alan"},{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"first_name":"Olga","last_name":"Ortega-Martinez","full_name":"Ortega-Martinez, Olga"},{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Roger K","full_name":"Butlin, Roger K","last_name":"Butlin"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"}],"file_date_updated":"2025-01-27T13:33:14Z","citation":{"ieee":"A. Le Moan <i>et al.</i>, “Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes,” <i>Evolution Letters</i>, vol. 8, no. 4. Oxford University Press, pp. 575–586, 2024.","short":"A. Le Moan, S. Stankowski, M. Rafajlović, O. Ortega-Martinez, R. Faria, R.K. Butlin, K. Johannesson, Evolution Letters 8 (2024) 575–586.","ista":"Le Moan A, Stankowski S, Rafajlović M, Ortega-Martinez O, Faria R, Butlin RK, Johannesson K. 2024. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. Evolution Letters. 8(4), 575–586.","apa":"Le Moan, A., Stankowski, S., Rafajlović, M., Ortega-Martinez, O., Faria, R., Butlin, R. K., &#38; Johannesson, K. (2024). Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. <i>Evolution Letters</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/evlett/qrae014\">https://doi.org/10.1093/evlett/qrae014</a>","ama":"Le Moan A, Stankowski S, Rafajlović M, et al. Coupling of twelve putative chromosomal inversions maintains a strong barrier to gene flow between snail ecotypes. <i>Evolution Letters</i>. 2024;8(4):575-586. doi:<a href=\"https://doi.org/10.1093/evlett/qrae014\">10.1093/evlett/qrae014</a>","chicago":"Le Moan, Alan, Sean Stankowski, Marina Rafajlović, Olga Ortega-Martinez, Rui Faria, Roger K Butlin, and Kerstin Johannesson. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” <i>Evolution Letters</i>. Oxford University Press, 2024. <a href=\"https://doi.org/10.1093/evlett/qrae014\">https://doi.org/10.1093/evlett/qrae014</a>.","mla":"Le Moan, Alan, et al. “Coupling of Twelve Putative Chromosomal Inversions Maintains a Strong Barrier to Gene Flow between Snail Ecotypes.” <i>Evolution Letters</i>, vol. 8, no. 4, Oxford University Press, 2024, pp. 575–86, doi:<a href=\"https://doi.org/10.1093/evlett/qrae014\">10.1093/evlett/qrae014</a>."},"publication_status":"published","publication":"Evolution Letters","article_processing_charge":"Yes","year":"2024","page":"575-586","oa_version":"Published Version"},{"isi":1,"day":"01","status":"public","abstract":[{"lang":"eng","text":"Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies."}],"date_created":"2025-01-27T13:40:34Z","publisher":"Annual Reviews","scopus_import":"1","date_published":"2024-07-01T00:00:00Z","quality_controlled":"1","type":"journal_article","doi":"10.1146/annurev-biophys-070323-022428","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"PaSc"}],"has_accepted_license":"1","article_type":"original","file":[{"checksum":"c90861542ae3f9147939030d5bafed3c","file_name":"2024_AnnualReviews_Schanda.pdf","creator":"dernst","relation":"main_file","access_level":"open_access","file_id":"18911","file_size":3025589,"success":1,"date_created":"2025-01-27T13:44:59Z","content_type":"application/pdf","date_updated":"2025-01-27T13:44:59Z"}],"file_date_updated":"2025-01-27T13:44:59Z","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul"},{"first_name":"Gilad","full_name":"Haran, Gilad","last_name":"Haran"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1936-122X"],"eissn":["1936-1238"]},"publication":"Annual Review of Biophysics","publication_status":"published","citation":{"mla":"Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.” <i>Annual Review of Biophysics</i>, vol. 53, Annual Reviews, 2024, pp. 247–73, doi:<a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">10.1146/annurev-biophys-070323-022428</a>.","chicago":"Schanda, Paul, and Gilad Haran. “NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.” <i>Annual Review of Biophysics</i>. Annual Reviews, 2024. <a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">https://doi.org/10.1146/annurev-biophys-070323-022428</a>.","ama":"Schanda P, Haran G. NMR and single-molecule FRET insights into fast protein motions and their relation to function. <i>Annual Review of Biophysics</i>. 