[{"date_updated":"2025-09-08T09:22:11Z","publication_status":"published","ddc":["570"],"OA_type":"gold","author":[{"full_name":"Kettel, Paulina","first_name":"Paulina","last_name":"Kettel"},{"full_name":"Marosits, Laura","first_name":"Laura","last_name":"Marosits"},{"first_name":"Elena","full_name":"Spinetti, Elena","last_name":"Spinetti"},{"last_name":"Rechberger","full_name":"Rechberger, Michael","first_name":"Michael"},{"last_name":"Giannini","id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","full_name":"Giannini, Caterina"},{"last_name":"Radler","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","first_name":"Philipp"},{"last_name":"Niedermoser","full_name":"Niedermoser, Isabell","first_name":"Isabell"},{"first_name":"Irmgard","full_name":"Fischer, Irmgard","last_name":"Fischer"},{"full_name":"Versteeg, Gijs A.","first_name":"Gijs A.","last_name":"Versteeg"},{"full_name":"Loose, Martin","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","last_name":"Loose"},{"last_name":"Covino","full_name":"Covino, Roberto","first_name":"Roberto"},{"last_name":"Karagöz","first_name":"G. Elif","full_name":"Karagöz, G. Elif"}],"month":"10","publication":"EMBO Journal","language":[{"iso":"eng"}],"_id":"18073","title":"Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering","status":"public","scopus_import":"1","file":[{"date_created":"2025-01-13T08:43:20Z","success":1,"date_updated":"2025-01-13T08:43:20Z","checksum":"04f4df1a561083f2846676442fc4eb3c","file_size":10080854,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2024_Embo_Kettel.pdf","file_id":"18827","creator":"dernst"}],"article_type":"original","external_id":{"pmid":["39232130"],"isi":["001306286100002"]},"date_created":"2024-09-15T22:01:42Z","oa_version":"Published Version","page":"4668-4698","abstract":[{"text":"Conserved signaling cascades monitor protein-folding homeostasis to ensure proper cellular function. One of the evolutionary conserved key players is IRE1, which maintains endoplasmic reticulum (ER) homeostasis through the unfolded protein response (UPR). Upon accumulation of misfolded proteins in the ER, IRE1 forms clusters on the ER membrane to initiate UPR signaling. What regulates IRE1 cluster formation is not fully understood. Here, we show that the ER lumenal domain (LD) of human IRE1α forms biomolecular condensates in vitro. IRE1α LD condensates were stabilized both by binding to unfolded polypeptides as well as by tethering to model membranes, suggesting their role in assembling IRE1α into signaling-competent stable clusters. Molecular dynamics simulations indicated that weak multivalent interactions drive IRE1α LD clustering. Mutagenesis experiments identified disordered regions in IRE1α LD to control its clustering in vitro and in cells. Importantly, dysregulated clustering of IRE1α mutants led to defects in IRE1α signaling. Our results revealed that disordered regions in IRE1α LD control its clustering and suggest their role as a common strategy in regulating protein assembly on membranes.","lang":"eng"}],"isi":1,"volume":43,"year":"2024","quality_controlled":"1","day":"15","OA_place":"publisher","intvolume":"        43","date_published":"2024-10-15T00:00:00Z","citation":{"ama":"Kettel P, Marosits L, Spinetti E, et al. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. <i>EMBO Journal</i>. 2024;43(20):4668-4698. doi:<a href=\"https://doi.org/10.1038/s44318-024-00207-0\">10.1038/s44318-024-00207-0</a>","short":"P. Kettel, L. Marosits, E. Spinetti, M. Rechberger, C. Giannini, P. Radler, I. Niedermoser, I. Fischer, G.A. Versteeg, M. Loose, R. Covino, G.E. Karagöz, EMBO Journal 43 (2024) 4668–4698.","mla":"Kettel, Paulina, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” <i>EMBO Journal</i>, vol. 43, no. 20, Embo Press, 2024, pp. 4668–98, doi:<a href=\"https://doi.org/10.1038/s44318-024-00207-0\">10.1038/s44318-024-00207-0</a>.","apa":"Kettel, P., Marosits, L., Spinetti, E., Rechberger, M., Giannini, C., Radler, P., … Karagöz, G. E. (2024). Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.1038/s44318-024-00207-0\">https://doi.org/10.1038/s44318-024-00207-0</a>","chicago":"Kettel, Paulina, Laura Marosits, Elena Spinetti, Michael Rechberger, Caterina Giannini, Philipp Radler, Isabell Niedermoser, et al. “Disordered Regions in the IRE1α ER Lumenal Domain Mediate Its Stress-Induced Clustering.” <i>EMBO Journal</i>. Embo Press, 2024. <a href=\"https://doi.org/10.1038/s44318-024-00207-0\">https://doi.org/10.1038/s44318-024-00207-0</a>.","ieee":"P. Kettel <i>et al.</i>, “Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering,” <i>EMBO Journal</i>, vol. 43, no. 20. Embo Press, pp. 4668–4698, 2024.","ista":"Kettel P, Marosits L, Spinetti E, Rechberger M, Giannini C, Radler P, Niedermoser I, Fischer I, Versteeg GA, Loose M, Covino R, Karagöz GE. 2024. Disordered regions in the IRE1α ER lumenal domain mediate its stress-induced clustering. EMBO Journal. 43(20), 4668–4698."},"department":[{"_id":"MaLo"},{"_id":"JiFr"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Embo Press","issue":"20","article_processing_charge":"Yes","publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"We thank late Thomas Peterbauer at the Max Perutz Labs Biooptics Light Microscopy Facility for his help and support. We are grateful to Kitti Csalyi and Thomas Sauer at Max Perutz Labs Biooptics FACS facility for their help. We thank Grzegorz Scibisz and Sertan Atilla for their support with the expression and purification of mCherry-IRE1α LD-10His. We are grateful to Aleksandra S Anisimova with her help in the generation of stable cell lines and the statistical analyses of the data. We thank Venja Vieweger for her help with the characterization of the WLLI and D123P IRE1 mutants in cells. We are thankful to Monika Kubickova for the help with the AUC experiments. We acknowledge CF BIC of CIISB, Instruct-CZ Centre, supported by MEYS CR (LM2023042)) and European Regional Development Fund-Project, UP CIISB“ (No. CZ.02.1.01/0.0/0.0/18_046/0015974). We thank the members of the Karagöz lab for the critical reading and editing of the manuscript. We are thankful to our colleagues Diego Acosta-Alvear, Vladislav Belyy, Jirka Peschek, Yasin Dagdas, Javier Martinez, Sascha Martens and Alwin Köhler for their invaluable input on the manuscript. We are grateful to Life Science Editors, especially Katrina Woolcock for her useful edits and comments on the manuscript. We acknowledge funding from Austrian Science Fund (FWF-SFB F79 and FWF-W 1261) to GEK. PK acknowledges the support of the Max Perutz PhD fellowship. GAV is funded by Stand-Alone grants (P30231-B, P30415-B, P36572), Special Research Grant (SFB grant F79), and Doctoral School grant (DK grant W1261) from the Austrian Science Fund (FWF). ES and RC acknowledge support and funding by the Frankfurt Institute of Advanced Studies, the LOEWE Center for Multiscale Modelling in Life Sciences of the state of Hesse, the Collaborative Research Center 1507 “Membrane-associated Protein Assemblies, Machineries, and Supercomplexes” (Project ID 450648163), and the International Max Planck Research School on Cellular Biophysics (to RC), the Center for Scientific Computing of the Goethe University and the Jülich Supercomputing Centre for computational resources and support.","file_date_updated":"2025-01-13T08:43:20Z","pmid":1,"type":"journal_article","doi":"10.1038/s44318-024-00207-0","oa":1},{"publication_identifier":{"isbn":["9783959773164"]},"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["LIPIcs"],"citation":{"ista":"Attali D, Kourimska H, Fillmore CD, Ghosh I, Lieutier A, Stephenson ER, Wintraecken M. 2024. The ultimate frontier: An optimality construction for homotopy inference (media exposition). 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 87.","apa":"Attali, D., Kourimska, H., Fillmore, C. D., Ghosh, I., Lieutier, A., Stephenson, E. R., &#38; Wintraecken, M. (2024). The ultimate frontier: An optimality construction for homotopy inference (media exposition). In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.87\">https://doi.org/10.4230/LIPIcs.SoCG.2024.87</a>","ieee":"D. Attali <i>et al.</i>, “The ultimate frontier: An optimality construction for homotopy inference (media exposition),” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293.","chicago":"Attali, Dominique, Hana Kourimska, Christopher D Fillmore, Ishika Ghosh, Andre Lieutier, Elizabeth R Stephenson, and Mathijs Wintraecken. “The Ultimate Frontier: An Optimality Construction for Homotopy Inference (Media Exposition).” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.87\">https://doi.org/10.4230/LIPIcs.SoCG.2024.87</a>.","mla":"Attali, Dominique, et al. “The Ultimate Frontier: An Optimality Construction for Homotopy Inference (Media Exposition).” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 87, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.87\">10.4230/LIPIcs.SoCG.2024.87</a>.","short":"D. Attali, H. Kourimska, C.D. Fillmore, I. Ghosh, A. Lieutier, E.R. Stephenson, M. Wintraecken, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","ama":"Attali D, Kourimska H, Fillmore CD, et al. The ultimate frontier: An optimality construction for homotopy inference (media exposition). In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.87\">10.4230/LIPIcs.SoCG.2024.87</a>"},"department":[{"_id":"HeEd"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_published":"2024-06-06T00:00:00Z","intvolume":"       293","day":"06","quality_controlled":"1","oa":1,"doi":"10.4230/LIPIcs.SoCG.2024.87","conference":{"location":"Athens, Greece","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry","start_date":"2024-06-11"},"file_date_updated":"2024-09-19T10:30:37Z","type":"conference","corr_author":"1","has_accepted_license":"1","acknowledgement":"This research has been supported by the European Research Council (ERC), grant No. 788183, by the Wittgenstein Prize, Austrian Science Fund (FWF), grant No. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant No. I02979-N35. Mathijs Wintraecken: Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411, the Austrian science fund (FWF) grant No. M-3073, and the welcome package from IDEX of the Université Côte d’Azur.\r\nWe thank Jean-Daniel Boissonnat, Herbert Edelsbrunner, and Mariette Yvinec for discussion.","article_number":"87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"The ultimate frontier: An optimality construction for homotopy inference (media exposition)","status":"public","file":[{"file_name":"2024_LIPICs_Attali.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"18098","date_updated":"2024-09-19T10:30:37Z","success":1,"date_created":"2024-09-19T10:30:37Z","checksum":"9355c2e60b8ec285e1b22719c5b73f1a","file_size":3507177}],"_id":"18097","publication":"40th International Symposium on Computational Geometry","language":[{"iso":"eng"}],"author":[{"first_name":"Dominique","full_name":"Attali, Dominique","last_name":"Attali"},{"id":"D9B8E14C-3C26-11EA-98F5-1F833DDC885E","last_name":"Kourimska","first_name":"Hana","orcid":"0000-0001-7841-0091","full_name":"Kourimska, Hana"},{"full_name":"Fillmore, Christopher D","first_name":"Christopher D","id":"35638A5C-AAC7-11E9-B0BF-5503E6697425","last_name":"Fillmore"},{"last_name":"Ghosh","id":"ee449b28-344d-11ef-a6d5-9ca430e9e9ff","first_name":"Ishika","full_name":"Ghosh, Ishika"},{"last_name":"Lieutier","first_name":"Andre","full_name":"Lieutier, Andre"},{"full_name":"Stephenson, Elizabeth R","orcid":"0000-0002-6862-208X","first_name":"Elizabeth R","last_name":"Stephenson","id":"2D04F932-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7472-2220","first_name":"Mathijs","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"month":"06","ddc":["000"],"date_updated":"2025-04-15T07:16:58Z","publication_status":"published","volume":293,"project":[{"call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183"},{"grant_number":"Z00342","call_identifier":"FWF","name":"Mathematics, Computer Science","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses","grant_number":"M03073"}],"year":"2024","abstract":[{"text":"In our companion paper \"Tight bounds for the learning of homotopy à la Niyogi, Smale, and Weinberger for subsets of Euclidean spaces and of Riemannian manifolds\" we gave optimal bounds (in terms of the two one-sided Hausdorff distances) on a sample P of an input shape 𝒮 (either manifold or general set with positive reach) such that one can infer the homotopy of 𝒮 from the union of balls with some radius centred at P, both in Euclidean space and in a Riemannian manifold of bounded curvature. The construction showing the optimality of the bounds is not straightforward. The purpose of this video is to visualize and thus elucidate said construction in the Euclidean setting.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","date_created":"2024-09-19T10:29:48Z"},{"article_type":"original","title":"Commutative avatars of representations of semisimple Lie groups","scopus_import":"1","status":"public","file":[{"creator":"dernst","file_id":"18127","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2024_PNAS_Hausel.pdf","file_size":3764695,"checksum":"df80c873633c6734d2e324841e69db58","date_created":"2024-09-23T11:22:56Z","success":1,"date_updated":"2024-09-23T11:22:56Z"}],"_id":"18108","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","author":[{"id":"4A0666D8-F248-11E8-B48F-1D18A9856A87","last_name":"Hausel","full_name":"Hausel, Tamás","first_name":"Tamás","orcid":"0000-0002-9582-2634"}],"month":"09","ddc":["510"],"OA_type":"hybrid","APC_amount":"2742,92 EUR","date_updated":"2025-05-08T09:57:59Z","publication_status":"published","project":[{"grant_number":"P35847","name":"Geometry of the tip of the global nilpotent cone","_id":"34b2c9cb-11ca-11ed-8bc3-a50ba74ca4a3"}],"volume":121,"year":"2024","abstract":[{"text":"Here we announce the construction and properties of a big commutative subalgebra of the Kirillov algebra attached to a finite dimensional irreducible representation of a complex semisimple Lie group. They are commutative finite flat algebras over the cohomology of the classifying space of the group. They are isomorphic with the equivariant intersection cohomology of affine Schubert varieties, endowing the latter with a new ring structure. Study of the finer aspects of the structure of the big algebras will also furnish the stalks of the intersection cohomology with ring structure, thus ringifying Lusztig’s q-weight multiplicity polynomials i.e., certain affine Kazhdan–Lusztig polynomials.","lang":"eng"}],"oa_version":"Published Version","related_material":{"link":[{"url":"https://ista.ac.at/en/news/big-algebras-a-dictionary-of-abstract-math/","relation":"press_release"}]},"external_id":{"pmid":["39259592"]},"date_created":"2024-09-22T22:01:41Z","publication_identifier":{"eissn":["1091-6490"]},"article_processing_charge":"Yes (in subscription journal)","department":[{"_id":"TaHa"}],"citation":{"short":"T. Hausel, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Hausel T. Commutative avatars of representations of semisimple Lie groups. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(38). doi:<a href=\"https://doi.org/10.1073/pnas.2319341121\">10.1073/pnas.2319341121</a>","chicago":"Hausel, Tamás. “Commutative Avatars of Representations of Semisimple Lie Groups.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2319341121\">https://doi.org/10.1073/pnas.2319341121</a>.","ieee":"T. Hausel, “Commutative avatars of representations of semisimple Lie groups,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 38. National Academy of Sciences, 2024.","apa":"Hausel, T. (2024). Commutative avatars of representations of semisimple Lie groups. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2319341121\">https://doi.org/10.1073/pnas.2319341121</a>","ista":"Hausel T. 2024. Commutative avatars of representations of semisimple Lie groups. Proceedings of the National Academy of Sciences of the United States of America. 121(38), e2319341121.","mla":"Hausel, Tamás. “Commutative Avatars of Representations of Semisimple Lie Groups.