2024;53:247-273. doi:<a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">10.1146/annurev-biophys-070323-022428</a>","apa":"Schanda, P., &#38; Haran, G. (2024). NMR and single-molecule FRET insights into fast protein motions and their relation to function. <i>Annual Review of Biophysics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-biophys-070323-022428\">https://doi.org/10.1146/annurev-biophys-070323-022428</a>","ista":"Schanda P, Haran G. 2024. NMR and single-molecule FRET insights into fast protein motions and their relation to function. Annual Review of Biophysics. 53, 247–273.","ieee":"P. Schanda and G. Haran, “NMR and single-molecule FRET insights into fast protein motions and their relation to function,” <i>Annual Review of Biophysics</i>, vol. 53. Annual Reviews, pp. 247–273, 2024.","short":"P. Schanda, G. Haran, Annual Review of Biophysics 53 (2024) 247–273."},"year":"2024","article_processing_charge":"No","oa_version":"Published Version","corr_author":"1","project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","grant_number":"I05812"}],"page":"247-273","pmid":1,"acknowledgement":"G.H. is the incumbent of the Hilda Pomeraniec Memorial Professorial Chair. He has been partially funded by the European Research Council under the European Union's Horizon 2020 research and innovation program (grant 742637, SMALLOSTERY), by National Science Foundation–US-Israel Binational Science Foundation grant 2021700, and by an Israel Science Foundation Breakthrough grant (1924/22). P.S. acknowledges funding from the Austrian Science Fund (project “AlloSpace,” I05812) and intramural funding from the Institute of Science and Technology Austria.","OA_type":"hybrid","OA_place":"publisher","date_updated":"2025-09-09T12:06:24Z","_id":"18910","title":"NMR and single-molecule FRET insights into fast protein motions and their relation to function","intvolume":"        53","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"volume":53,"month":"07","external_id":{"isi":["001278237500012"],"pmid":["38346243"]}},{"publication":"SIGGRAPH '24: ACM SIGGRAPH 2024 Conference Papers","article_number":"134","publication_status":"published","citation":{"apa":"Tojo, K., Shamir, A., Bickel, B., &#38; Umetani, N. (2024). Fabricable 3D wire art. In <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. Denver, CO, United States: ACM. <a href=\"https://doi.org/10.1145/3641519.3657453\">https://doi.org/10.1145/3641519.3657453</a>","ista":"Tojo K, Shamir A, Bickel B, Umetani N. 2024. Fabricable 3D wire art. SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 134.","ieee":"K. Tojo, A. Shamir, B. Bickel, and N. Umetani, “Fabricable 3D wire art,” in <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>, Denver, CO, United States, 2024.","short":"K. Tojo, A. Shamir, B. Bickel, N. Umetani, in:, SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers, ACM, 2024.","mla":"Tojo, Kenji, et al. “Fabricable 3D Wire Art.” <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>, 134, ACM, 2024, doi:<a href=\"https://doi.org/10.1145/3641519.3657453\">10.1145/3641519.3657453</a>.","ama":"Tojo K, Shamir A, Bickel B, Umetani N. Fabricable 3D wire art. In: <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. ACM; 2024. doi:<a href=\"https://doi.org/10.1145/3641519.3657453\">10.1145/3641519.3657453</a>","chicago":"Tojo, Kenji, Ariel Shamir, Bernd Bickel, and Nobuyuki Umetani. “Fabricable 3D Wire Art.” In <i>SIGGRAPH ’24: ACM SIGGRAPH 2024 Conference Papers</i>. ACM, 2024. <a href=\"https://doi.org/10.1145/3641519.3657453\">https://doi.org/10.1145/3641519.3657453</a>."