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 38, e2319341121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2319341121\">10.1073/pnas.2319341121</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"38","publisher":"National Academy of Sciences","date_published":"2024-09-17T00:00:00Z","OA_place":"publisher","intvolume":"       121","day":"17","quality_controlled":"1","oa":1,"doi":"10.1073/pnas.2319341121","file_date_updated":"2024-09-23T11:22:56Z","type":"journal_article","pmid":1,"corr_author":"1","has_accepted_license":"1","acknowledgement":"We thank Nigel Hitchin for discussions and the joint projects this paper has grown out from. We thank Vladyslav Zveryk for collaboration on Theorem 2.3 and on the corresponding Magma code which implements big algebras. We thank Hiraku Nakajima for discussions and pointing out Theorem 3.1.2, a result generalizing our original observation in the= = 0 case. Special thanks go to Leonid Rybnikov for patiently explaining his works, in particular crucial to Theorem 2.1. We thank Michel Brion, Michael Finkelberg, Oscar García-Prada, Jakub Löwit, Joel Kamnitzer, Friedrich Knop, Michael McBreen, Anton Mellit, Takuro Mochizuki, Shon Ngô, Kamil Rychlewicz, Shiyu Shen, Leslie Spencer, Balázs Szendr ˝ oi, András Szenes, and Oksana\r\nYakimova for comments and discussions. Kamil Rychlewicz and Daniel Bedats helped with the Mathematica files for the figures, and we used the SM_isospin Tikz package of Izaak Neutelings for drawing the baryon multiplets. We thank the referees for many useful comments. We acknowledge funding from FWF grant “Geometry of the tip of the global nilpotent cone” no. P 35847.","article_number":"e2319341121","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"acknowledgement":"We thank Michael Carroll (Harvard Medical School, Boston) for providing Ighmtm1Che, C4−/−, and C3−/− mice; Mark Suter (University of Zurich, Zurich) for providing Aicda−/− mice; Marina Botto (Imperial College London, London) for providing C1q−/− and fB−/− mice; Craig Gerard (Harvard Medical School, Boston) for providing C3aR−/− mice; Falk Nimmerjahn (University Erlangen-Nuernberg, Erlangen) for providing Fcgr−/−Fcgr2b−/− mice; Karl Lang (University of Duisburg-Essen, Essen) for providing Fcmr−/− mice; Hans Hengartner and Rolf Zinkernagel (ETH Zurich, Zurich) for providing KL25 mice; Mark Zabel (University Hospital of Zurich, Zurich) for providing CR2−/− mice; Christie Ballantyne (Baylor College of Medicine, Houston) for providing CD11c−/− mice; and Siamon Gordon (University of Oxford, Oxford) for providing CD11b−/− mice. A.V. wishes to thank Michael Grünaug and dedicates this work to Annette, Rita, and Hans.\r\nThis project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. \r\n947611) (K.S.). This study was supported by the Deutsche Forschungsgemeinschaft through the collaborative research center 914 project B02 (K.S. and S.M.), project B04 (A.V.), project A01 (M.M.), project B01 (M.S.), the collaborative research center 1123 project B07 (K.S. and S.M.), the collaborative research center 359 (project A03 [K.S.] and B02 [M.S.]), the international research training group 1911 project B09 (A.V.), the clinical research unit 303 project 7 (A.V.), cluster of excellence 2167 (A.V.), collaborative research center 1526 project 05 (A.V.), the ANR-DFG project JAKPOT (K.S.), LMUexcellent (K.S.), and the Deutsche Zentrum für Herz-Kreislauf-Forschung (PostDoc Grant and partner site project [K.S. and S.M.]). M.I. is supported by the European Research Council (ERC) Advanced Grant 101141363, ERC Proof of Concept Grant 101138728, Italian Association for Cancer Research (AIRC) Grants 19891 and \r\n22737, Italian Ministry for University and Research Grants PE00000007 (INF-ACT) and PRIN \r\n2022FMESXL, Funded Research Agreement from Asher Biotherapeutics, VIR Biotechnology, and BlueJay Therapeutics. V.F. is supported by the Italian Ministry for University and Research Grants PE00000007 (INF-ACT) and Fondazione Prossimo Mio.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"journal_article","pmid":1,"file_date_updated":"2024-09-30T09:16:03Z","oa":1,"doi":"10.1016/j.immuni.2024.08.007","day":"10","quality_controlled":"1","date_published":"2024-09-10T00:00:00Z","intvolume":"        57","issue":"9","publisher":"Elsevier","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"MiSi"}],"citation":{"mla":"Stark, Konstantin, et al. “Antibodies and Complement Are Key Drivers of Thrombosis.” <i>Immunity</i>, vol. 57, no. 9, Elsevier, 2024, pp. 2140–56, doi:<a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">10.1016/j.immuni.2024.08.007</a>.","ista":"Stark K, Kilani B, Stockhausen S, Busse J, Schubert I, Tran TD, Gärtner FR, Leunig A, Pekayvaz K, Nicolai L, Fumagalli V, Stermann J, Stephan F, David C, Müller MB, Heyman B, Lux A, Da Palma Guerreiro A, Frenzel LP, Schmidt CQ, Dopler A, Moser M, Chandraratne S, Von Brühl ML, Lorenz M, Korff T, Rudelius M, Popp O, Kirchner M, Mertins P, Nimmerjahn F, Iannacone M, Sperandio M, Engelmann B, Verschoor A, Massberg S. 2024. Antibodies and complement are key drivers of thrombosis. Immunity. 57(9), 2140–2156.","ieee":"K. Stark <i>et al.</i>, “Antibodies and complement are key drivers of thrombosis,” <i>Immunity</i>, vol. 57, no. 9. Elsevier, pp. 2140–2156, 2024.","chicago":"Stark, Konstantin, Badr Kilani, Sven Stockhausen, Johanna Busse, Irene Schubert, Thuy Duong Tran, Florian R Gärtner, et al. “Antibodies and Complement Are Key Drivers of Thrombosis.” <i>Immunity</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">https://doi.org/10.1016/j.immuni.2024.08.007</a>.","apa":"Stark, K., Kilani, B., Stockhausen, S., Busse, J., Schubert, I., Tran, T. D., … Massberg, S. (2024). Antibodies and complement are key drivers of thrombosis. <i>Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">https://doi.org/10.1016/j.immuni.2024.08.007</a>","ama":"Stark K, Kilani B, Stockhausen S, et al. Antibodies and complement are key drivers of thrombosis. <i>Immunity</i>. 2024;57(9):2140-2156. doi:<a href=\"https://doi.org/10.1016/j.immuni.2024.08.007\">10.1016/j.immuni.2024.08.007</a>","short":"K. Stark, B. Kilani, S. Stockhausen, J. Busse, I. Schubert, T.D. Tran, F.R. Gärtner, A. Leunig, K. Pekayvaz, L. Nicolai, V. Fumagalli, J. Stermann, F. Stephan, C. David, M.B. Müller, B. Heyman, A. Lux, A. Da Palma Guerreiro, L.P. Frenzel, C.Q. Schmidt, A. Dopler, M. Moser, S. Chandraratne, M.L. Von Brühl, M. Lorenz, T. Korff, M. Rudelius, O. Popp, M. Kirchner, P. Mertins, F. Nimmerjahn, M. Iannacone, M. Sperandio, B. Engelmann, A. Verschoor, S. Massberg, Immunity 57 (2024) 2140–2156."},"publication_identifier":{"eissn":["1097-4180"]},"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-09-22T22:01:42Z","external_id":{"isi":["001317438500001"],"pmid":["39226900"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Venous thromboembolism (VTE) is a common, deadly disease with an increasing incidence despite preventive efforts. Clinical observations have associated elevated antibody concentrations or antibody-based therapies with thrombotic events. However, how antibodies contribute to thrombosis is unknown. Here, we show that reduced blood flow enabled immunoglobulin M (IgM) to bind to FcμR and the polymeric immunoglobulin receptor (pIgR), initiating endothelial activation and platelet recruitment. Subsequently, the procoagulant surface of activated platelets accommodated antigen- and FcγR-independent IgG deposition. This leads to classical complement activation, setting in motion a prothrombotic vicious circle. Key elements of this mechanism were present in humans in the setting of venous stasis as well as in the dysregulated immunothrombosis of COVID-19. This antibody-driven thrombosis can be prevented by pharmacologically targeting complement. Hence, our results uncover antibodies as previously unrecognized central regulators of thrombosis. These findings carry relevance for therapeutic application of antibodies and open innovative avenues to target thrombosis without compromising hemostasis."}],"page":"2140-2156","year":"2024","isi":1,"volume":57,"ddc":["570"],"publication_status":"published","date_updated":"2025-09-08T09:50:13Z","month":"09","author":[{"last_name":"Stark","full_name":"Stark, Konstantin","first_name":"Konstantin"},{"last_name":"Kilani","first_name":"Badr","full_name":"Kilani, Badr"},{"first_name":"Sven","full_name":"Stockhausen, Sven","last_name":"Stockhausen"},{"last_name":"Busse","first_name":"Johanna","full_name":"Busse, Johanna"},{"last_name":"Schubert","first_name":"Irene","full_name":"Schubert, Irene"},{"first_name":"Thuy Duong","full_name":"Tran, Thuy Duong","last_name":"Tran"},{"full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","first_name":"Florian R","last_name":"Gärtner","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Leunig","full_name":"Leunig, Alexander","first_name":"Alexander"},{"first_name":"Kami","full_name":"Pekayvaz, Kami","last_name":"Pekayvaz"},{"last_name":"Nicolai","full_name":"Nicolai, Leo","first_name":"Leo"},{"first_name":"Valeria","full_name":"Fumagalli, Valeria","last_name":"Fumagalli"},{"last_name":"Stermann","full_name":"Stermann, Julia","first_name":"Julia"},{"last_name":"Stephan","first_name":"Felix","full_name":"Stephan, Felix"},{"first_name":"Christian","full_name":"David, Christian","last_name":"David"},{"last_name":"Müller","first_name":"Martin B.","full_name":"Müller, Martin B."},{"full_name":"Heyman, Birgitta","first_name":"Birgitta","last_name":"Heyman"},{"last_name":"Lux","first_name":"Anja","full_name":"Lux, Anja"},{"last_name":"Da Palma Guerreiro","first_name":"Alexandra","full_name":"Da Palma Guerreiro, Alexandra"},{"last_name":"Frenzel","full_name":"Frenzel, Lukas P.","first_name":"Lukas P."