},"author":[{"full_name":"Tojo, Kenji","last_name":"Tojo","first_name":"Kenji"},{"last_name":"Shamir","full_name":"Shamir, Ariel","first_name":"Ariel"},{"last_name":"Bickel","full_name":"Bickel, Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"first_name":"Nobuyuki","last_name":"Umetani","full_name":"Umetani, Nobuyuki"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9798400705250"]},"corr_author":"1","oa_version":"None","year":"2024","conference":{"location":"Denver, CO, United States","end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28"},"article_processing_charge":"No","date_updated":"2025-09-09T12:06:57Z","_id":"18912","acknowledgement":"The authors thank the anonymous reviewers for their valuable comments and suggestions for improving the paper. This work was supported by JSPS KAKENHI Grant Numbers JP21K11910, 23KJ0699 and JST AdCORP, Grant Number JPMJKB2302, Japan. This work was partially supported by Israel Science Foundation Grant number 1390/19 and Joint NSFC-ISF Research Grant no. 3077/23. We thank Riku Toyota for his useful advice on wire selection and Takeo Igarashi for his assistance in arranging the collaboration of the authors.","OA_type":"closed access","month":"07","external_id":{"isi":["001282218200059"]},"title":"Fabricable 3D wire art","day":"01","isi":1,"status":"public","abstract":[{"text":"This paper presents a computational method for automatically creating fabricable 3D wire sculptures from various input modalities, including 3D models, images, and even text. There are several challenges to wire art creation. For example, artists must express the desired visual as a sparse wire representation. It is also difficult to manually bend wires in the air without guidance to fabricate the designed 3D curves. Our workflow solves these challenges by using two core techniques. First, we present an algorithm that automatically generates a fabricable 3D curve representation of the target based on a loss function that measures the semantic distance between the rendered curve and the target. The loss function can be defined using different pre-trained vision-language neural networks to generate wire art from different input types. The loss function is then optimized using differentiable rendering specifically targeting 3D parametric curves. Our method can incorporate various fabrication constraints on the wire as additional regularization terms in the optimization process. Second, we present an algorithm to generate a 3D printable jig structure that can be used to fabricate the generated wire path. The major challenge in the jig generation stems from the design of an intersection-free surface mesh for 3D printing, which we address with our inflation algorithm. The experimental results indicate that our method can handle a wider range of input types and can produce physically fabricable wire shapes compared to previous wire generation methods. Various wire arts have been fabricated using our 3D-printed jig to demonstrate its effectiveness in 3D wire bending.","lang":"eng"}],"type":"conference","date_created":"2025-01-27T13:47:35Z","publisher":"ACM","scopus_import":"1","quality_controlled":"1","date_published":"2024-07-01T00:00:00Z","doi":"10.1145/3641519.3657453","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"BeBi"}]},{"scopus_import":"1","publisher":"ACM","date_created":"2025-01-27T13:57:00Z","date_published":"2024-07-01T00:00:00Z","quality_controlled":"1","type":"conference","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1145/3634737.3656997","file":[{"checksum":"1e743ddf49d35390eb56e11eb0759150","file_name":"2024_ACMAsiaCCS_Giuliari.pdf","relation":"main_file","creator":"dernst","access_level":"open_access","file_id":"18914","file_size":951940,"success":1,"date_created":"2025-01-27T14:04:12Z","content_type":"application/pdf","date_updated":"2025-01-27T14:04:12Z"}],"department":[{"_id":"ElKo"}],"has_accepted_license":"1","isi":1,"day":"01","status":"public","abstract":[{"lang":"eng","text":"With the proliferation of blockchain technology in high-value sectors, consensus protocols are becoming critical infrastructures. The rapid innovation cycle in Byzantine fault tolerant (BFT) consensus protocols has culminated in HotStuff, which provides linear message complexity in the partially synchronous setting. To achieve this, HotStuff leverages a leader that collects, aggregates, and broadcasts the messages of other validators. This paper analyzes the security implications of such approaches in practice, from the perspective of liveness and availability.\r\nBy implementing attacks in a globally-distributed testbed, we show that state-of-the-art leader-based protocols are vulnerable to denial-of-service (DoS) attacks on the leader. Our attacks, demonstrated on committees of up to 64 validators, manage to disrupt liveness within seconds, using only a few tens of Mbps of attack bandwidth per validator. Crucially, the cost and effectiveness of the attacks are independent of the committee size. Based on the outcome of these experiments, we then propose and test effective mitigations. Our findings show that advancements in both protocol design and network-layer defenses can greatly improve the practical resilience of BFT consensus protocols."}],"acknowledgement":"This work was mostly realized while Alberto Sonnino and Lefteris Kokoris-Kogias were employed at Meta. We gratefully acknowledge support for this project from ETH Zurich and Mysten Labs.","OA_place":"publisher","OA_type":"hybrid","date_updated":"2025-09-09T12:07:28Z","_id":"18913","title":"An empirical study of consensus protocols’ DoS resilience","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["000"],"month":"07","oa":1,"external_id":{"isi":["001283918100095"]},"author":[{"full_name":"Giuliari, Giacomo","last_name":"Giuliari","first_name":"Giacomo"},{"last_name":"Sonnino","full_name":"Sonnino, Alberto","first_name":"Alberto"},{"full_name":"Frei, Marc","last_name":"Frei","first_name":"Marc"},{"first_name":"Fabio","full_name":"Streun, Fabio","last_name":"Streun"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"last_name":"Perrig","full_name":"Perrig, Adrian","first_name":"Adrian"}],"file_date_updated":"2025-01-27T14:04:12Z","publication_identifier":{"isbn":["9798400704826"]},"language":[{"iso":"eng"}],"publication":"Proceedings of the 19th ACM Asia Conference on Computer and Communications Security","citation":{"short":"G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, A. Perrig, in:, Proceedings of the 19th ACM Asia Conference on Computer and Communications Security, ACM, 2024, pp. 1345–1360.","ieee":"G. Giuliari, A. Sonnino, M. Frei, F. Streun, E. Kokoris Kogias, and A. Perrig, “An empirical study of consensus protocols’ DoS resilience,” in <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>, Singapore, Singapore, 2024, pp. 1345–1360.","ista":"Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. 2024. An empirical study of consensus protocols’ DoS resilience. Proceedings of the 19th ACM Asia Conference on Computer and Communications Security. ASIACCS: Asia Conference on Computer and Communications Security, 1345–1360.","apa":"Giuliari, G., Sonnino, A., Frei, M., Streun, F., Kokoris Kogias, E., &#38; Perrig, A. (2024). An empirical study of consensus protocols’ DoS resilience. In <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i> (pp. 1345–1360). Singapore, Singapore: ACM. <a href=\"https://doi.org/10.1145/3634737.3656997\">https://doi.org/10.1145/3634737.3656997</a>","ama":"Giuliari G, Sonnino A, Frei M, Streun F, Kokoris Kogias E, Perrig A. An empirical study of consensus protocols’ DoS resilience. In: <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>. ACM; 2024:1345-1360. doi:<a href=\"https://doi.org/10.1145/3634737.3656997\">10.1145/3634737.3656997</a>","chicago":"Giuliari, Giacomo, Alberto Sonnino, Marc Frei, Fabio Streun, Eleftherios Kokoris Kogias, and Adrian Perrig. “An Empirical Study of Consensus Protocols’ DoS Resilience.” In <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>, 1345–60. ACM, 2024. <a href=\"https://doi.org/10.1145/3634737.3656997\">https://doi.org/10.1145/3634737.3656997</a>.","mla":"Giuliari, Giacomo, et al. “An Empirical Study of Consensus Protocols’ DoS Resilience.” <i>Proceedings of the 19th ACM Asia Conference on Computer and Communications Security</i>, ACM, 2024, pp. 1345–60, doi:<a href=\"https://doi.org/10.1145/3634737.3656997\">10.1145/3634737.3656997</a>."