},{"first_name":"Christoph Q.","full_name":"Schmidt, Christoph Q.","last_name":"Schmidt"},{"first_name":"Arthur","full_name":"Dopler, Arthur","last_name":"Dopler"},{"first_name":"Markus","full_name":"Moser, Markus","last_name":"Moser"},{"last_name":"Chandraratne","first_name":"Sue","full_name":"Chandraratne, Sue"},{"last_name":"Von Brühl","full_name":"Von Brühl, Marie Luise","first_name":"Marie Luise"},{"last_name":"Lorenz","first_name":"Michael","full_name":"Lorenz, Michael"},{"last_name":"Korff","first_name":"Thomas","full_name":"Korff, Thomas"},{"last_name":"Rudelius","first_name":"Martina","full_name":"Rudelius, Martina"},{"full_name":"Popp, Oliver","first_name":"Oliver","last_name":"Popp"},{"last_name":"Kirchner","first_name":"Marieluise","full_name":"Kirchner, Marieluise"},{"first_name":"Philipp","full_name":"Mertins, Philipp","last_name":"Mertins"},{"last_name":"Nimmerjahn","full_name":"Nimmerjahn, Falk","first_name":"Falk"},{"last_name":"Iannacone","first_name":"Matteo","full_name":"Iannacone, Matteo"},{"full_name":"Sperandio, Markus","first_name":"Markus","last_name":"Sperandio"},{"last_name":"Engelmann","full_name":"Engelmann, Bernd","first_name":"Bernd"},{"last_name":"Verschoor","full_name":"Verschoor, Admar","first_name":"Admar"},{"last_name":"Massberg","full_name":"Massberg, Steffen","first_name":"Steffen"}],"_id":"18109","publication":"Immunity","language":[{"iso":"eng"}],"article_type":"original","scopus_import":"1","file":[{"checksum":"4683de43d06a8fd8e3fc91af4ddc1ba2","file_size":6892750,"date_created":"2024-09-30T09:16:03Z","success":1,"date_updated":"2024-09-30T09:16:03Z","file_id":"18162","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2024_Immunity_Stark.pdf"}],"status":"public","title":"Antibodies and complement are key drivers of thrombosis"},{"oa":1,"doi":"10.1103/PhysRevB.110.L100304","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02102"}],"type":"journal_article","corr_author":"1","acknowledgement":"The authors acknowledge useful discussions with M. Serbyn, Z. Papic, and A. Nunnenkamp. ´\r\nP.B. is supported by the Erwin Schrödinger Center for Quantum Science & Technology (ESQ) of the Österreichische Akademie der Wissenschaften (ÖAW) under the Discovery Grant. M.L. acknowledges support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement\r\nNo. 850899). The numerical simulations were performed using the ITensor library [68] on the Vienna Scientific Cluster (VSC).","article_number":"L100304","publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_processing_charge":"No","department":[{"_id":"MaSe"}],"citation":{"ama":"Brighi P, Ljubotina M. Anomalous transport in the kinetically constrained quantum East-West model. <i>Physical Review B</i>. 2024;110(10). doi:<a href=\"https://doi.org/10.1103/PhysRevB.110.L100304\">10.1103/PhysRevB.110.L100304</a>","short":"P. Brighi, M. Ljubotina, Physical Review B 110 (2024).","mla":"Brighi, Pietro, and Marko Ljubotina. “Anomalous Transport in the Kinetically Constrained Quantum East-West Model.” <i>Physical Review B</i>, vol. 110, no. 10, L100304, American Physical Society, 2024, doi:<a href=\"https://doi.org/10.1103/PhysRevB.110.L100304\">10.1103/PhysRevB.110.L100304</a>.","ista":"Brighi P, Ljubotina M. 2024. Anomalous transport in the kinetically constrained quantum East-West model. Physical Review B. 110(10), L100304.","apa":"Brighi, P., &#38; Ljubotina, M. (2024). Anomalous transport in the kinetically constrained quantum East-West model. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.110.L100304\">https://doi.org/10.1103/PhysRevB.110.L100304</a>","chicago":"Brighi, Pietro, and Marko Ljubotina. “Anomalous Transport in the Kinetically Constrained Quantum East-West Model.” <i>Physical Review B</i>. American Physical Society, 2024. <a href=\"https://doi.org/10.1103/PhysRevB.110.L100304\">https://doi.org/10.1103/PhysRevB.110.L100304</a>.","ieee":"P. Brighi and M. Ljubotina, “Anomalous transport in the kinetically constrained quantum East-West model,” <i>Physical Review B</i>, vol. 110, no. 10. American Physical Society, 2024."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Physical Society","issue":"10","date_published":"2024-09-11T00:00:00Z","intvolume":"       110","arxiv":1,"day":"11","quality_controlled":"1","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","grant_number":"850899"}],"volume":110,"isi":1,"year":"2024","abstract":[{"text":"We study a chaotic particle-conserving kinetically constrained model, with a single parameter which allows us to break reflection symmetry. Through extensive numerical simulations we find that the domain wall state shows a variety of dynamical behaviors from localization all the way to ballistic transport, depending on the value of the reflection breaking parameter. Surprisingly, such anomalous behavior is not mirrored in infinite-temperature dynamics, which appear to scale diffusively, in line with expectations for generic interacting models. However, studying the particle density gradient, we show that the lack of reflection symmetry affects infinite-temperature dynamics, resulting in an asymmetric dynamical structure factor. This is in disagreement with normal diffusion and suggests that the model may also exhibit anomalous dynamics at infinite temperature in the thermodynamic limit. Finally, we observe low-entangled eigenstates in the spectrum of the model, a telltale sign of quantum many-body scars.","lang":"eng"}],"ec_funded":1,"oa_version":"Preprint","external_id":{"arxiv":["2405.02102"],"isi":["001361617100003"]},"date_created":"2024-09-22T22:01:42Z","article_type":"letter_note","title":"Anomalous transport in the kinetically constrained quantum East-West model","scopus_import":"1","status":"public","_id":"18110","publication":"Physical Review B","language":[{"iso":"eng"}],"author":[{"first_name":"Pietro","orcid":"0000-0002-7969-2729","full_name":"Brighi, Pietro","id":"4115AF5C-F248-11E8-B48F-1D18A9856A87","last_name":"Brighi"},{"first_name":"Marko","orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","last_name":"Ljubotina"}],"month":"09","date_updated":"2025-09-08T09:49:29Z","publication_status":"published"},{"title":"Tidal disruption events from stripped stars","scopus_import":"1","status":"public","file":[{"date_updated":"2024-09-30T08:54:26Z","success":1,"date_created":"2024-09-30T08:54:26Z","checksum":"050ddf873244839825714cca42b5d857","file_size":844227,"file_name":"2024_AstrophysicalJourn_Mockler.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18161","creator":"dernst"}],"article_type":"original","publication":"Astrophysical Journal Letters","language":[{"iso":"eng"}],"_id":"18111","month":"09","author":[{"full_name":"Mockler, Brenna","first_name":"Brenna","last_name":"Mockler"},{"first_name":"Monica","full_name":"Gallegos-Garcia, Monica","last_name":"Gallegos-Garcia"},{"orcid":"0000-0002-6960-6911","first_name":"Ylva Louise Linsdotter","full_name":"Götberg, Ylva Louise Linsdotter","last_name":"Götberg","id":"d0648d0c-0f64-11ee-a2e0-dd0faa2e4f7d"},{"full_name":"Miller, Jon M.","first_name":"Jon M.","last_name":"Miller"},{"last_name":"Ramirez-Ruiz","full_name":"Ramirez-Ruiz, Enrico","first_name":"Enrico"}],"date_updated":"2025-09-08T09:48:50Z","publication_status":"published","ddc":["520"],"isi":1,"volume":973,"year":"2024","abstract":[{"lang":"eng","text":"Observations of tidal disruption events (TDEs) show signs of nitrogen enrichment reminiscent of other astrophysical sources such as active galactic nuclei and star-forming galaxies. Given that TDEs probe the gas from a single star, it is possible to test whether the observed enrichment is consistent with expectations from the CNO cycle by looking at the observed nitrogen/carbon (N/C) abundance ratios. Given that ≈20% of solar-mass stars (and an even larger fraction of more massive stars) live in close binaries, it is worthwhile to also consider what TDEs from stars influenced by binary evolution would look like. We show here that TDEs from stars stripped of their hydrogen-rich (and nitrogen-poor) envelopes through previous binary-induced mass loss can produce much higher observable N/C enhancements than even TDEs from massive stars. Additionally, we predict that the time dependence of the N/C abundance ratio in the mass fallback rate of stripped stars will follow the inverse behavior of main-sequence stars, enabling a more accurate characterization of the disrupted star."