},"publication_status":"published","year":"2024","article_processing_charge":"Yes (in subscription journal)","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security","start_date":"2024-07-01","location":"Singapore, Singapore","end_date":"2024-07-05"},"oa_version":"Published Version","page":"1345-1360"},{"month":"05","volume":20,"external_id":{"isi":["001162208200002"]},"title":"Through the slopes of a light-induced phase transition","intvolume":"        20","date_updated":"2025-09-09T12:08:10Z","_id":"18919","OA_type":"closed access","corr_author":"1","oa_version":"None","page":"684-685","year":"2024","article_processing_charge":"No","publication":"Nature Physics","publication_status":"published","citation":{"apa":"Baykusheva, D. R. (2024). Through the slopes of a light-induced phase transition. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-024-02401-7\">https://doi.org/10.1038/s41567-024-02401-7</a>","ista":"Baykusheva DR. 2024. Through the slopes of a light-induced phase transition. Nature Physics. 20(5), 684–685.","ieee":"D. R. Baykusheva, “Through the slopes of a light-induced phase transition,” <i>Nature Physics</i>, vol. 20, no. 5. Springer Nature, pp. 684–685, 2024.","short":"D.R. Baykusheva, Nature Physics 20 (2024) 684–685.","mla":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” <i>Nature Physics</i>, vol. 20, no. 5, Springer Nature, 2024, pp. 684–85, doi:<a href=\"https://doi.org/10.1038/s41567-024-02401-7\">10.1038/s41567-024-02401-7</a>.","ama":"Baykusheva DR. Through the slopes of a light-induced phase transition. <i>Nature Physics</i>. 2024;20(5):684-685. doi:<a href=\"https://doi.org/10.1038/s41567-024-02401-7\">10.1038/s41567-024-02401-7</a>","chicago":"Baykusheva, Denitsa Rangelova. “Through the Slopes of a Light-Induced Phase Transition.” <i>Nature Physics</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41567-024-02401-7\">https://doi.org/10.1038/s41567-024-02401-7</a>."},"author":[{"first_name":"Denitsa Rangelova","id":"71b4d059-2a03-11ee-914d-dfa3beed6530","full_name":"Baykusheva, Denitsa Rangelova","last_name":"Baykusheva"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"doi":"10.1038/s41567-024-02401-7","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"DeBa"}],"article_type":"letter_note","type":"journal_article","issue":"5","publisher":"Springer Nature","date_created":"2025-01-27T14:29:20Z","scopus_import":"1","quality_controlled":"1","date_published":"2024-05-01T00:00:00Z","status":"public","abstract":[{"text":"The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling.","lang":"eng"}],"day":"01","isi":1},{"publisher":"American Association for the Advancement of Science","date_created":"2025-01-27T14:32:34Z","scopus_import":"1","date_published":"2024-04-01T00:00:00Z","quality_controlled":"1","type":"journal_article","issue":"15","doi":"10.1126/sciadv.adk1954","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"EM-Fac"}],"has_accepted_license":"1","article_type":"original","file":[{"date_created":"2025-01-27T14:40:08Z","date_updated":"2025-01-27T14:40:08Z","content_type":"application/pdf","creator":"dernst","relation":"main_file","file_name":"2024_ScienceAdv_Homola.pdf","checksum":"291dd7ceccbe6bfd8e0a9157584f88e9","success":1,"file_size":40623405,"file_id":"18921","access_level":"open_access"}],"day":"01","status":"public","abstract":[{"lang":"eng","text":"The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis."}],"pmid":1,"acknowledgement":"We acknowledge (i) the Cryo-Electron Microscopy and Tomography Core Facility and Proteomics Core Facility of the Central European Institute of Technology (CEITEC), Masaryk University, supported by the Ministry of Education, Youth, and Sports of the Czech Republic (grant LM2018127); (ii) the Cellular Imaging Core Facility supported by the Czech-BioImaging large RI project (LM2018129 funded by MEYS CR); and (iii) Plant Sciences Core Facility for support with obtaining scientific data presented here. We acknowledge support from the project National Institute of Virology and Bacteriology (Program EXCELES, ID project no. LX22NPO5103), funded by the European Union - Next Generation EU. This work received funding from the Czech Science Foundation grant GX 19-259882X to P.P., from European Regional Development Fund-Project “MSCAfellow2@MUNI” (no. CZ.02.2.69/0.0/0.0/18_070/0009846) to C.R.B., and from Brno PhD talent scholarship funded by Brno city municipality to M.H.","OA_type":"gold","OA_place":"publisher","related_material":{"link":[{"url":" https://github.com/fuzikt/tomostarpy.","relation":"software"}]},"date_updated":"2025-05-14T09:29:04Z","_id":"18920","title":"Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi","intvolume":"        10","ddc":["570"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"volume":10,"month":"04","external_id":{"pmid":["38598627"]},"file_date_updated":"2025-01-27T14:40:08Z","DOAJ_listed":"1","author":[{"full_name":"Homola, Miroslav","last_name":"Homola","first_name":"Miroslav"},{"first_name":"Renate Carina","id":"3b7984c9-17ff-11ed-b6fe-f943c4a5b626","full_name":"Büttner, Renate Carina","last_name":"Büttner"},{"first_name":"Tibor","full_name":"Füzik, Tibor","last_name":"Füzik"},{"first_name":"Pavel","full_name":"Křepelka, Pavel","last_name":"Křepelka"},{"full_name":"Holbová, Radka","last_name":"Holbová","first_name":"Radka"},{"full_name":"Nováček, Jiří","last_name":"Nováček","first_name":"Jiří"},{"first_name":"Marten L.","full_name":"Chaillet, Marten L.","last_name":"Chaillet"},{"first_name":"Jakub","last_name":"Žák","full_name":"Žák, Jakub"},{"full_name":"Grybchuk, Danyil","last_name":"Grybchuk","first_name":"Danyil"},{"first_name":"Friedrich","last_name":"Förster","full_name":"Förster, Friedrich"},{"full_name":"Wilson, William H.","last_name":"Wilson","first_name":"William H."},{"full_name":"Schroeder, Declan C.","last_name":"Schroeder","first_name":"Declan C."},{"first_name":"Pavel","last_name":"Plevka","full_name":"Plevka, Pavel"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2375-2548"]},"publication":"Science Advances","publication_status":"published","article_number":"eadk1954 ","citation":{"ieee":"M. Homola <i>et al.</i>, “Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi,” <i>Science Advances</i>, vol. 10, no. 15. American Association for the Advancement of Science, 2024.","short":"M. Homola, R.C. Büttner, T. Füzik, P. Křepelka, R. Holbová, J. Nováček, M.L. Chaillet, J. Žák, D. Grybchuk, F. Förster, W.H. Wilson, D.C. Schroeder, P. Plevka, Science Advances 10 (2024).","ista":"Homola M, Büttner RC, Füzik T, Křepelka P, Holbová R, Nováček J, Chaillet ML, Žák J, Grybchuk D, Förster F, Wilson WH, Schroeder DC, Plevka P. 2024. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. Science Advances. 10(15), eadk1954.","apa":"Homola, M., Büttner, R. C., Füzik, T., Křepelka, P., Holbová, R., Nováček, J., … Plevka, P. (2024). Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>","chicago":"Homola, Miroslav, Renate Carina Büttner, Tibor Füzik, Pavel Křepelka, Radka Holbová, Jiří Nováček, Marten L. Chaillet, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>. American Association for the Advancement of Science, 2024. <a href=\"https://doi.org/10.1126/sciadv.adk1954\">https://doi.org/10.1126/sciadv.adk1954</a>.","ama":"Homola M, Büttner RC, Füzik T, et al. Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi. <i>Science Advances</i>. 2024;10(15). doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>","mla":"Homola, Miroslav, et al. “Structure and Replication Cycle of a Virus Infecting Climate-Modulating Alga Emiliania Huxleyi.” <i>Science Advances</i>, vol. 10, no. 15, eadk1954, American Association for the Advancement of Science, 2024, doi:<a href=\"https://doi.org/10.1126/sciadv.adk1954\">10.1126/sciadv.adk1954</a>."},"year":"2024","article_processing_charge":"Yes","oa_version":"Published Version"},{"status":"public","abstract":[{"text":"Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them.","lang":"eng"}],"day":"01","isi":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1109/focs61266.2024.00015","department":[{"_id":"MoHe"}],"type":"conference","scopus_import":"1","date_created":"2025-01-27T14:50:23Z","publisher":"IEEE","date_published":"2024-10-01T00:00:00Z","quality_controlled":"1","oa_version":"None","corr_author":"1","page":"62-85","year":"2024","conference":{"start_date":"2024-10-27","name":"FOCS: Foundations of Computer Science","end_date":"2024-10-30","location":"Chicago, IL, United States"},"article_processing_charge":"No","publication":"65th Annual Symposium on Foundations of Computer Science","citation":{"ieee":"L. Georgiadis, G. F. Italiano, and E. Kosinas, “Computing the 3-edge-connected components of directed graphs in linear time,” in <i>65th Annual Symposium on Foundations of Computer Science</i>, Chicago, IL, United States, 2024, pp. 62–85.","short":"L. Georgiadis, G.F. Italiano, E. Kosinas, in:, 65th Annual Symposium on Foundations of Computer Science, IEEE, 2024, pp. 62–85.","ista":"Georgiadis L, Italiano GF, Kosinas E. 2024. Computing the 3-edge-connected components of directed graphs in linear time. 65th Annual Symposium on Foundations of Computer Science. FOCS: Foundations of Computer Science, 62–85.","apa":"Georgiadis, L., Italiano, G. F., &#38; Kosinas, E. (2024). Computing the 3-edge-connected components of directed graphs in linear time. In <i>65th Annual Symposium on Foundations of Computer Science</i> (pp. 62–85). Chicago, IL, United States: IEEE. <a href=\"https://doi.org/10.1109/focs61266.2024.00015\">https://doi.org/10.1109/focs61266.2024.00015</a>","chicago":"Georgiadis, Loukas, Giuseppe F. Italiano, and Evangelos Kosinas. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” In <i>65th Annual Symposium on Foundations of Computer Science</i>, 62–85. IEEE, 2024. <a href=\"https://doi.org/10.1109/focs61266.2024.00015\">https://doi.org/10.1109/focs61266.2024.00015</a>.","ama":"Georgiadis L, Italiano GF, Kosinas E. Computing the 3-edge-connected components of directed graphs in linear time. In: <i>65th Annual Symposium on Foundations of Computer Science</i>. IEEE; 2024:62-85. doi:<a href=\"https://doi.org/10.1109/focs61266.2024.00015\">10.1109/focs61266.2024.00015</a>","mla":"Georgiadis, Loukas, et al. “Computing the 3-Edge-Connected Components of Directed Graphs in Linear Time.” <i>65th Annual Symposium on Foundations of Computer Science</i>, IEEE, 2024, pp. 62–85, doi:<a href=\"https://doi.org/10.1109/focs61266.2024.00015\">10.1109/focs61266.2024.00015</a>."},"publication_status":"published","author":[{"first_name":"Loukas","last_name":"Georgiadis","full_name":"Georgiadis, Loukas"},{"first_name":"Giuseppe F.","full_name":"Italiano, Giuseppe F.","last_name":"Italiano"},{"last_name":"Kosinas","full_name":"Kosinas, Evangelos","id":"4c7f9625-dbbc-11ee-9d86-bdcc2db5a949","first_name":"Evangelos"}],"publication_identifier":{"isbn":["9798331516741"]},"language":[{"iso":"eng"}],"month":"10","external_id":{"isi":["001419526400005"]},"title":"Computing the 3-edge-connected components of directed graphs in linear time","date_updated":"2025-09-09T12:08:47Z","_id":"18922","acknowledgement":"Giuseppe F. Italiano was partially supported by the Italian Ministry of\r\nUniversity and Reseach under PRIN Project n. 2022TS4Y3N - EXPAND: scalable algorithms for EXPloratory Analyses of heterogeneous and dynamic Networked Data.