}],"oa_version":"Published Version","date_created":"2024-09-22T22:01:42Z","external_id":{"isi":["001310592900001"]},"article_processing_charge":"Yes","publication_identifier":{"issn":["2041-8205"],"eissn":["2041-8213"]},"department":[{"_id":"YlGo"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Mockler, Brenna, et al. “Tidal Disruption Events from Stripped Stars.” <i>Astrophysical Journal Letters</i>, vol. 973, no. 1, L9, IOP Publishing, 2024, doi:<a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">10.3847/2041-8213/ad6c34</a>.","chicago":"Mockler, Brenna, Monica Gallegos-Garcia, Ylva Louise Linsdotter Götberg, Jon M. Miller, and Enrico Ramirez-Ruiz. “Tidal Disruption Events from Stripped Stars.” <i>Astrophysical Journal Letters</i>. IOP Publishing, 2024. <a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">https://doi.org/10.3847/2041-8213/ad6c34</a>.","apa":"Mockler, B., Gallegos-Garcia, M., Götberg, Y. L. L., Miller, J. M., &#38; Ramirez-Ruiz, E. (2024). Tidal disruption events from stripped stars. <i>Astrophysical Journal Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">https://doi.org/10.3847/2041-8213/ad6c34</a>","ieee":"B. Mockler, M. Gallegos-Garcia, Y. L. L. Götberg, J. M. Miller, and E. Ramirez-Ruiz, “Tidal disruption events from stripped stars,” <i>Astrophysical Journal Letters</i>, vol. 973, no. 1. IOP Publishing, 2024.","ista":"Mockler B, Gallegos-Garcia M, Götberg YLL, Miller JM, Ramirez-Ruiz E. 2024. Tidal disruption events from stripped stars. Astrophysical Journal Letters. 973(1), L9.","ama":"Mockler B, Gallegos-Garcia M, Götberg YLL, Miller JM, Ramirez-Ruiz E. Tidal disruption events from stripped stars. <i>Astrophysical Journal Letters</i>. 2024;973(1). doi:<a href=\"https://doi.org/10.3847/2041-8213/ad6c34\">10.3847/2041-8213/ad6c34</a>","short":"B. Mockler, M. Gallegos-Garcia, Y.L.L. Götberg, J.M. Miller, E. Ramirez-Ruiz, Astrophysical Journal Letters 973 (2024)."},"issue":"1","publisher":"IOP Publishing","intvolume":"       973","date_published":"2024-09-12T00:00:00Z","quality_controlled":"1","day":"12","DOAJ_listed":"1","doi":"10.3847/2041-8213/ad6c34","oa":1,"file_date_updated":"2024-09-30T08:54:26Z","type":"journal_article","article_number":"L9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","acknowledgement":"This work was performed in part at Aspen Center for Physics, which is supported by National Science Foundation grant PHY-2210452. We thank the participants and organizers of the summer Aspen 2023 workshop on “Stellar Interactions and the Transients They Cause” for fruitful discussions. B.M. is grateful for support from the Carnegie Theoretical Astrophysics\r\nCenter. M.G.-G. is grateful for the support from Northwestern University’s Presidential Fellowship. E.R.-R. thanks the Heising-Simons Foundation, NSF (AST-2150255 and AST2307710), Swift (80NSSC21K1409, 80NSSC19K1391), and Chandra (22-0142) for support. "},{"corr_author":"1","acknowledgement":"Authors would like to thank Ruslan Svirschevski for his help in solving technical issues with AQLM and baselines. We also thank Tim Dettmers for helpful discussions on the structure of weights in modern LLMs and size-accuracy trade-offs. The authors would also like to thank Daniil Pavlov for his assistance with CPU benchmarking. Finally, authors would like to thank the communities of ML enthusiasts known as LocalLLaMA5 and Petals community on discord6\r\nfor the crowd wisdom about running LLMs on consumer devices. Egiazarian Vage and Denis Kuznedelev and Andrei Panferov were supported by the grant for research centers in the field of AI provided by the Analytical Center for the Government of the Russian Federation (ACRF) in\r\naccordance with the agreement on the provision of subsidies (identifier of the agreement 000000D730321P5Q0002) and the agreement with HSE University No. 70-2021-00139.","oa":1,"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2401.06118"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","location":"Vienna, Austria","end_date":"2024-07-27"},"type":"conference","date_published":"2024-09-01T00:00:00Z","intvolume":"       235","arxiv":1,"day":"01","quality_controlled":"1","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"citation":{"mla":"Egiazarian, Vage, et al. “Extreme Compression of Large Language Models via Additive Quantization.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 12284–303.","ista":"Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A. 2024. Extreme compression of large language models via additive quantization. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 12284–12303.","chicago":"Egiazarian, Vage, Andrei Panferov, Denis Kuznedelev, Elias Frantar, Artem Babenko, and Dan-Adrian Alistarh. “Extreme Compression of Large Language Models via Additive Quantization.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:12284–303. ML Research Press, 2024.","ieee":"V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, and D.-A. Alistarh, “Extreme compression of large language models via additive quantization,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 12284–12303.","apa":"Egiazarian, V., Panferov, A., Kuznedelev, D., Frantar, E., Babenko, A., &#38; Alistarh, D.-A. (2024). Extreme compression of large language models via additive quantization. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 12284–12303). Vienna, Austria: ML Research Press.","ama":"Egiazarian V, Panferov A, Kuznedelev D, Frantar E, Babenko A, Alistarh D-A. Extreme compression of large language models via additive quantization. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:12284-12303.","short":"V. Egiazarian, A. Panferov, D. Kuznedelev, E. Frantar, A. Babenko, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 12284–12303."},"alternative_title":["PMLR"],"publisher":"ML Research Press","oa_version":"Preprint","external_id":{"arxiv":["2401.06118"]},"date_created":"2024-09-22T22:01:43Z","volume":235,"year":"2024","abstract":[{"text":"The emergence of accurate open large language models (LLMs) has led to a race towards performant quantization techniques which can enable their execution on end-user devices. In this paper, we revisit the problem of “extreme” LLM compression—defined as targeting extremely low bit counts, such as 2 to 3 bits per parameter—from the point of view of classic methods in Multi-Codebook Quantization (MCQ). Our algorithm, called AQLM, generalizes the classic Additive Quantization (AQ) approach for information retrieval to advance the state-of-the-art in LLM compression, via two innovations: 1) learned additive quantization of weight matrices in input-adaptive fashion, and 2) joint optimization of codebook parameters across each transformer blocks. Broadly, AQLM is the first scheme that is Pareto optimal in terms of accuracy-vs-model-size when compressing to less than 3 bits per parameter, and significantly improves upon all known schemes in the extreme compression (2bit) regime. In addition, AQLM is practical: we provide fast GPU and CPU implementations of AQLM for token generation, which enable us to match or outperform optimized FP16 implementations for speed, while executing in a much smaller memory footprint.","lang":"eng"}],"page":"12284-12303","month":"09","author":[{"last_name":"Egiazarian","full_name":"Egiazarian, Vage","first_name":"Vage"},{"id":"2c18daae-4dbe-11ef-8491-98ce2d960f09","last_name":"Panferov","full_name":"Panferov, Andrei","first_name":"Andrei"},{"full_name":"Kuznedelev, Denis","first_name":"Denis","last_name":"Kuznedelev"},{"last_name":"Frantar","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","full_name":"Frantar, Elias","first_name":"Elias"},{"last_name":"Babenko","first_name":"Artem","full_name":"Babenko, Artem"},{"orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-10-01T08:13:05Z","publication_status":"published","title":"Extreme compression of large language models via additive quantization","scopus_import":"1","status":"public","_id":"18113","publication":"Proceedings of the 41st International Conference on Machine Learning","language":[{"iso":"eng"}]},{"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2402.13077"}],"conference":{"location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21"},"type":"conference","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","publisher":"ML Research Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"A.A. Pervez, F. Locatello, E. Gavves, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 40484–40501.","ama":"Pervez AA, Locatello F, Gavves E. Mechanistic neural networks for scientific machine learning. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:40484-40501.","apa":"Pervez, A. A., Locatello, F., &#38; Gavves, E. (2024). Mechanistic neural networks for scientific machine learning. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 40484–40501). Vienna, Austria: ML Research Press.","chicago":"Pervez, Adeel A, Francesco Locatello, and Efstratios Gavves. “Mechanistic Neural Networks for Scientific Machine Learning.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:40484–501. ML Research Press, 2024.","ieee":"A. A. Pervez, F. Locatello, and E. Gavves, “Mechanistic neural networks for scientific machine learning,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 40484–40501.","ista":"Pervez AA, Locatello F, Gavves E. 2024. Mechanistic neural networks for scientific machine learning. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 40484–40501.","mla":"Pervez, Adeel A., et al. “Mechanistic Neural Networks for Scientific Machine Learning.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 40484–501."},"department":[{"_id":"FrLo"}],"alternative_title":["PMLR"],"date_published":"2024-09-01T00:00:00Z","intvolume":"       235","arxiv":1,"day":"01","quality_controlled":"1","year":"2024","volume":235,"abstract":[{"lang":"eng","text":"This paper presents Mechanistic Neural Networks, a neural network design for machine learning applications in the sciences. It incorporates a new Mechanistic Block in standard architectures to explicitly learn governing differential equations as representations, revealing the underlying dynamics of data and enhancing interpretability and efficiency in data modeling. Central to our approach is a novel Relaxed Linear Programming Solver (NeuRLP) inspired by a technique that reduces solving linear ODEs to solving linear programs. This integrates well with neural networks and surpasses the limitations of traditional ODE solvers enabling scalable GPU parallel processing. Overall, Mechanistic Neural Networks demonstrate their versatility for scientific machine learning applications, adeptly managing tasks from equation discovery to dynamic systems modeling. We prove their comprehensive capabilities in analyzing and interpreting complex scientific data across various applications, showing significant performance against specialized state-of-the-art methods. Source code is available at https://github.com/alpz/mech-nn."}],"page":"40484-40501","oa_version":"Published Version","related_material":{"link":[{"url":"https://github.com/alpz/mech-nn","relation":"software"}]},"date_created":"2024-09-22T22:01:43Z","external_id":{"arxiv":["2402.13077"]},"scopus_import":"1","status":"public","title":"Mechanistic neural networks for scientific machine learning","_id":"18114","language":[{"iso":"eng"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","month":"09","author":[{"first_name":"Adeel A","full_name":"Pervez, Adeel A","last_name":"Pervez","id":"fca6d90c-d47f-11ee-bc87-93ff51604981"},{"full_name":"Locatello, Francesco","orcid":"0000-0002-4850-0683","first_name":"Francesco","last_name":"Locatello","id":"26cfd52f-2483-11ee-8040-88983bcc06d4"},{"last_name":"Gavves","full_name":"Gavves, Efstratios","first_name":"Efstratios"}],"publication_status":"published","date_updated":"2024-10-01T08:01:17Z"},{"author":[{"full_name":"Axiotis, Kyriakos","first_name":"Kyriakos","last_name":"Axiotis"},{"first_name":"Vincent","full_name":"Cohen-Addad, Vincent","last_name":"Cohen-Addad"},{"last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H"},{"full_name":"Jerome, Sammy","first_name":"Sammy","last_name":"Jerome"},{"full_name":"Mirrokni, Vahab","first_name":"Vahab","last_name":"Mirrokni"},{"id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","first_name":"David","full_name":"Saulpic, David"},{"full_name":"Woodruff, David P.","first_name":"David P.","last_name":"Woodruff"},{"first_name":"Michael","full_name":"Wunder, Michael","last_name":"Wunder"}],"month":"09","date_updated":"2025-04-14T13:50:50Z","publication_status":"published","title":"Data-efficient learning via clustering-based sensitivity sampling: Foundation models and beyond","scopus_import":"1","status":"public","_id":"18115","language":[{"iso":"eng"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","oa_version":"Published Version","external_id":{"arxiv":["2402.17327"]},"date_created":"2024-09-22T22:01:44Z","volume":235,"project":[{"grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures"},{"grant_number":"Z00422","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms"},{"name":"Static and Dynamic Hierarchical Graph Decompositions","_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","grant_number":"I05982"},{"grant_number":"P33775","name":"Fast Algorithms for a Reactive Network Layer","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program"}],"year":"2024","abstract":[{"text":"We study the data selection problem, whose aim is to select a small representative subset of data that can be used to efficiently train a machine learning model. We present a new data selection approach based on k-means clustering and sensitivity sampling. Assuming access to an embedding representation of the data with respect to which the model loss is Holder continuous, our approach provably allows selecting a set of “typical” k+1/ε2 elements whose average loss corresponds to the average loss of the whole dataset, up to a multiplicative (1±ε)\r\n factor and an additive ελΦk, where Φk represents the k-means cost for the input embeddings and λ is the Holder constant. We furthermore demonstrate the performance and scalability of our approach on fine-tuning foundation models and show that it outperforms state-of-the-art methods. We also show how it can be applied on linear regression, leading to a new sampling strategy that surprisingly matches the performance of leverage score sampling, while being conceptually simpler and more scalable.","lang":"eng"}],"ec_funded":1,"page":"2086-2107","date_published":"2024-09-01T00:00:00Z","intvolume":"       235","arxiv":1,"day":"01","quality_controlled":"1","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MoHe"}],"citation":{"short":"K. Axiotis, V. Cohen-Addad, M. Henzinger, S. Jerome, V. Mirrokni, D. Saulpic, D.P. Woodruff, M. Wunder, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 2086–2107.","ama":"Axiotis K, Cohen-Addad V, Henzinger M, et al. Data-efficient learning via clustering-based sensitivity sampling: Foundation models and beyond. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:2086-2107.","ista":"Axiotis K, Cohen-Addad V, Henzinger M, Jerome S, Mirrokni V, Saulpic D, Woodruff DP, Wunder M. 2024. Data-efficient learning via clustering-based sensitivity sampling: Foundation models and beyond. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 2086–2107.","apa":"Axiotis, K., Cohen-Addad, V., Henzinger, M., Jerome, S., Mirrokni, V., Saulpic, D., … Wunder, M. (2024). Data-efficient learning via clustering-based sensitivity sampling: Foundation models and beyond. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 2086–2107). Vienna, Austria: ML Research Press.","chicago":"Axiotis, Kyriakos, Vincent Cohen-Addad, Monika Henzinger, Sammy Jerome, Vahab Mirrokni, David Saulpic, David P. Woodruff, and Michael Wunder. “Data-Efficient Learning via Clustering-Based Sensitivity Sampling: Foundation Models and Beyond.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:2086–2107. ML Research Press, 2024.","ieee":"K. Axiotis <i>et al.</i>, “Data-efficient learning via clustering-based sensitivity sampling: Foundation models and beyond,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 2086–2107.","mla":"Axiotis, Kyriakos, et al. “Data-Efficient Learning via Clustering-Based Sensitivity Sampling: Foundation Models and Beyond.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 2086–107."