\r\n","OA_type":"closed access"},{"isi":1,"day":"01","abstract":[{"lang":"eng","text":"Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature."}],"main_file_link":[{"url":"https://schmiste.github.io/noms24.pdf","open_access":"1"}],"status":"public","date_published":"2024-05-01T00:00:00Z","quality_controlled":"1","publisher":"IEEE","date_created":"2025-01-27T15:06:45Z","scopus_import":"1","type":"conference","department":[{"_id":"KrCh"}],"doi":"10.1109/noms59830.2024.10575579","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2374-9709"],"isbn":["9798350327946"]},"author":[{"first_name":"Esra","id":"cb1ca1d8-dcc0-11ef-baa5-9f1b3ef75933","full_name":"Ceylan, Esra","last_name":"Ceylan"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"},{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","full_name":"Svoboda, Jakub"}],"publication_status":"published","citation":{"mla":"Ceylan, Esra, et al. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>, IEEE, 2024, doi:<a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">10.1109/noms59830.2024.10575579</a>.","ama":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In: <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. IEEE; 2024. doi:<a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">10.1109/noms59830.2024.10575579</a>","chicago":"Ceylan, Esra, Krishnendu Chatterjee, Stefan Schmid, and Jakub Svoboda. “Congestion-Free Rerouting of Network Flows: Hardness and an FPT Algorithm.” In <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. IEEE, 2024. <a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">https://doi.org/10.1109/noms59830.2024.10575579</a>.","ista":"Ceylan E, Chatterjee K, Schmid S, Svoboda J. 2024. Congestion-free rerouting of network flows: Hardness and an FPT algorithm. NOMS 2024-2024 IEEE Network Operations and Management Symposium. NOMS: Network Operations and Management Symposiu .","apa":"Ceylan, E., Chatterjee, K., Schmid, S., &#38; Svoboda, J. (2024). Congestion-free rerouting of network flows: Hardness and an FPT algorithm. In <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>. Seoul, Republic of Korea: IEEE. <a href=\"https://doi.org/10.1109/noms59830.2024.10575579\">https://doi.org/10.1109/noms59830.2024.10575579</a>","ieee":"E. Ceylan, K. Chatterjee, S. Schmid, and J. Svoboda, “Congestion-free rerouting of network flows: Hardness and an FPT algorithm,” in <i>NOMS 2024-2024 IEEE Network Operations and Management Symposium</i>, Seoul, Republic of Korea, 2024.","short":"E. Ceylan, K. Chatterjee, S. Schmid, J. Svoboda, in:, NOMS 2024-2024 IEEE Network Operations and Management Symposium, IEEE, 2024."},"publication":"NOMS 2024-2024 IEEE Network Operations and Management Symposium","conference":{"name":"NOMS: Network Operations and Management Symposiu ","start_date":"2024-05-06","location":"Seoul, Republic of Korea","end_date":"2024-05-10"},"article_processing_charge":"No","year":"2024","project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"894907","_id":"bd622a5c-d553-11ed-ba76-bae280ba8aff","name":"Graphical Games"}],"corr_author":"1","oa_version":"Submitted Version","ec_funded":1,"OA_type":"green","OA_place":"other","acknowledgement":"Research was supported by the Austrian Science Fund (FWF), project I 5025-N (DELTA), 2020-2024. Esra Ceylan’s research was supported by FFG, FEMtech Praktika für Studentinnen. Jakub Svoboda and Krishnendu Chatterjee were supported by the European Research Council (ERC) CoG 863818 (ForM-SMArt).","_id":"18925","date_updated":"2025-11-05T07:34:27Z","title":"Congestion-free rerouting of network flows: Hardness and an FPT algorithm","external_id":{"isi":["001270140300143"]},"oa":1,"month":"05"}]