},"alternative_title":["PMLR"],"publisher":"ML Research Press","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council (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. This work was partially done while David Saulpic was at the Institute for Science and Technology, Austria (ISTA). David Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the\r\nMarie Sklodowska-Curie grant agreement No 101034413. Work was done while David Woodruff was visiting Google Research.","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2402.17327"}],"conference":{"start_date":"2024-07-21","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27","location":"Vienna, Austria"},"type":"conference"},{"oa_version":"Published Version","external_id":{"arxiv":["2406.11649"]},"date_created":"2024-09-22T22:01:44Z","year":"2024","volume":235,"project":[{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","grant_number":"101019564"},{"_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"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"},{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"abstract":[{"text":"As a staple of data analysis and unsupervised learning, the problem of private clustering has been widely studied, under various privacy models. Centralized differential privacy is the first of them, and the problem has also been studied for the local and the shuffle variation. In each case, the goal is to design an algorithm that computes privately a clustering, with the smallest possible error. The study of each variation gave rise to new algorithm: the landscape of private clustering algorithm is therefore quite intricate. In this paper, we show that a 20 year-old algorithm can be slightly modified to work for any of those models. This provides a unified picture: while matching almost all previously known results, it allows us to improve some of them, and extend to a new privacy model, the continual observation setting, where the input is changing over time and the algorithm must output a new solution at each time step.","lang":"eng"}],"ec_funded":1,"page":"12046-12086","month":"09","author":[{"last_name":"La Tour","first_name":"Max Dupré","full_name":"La Tour, Max Dupré"},{"orcid":"0000-0002-5008-6530","first_name":"Monika H","full_name":"Henzinger, Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"last_name":"Saulpic","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","first_name":"David","full_name":"Saulpic, David"}],"publication_status":"published","date_updated":"2025-04-14T13:50:50Z","status":"public","scopus_import":"1","title":"Making old things new: A unified algorithm for differentially private clustering","_id":"18116","publication":"Proceedings of the 41st International Conference on Machine Learning","language":[{"iso":"eng"}],"corr_author":"1","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council (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.This work was partially done while David Saulpic was at the Institute for Science and Technology, Austria (ISTA). David Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 101034413.","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2406.11649","open_access":"1"}],"conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21","location":"Vienna, Austria","end_date":"2024-07-27"},"type":"conference","date_published":"2024-09-01T00:00:00Z","intvolume":"       235","day":"01","arxiv":1,"quality_controlled":"1","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","publisher":"ML Research Press","alternative_title":["PMLR"],"citation":{"mla":"La Tour, Max Dupré, et al. “Making Old Things New: A Unified Algorithm for Differentially Private Clustering.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 12046–86.","ista":"La Tour MD, Henzinger M, Saulpic D. 2024. Making old things new: A unified algorithm for differentially private clustering. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 12046–12086.","apa":"La Tour, M. D., Henzinger, M., &#38; Saulpic, D. (2024). Making old things new: A unified algorithm for differentially private clustering. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 12046–12086). Vienna, Austria: ML Research Press.","chicago":"La Tour, Max Dupré, Monika Henzinger, and David Saulpic. “Making Old Things New: A Unified Algorithm for Differentially Private Clustering.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:12046–86. ML Research Press, 2024.","ieee":"M. D. La Tour, M. Henzinger, and D. Saulpic, “Making old things new: A unified algorithm for differentially private clustering,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 12046–12086.","ama":"La Tour MD, Henzinger M, Saulpic D. Making old things new: A unified algorithm for differentially private clustering. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:12046-12086.","short":"M.D. La Tour, M. Henzinger, D. Saulpic, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 12046–12086."},"department":[{"_id":"MoHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"_id":"18117","language":[{"iso":"eng"}],"publication":"Proceedings of the 41st International Conference on Machine Learning","title":"RoSA: Accurate parameter-efficient fine-tuning via robust adaptation","status":"public","scopus_import":"1","date_updated":"2024-10-01T08:22:01Z","publication_status":"published","author":[{"first_name":"Mahdi","full_name":"Nikdan, Mahdi","last_name":"Nikdan","id":"66374281-f394-11eb-9cf6-869147deecc0"},{"first_name":"Soroush","orcid":"0009-0003-4119-6281","full_name":"Tabesh, Soroush","id":"06000900-6068-11ef-8d61-c2472ef2e752","last_name":"Tabesh"},{"id":"41888001-440d-11ef-8299-d0e838b8185e","last_name":"Crncevic","full_name":"Crncevic, Elvir","first_name":"Elvir"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh"}],"month":"09","abstract":[{"text":"We investigate parameter-efficient fine-tuning (PEFT) methods that can provide good accuracy under limited computational and memory budgets in the context of large language models (LLMs). We present a new PEFT method called Robust Adaptation (RoSA) inspired by robust principal component analysis that jointly trains low-rank\r\n and highly-sparse components on top of a set of fixed pretrained weights to efficiently approximate the performance of a full-fine-tuning (FFT) solution. Across a series of challenging generative tasks such as grade-school math and SQL query generation, which require fine-tuning for good performance, we show that RoSA outperforms LoRA, pure sparse fine-tuning, and alternative hybrid methods at the same parameter budget, and can even recover the performance of FFT on some tasks. We provide system support for RoSA to complement the training algorithm, specifically in the form of sparse GPU kernels which enable memory- and computationally-efficient training, and show that it is also compatible with low-precision base weights, resulting in the first joint representation combining quantization, low-rank and sparse approximations. Our code is available at https://github.com/IST-DASLab/RoSA.","lang":"eng"}],"page":"38187-38206","volume":235,"year":"2024","related_material":{"link":[{"url":"https://github.com/IST-DASLab/RoSA","relation":"software"}]},"date_created":"2024-09-22T22:01:44Z","external_id":{"arxiv":["2401.04679"]},"oa_version":"Preprint","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"citation":{"short":"M. Nikdan, S. Tabesh, E. Crncevic, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 38187–38206.","ama":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:38187-38206.","ieee":"M. Nikdan, S. Tabesh, E. Crncevic, and D.-A. Alistarh, “RoSA: Accurate parameter-efficient fine-tuning via robust adaptation,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 38187–38206.","chicago":"Nikdan, Mahdi, Soroush Tabesh, Elvir Crncevic, and Dan-Adrian Alistarh. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:38187–206. ML Research Press, 2024.","apa":"Nikdan, M., Tabesh, S., Crncevic, E., &#38; Alistarh, D.-A. (2024). RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 38187–38206). Vienna, Austria: ML Research Press.","ista":"Nikdan M, Tabesh S, Crncevic E, Alistarh D-A. 2024. RoSA: Accurate parameter-efficient fine-tuning via robust adaptation. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning vol. 235, 38187–38206.","mla":"Nikdan, Mahdi, et al. “RoSA: Accurate Parameter-Efficient Fine-Tuning via Robust Adaptation.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 38187–206."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ML Research Press","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","arxiv":1,"day":"01","quality_controlled":"1","date_published":"2024-09-01T00:00:00Z","intvolume":"       235","conference":{"start_date":"2024-07-21","name":"ICML: International Conference on Machine Learning","end_date":"2024-07-27","location":"Vienna, Austria"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2401.04679"}],"type":"conference","oa":1,"acknowledgement":"The authors would like to thank Eldar Kurtic for experimental support and useful suggestions throughout the project","corr_author":"1"},{"day":"01","arxiv":1,"quality_controlled":"1","date_published":"2024-09-01T00:00:00Z","intvolume":"       235","alternative_title":["PMLR"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"citation":{"short":"H. Zakerinia, A. Behjati, C. Lampert, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 58122–58139.","ama":"Zakerinia H, Behjati A, Lampert C. More flexible PAC-Bayesian meta-learning by learning learning algorithms. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:58122-58139.","apa":"Zakerinia, H., Behjati, A., &#38; Lampert, C. (2024). More flexible PAC-Bayesian meta-learning by learning learning algorithms. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 58122–58139). Vienna, Austria: ML Research Press.","chicago":"Zakerinia, Hossein, Amin Behjati, and Christoph Lampert. “More Flexible PAC-Bayesian Meta-Learning by Learning Learning Algorithms.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:58122–39. ML Research Press, 2024.","ieee":"H. Zakerinia, A. Behjati, and C. Lampert, “More flexible PAC-Bayesian meta-learning by learning learning algorithms,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 58122–58139.","ista":"Zakerinia H, Behjati A, Lampert C. 2024. More flexible PAC-Bayesian meta-learning by learning learning algorithms. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 58122–58139.","mla":"Zakerinia, Hossein, et al. “More Flexible PAC-Bayesian Meta-Learning by Learning Learning Algorithms.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 58122–39."},"publisher":"ML Research Press","publication_identifier":{"eissn":["2640-3498"]},"article_processing_charge":"No","corr_author":"1","conference":{"location":"Vienna, Austria","end_date":"2024-07-27","name":"ICML: International Conference on Machine Learning","start_date":"2024-07-21"},"main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2402.04054"}],"type":"conference","oa":1,"date_updated":"2024-10-01T09:30:03Z","publication_status":"published","month":"09","author":[{"id":"653bd8b6-f394-11eb-9cf6-c0bbf6cd78d4","last_name":"Zakerinia","full_name":"Zakerinia, Hossein","first_name":"Hossein"},{"first_name":"Amin","full_name":"Behjati, Amin","last_name":"Behjati"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"_id":"18118","publication":"Proceedings of the 41st International Conference on Machine Learning","language":[{"iso":"eng"}],"title":"More flexible PAC-Bayesian meta-learning by learning learning algorithms","scopus_import":"1","status":"public","external_id":{"arxiv":["2402.04054"]},"date_created":"2024-09-22T22:01:45Z","oa_version":"Published Version","abstract":[{"text":"We introduce a new framework for studying meta-learning methods using PAC-Bayesian theory. Its main advantage over previous work is that it allows for more flexibility in how the transfer of knowledge between tasks is realized. For previous approaches, this could only happen indirectly, by means of learning prior distributions over models. In contrast, the new generalization bounds that we prove express the process of meta-learning much more directly as learning the learning algorithm that should be used for future tasks. The flexibility of our framework makes it suitable to analyze a wide range of meta-learning mechanisms and even design new mechanisms. Other than our theoretical contributions we also show empirically that our framework improves the prediction quality in practical meta-learning mechanisms.","lang":"eng"}],"page":"58122-58139","volume":235,"year":"2024"},{"intvolume":"        15","date_published":"2024-07-02T00:00:00Z","quality_controlled":"1","day":"02","article_processing_charge":"Yes","publication_identifier":{"issn":["2041-1723"]},"publisher":"Springer Nature","citation":{"short":"M.A. Hajnal, D. Tran, Z. Szabó, A. Albert, K. Safaryan, M. Einstein, M. Vallejo Martelo, P.-O. Polack, P. Golshani, G. Orbán, Nature Communications 15 (2024).","ama":"Hajnal MA, Tran D, Szabó Z, et al. Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex in mice during decision making. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-024-49845-2\">10.1038/s41467-024-49845-2</a>","chicago":"Hajnal, Márton Albert, Duy Tran, Zsombor Szabó, Andrea Albert, Karen Safaryan, Michael Einstein, Mauricio Vallejo Martelo, Pierre-Olivier Polack, Peyman Golshani, and Gergő Orbán. “Shifts in Attention Drive Context-Dependent Subspace Encoding in Anterior Cingulate Cortex in Mice during Decision Making.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-024-49845-2\">https://doi.org/10.1038/s41467-024-49845-2</a>.","ieee":"M. A. Hajnal <i>et al.</i>, “Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex in mice during decision making,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","apa":"Hajnal, M. A., Tran, D., Szabó, Z., Albert, A., Safaryan, K., Einstein, M., … Orbán, G. (2024). Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex in mice during decision making. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-49845-2\">https://doi.org/10.1038/s41467-024-49845-2</a>","ista":"Hajnal MA, Tran D, Szabó Z, Albert A, Safaryan K, Einstein M, Vallejo Martelo M, Polack P-O, Golshani P, Orbán G. 2024. Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex in mice during decision making. Nature Communications. 15, 5559.","mla":"Hajnal, Márton Albert, et al. “Shifts in Attention Drive Context-Dependent Subspace Encoding in Anterior Cingulate Cortex in Mice during Decision Making.” <i>Nature Communications</i>, vol. 15, 5559, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-024-49845-2\">10.1038/s41467-024-49845-2</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"5559","has_accepted_license":"1","doi":"10.1038/s41467-024-49845-2","oa":1,"type":"journal_article","pmid":1,"file_date_updated":"2024-10-01T07:13:36Z","month":"07","author":[{"last_name":"Hajnal","full_name":"Hajnal, Márton Albert","first_name":"Márton Albert"},{"last_name":"Tran","first_name":"Duy","full_name":"Tran, Duy"},{"full_name":"Szabó, Zsombor","first_name":"Zsombor","orcid":"0009-0003-8524-4994","id":"47757b1e-3f56-11ef-9908-8ddefb4d05eb","last_name":"Szabó"},{"first_name":"Andrea","full_name":"Albert, Andrea","last_name":"Albert"},{"full_name":"Safaryan, Karen","first_name":"Karen","last_name":"Safaryan"},{"full_name":"Einstein, Michael","first_name":"Michael","last_name":"Einstein"},{"first_name":"Mauricio","full_name":"Vallejo Martelo, Mauricio","last_name":"Vallejo Martelo"},{"last_name":"Polack","first_name":"Pierre-Olivier","full_name":"Polack, Pierre-Olivier"},{"last_name":"Golshani","first_name":"Peyman","full_name":"Golshani, Peyman"},{"last_name":"Orbán","first_name":"Gergő","full_name":"Orbán, Gergő"}],"publication_status":"published","date_updated":"2024-10-01T07:14:56Z","ddc":["570"],"status":"public","scopus_import":"1","file":[{"file_size":4346510,"checksum":"22caa17a6691884c66c650c61227e903","date_created":"2024-10-01T07:13:36Z","success":1,"date_updated":"2024-10-01T07:13:36Z","creator":"dernst","file_id":"18163","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2024_NatureComm_Hajnal.pdf"}],"title":"Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex in mice during decision making","extern":"1","article_type":"original","language":[{"iso":"eng"}],"publication":"Nature Communications","_id":"18153","oa_version":"Published Version","external_id":{"pmid":["37873364"]},"date_created":"2024-09-28T06:59:03Z","year":"2024","volume":15,"abstract":[{"text":"Attention supports decision making by selecting the features that are relevant for decisions. Selective enhancement of the relevant features and inhibition of distractors has been proposed as potential neural mechanisms driving this selection process. Yet, how attention operates when relevance cannot be directly determined, and the attention signal needs to be internally constructed is less understood. Here we recorded from populations of neurons in the anterior cingulate cortex (ACC) of mice in an attention-shifting task where relevance of stimulus modalities changed across blocks of trials. In contrast with V1 recordings, decoding of the irrelevant modality gradually declined in ACC after an initial transient. Our analytical proof and a recurrent neural network model of the task revealed mutually inhibiting connections that produced context-gated suppression as observed in mice. Using this RNN model we predicted a correlation between contextual modulation of individual neurons and their stimulus drive, which we confirmed in ACC but not in V1.","lang":"eng"}]},{"acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) and the Hong Kong Research Grants Council ECS Project Number 26208122.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","conference":{"name":"FM: Formal Methods","start_date":"2024-09-09","location":"Milan, Italy","end_date":"2024-09-13"},"type":"conference","file_date_updated":"2024-10-01T09:56:54Z","oa":1,"doi":"10.1007/978-3-031-71162-6_31","day":"11","arxiv":1,"quality_controlled":"1","date_published":"2024-09-11T00:00:00Z","intvolume":"     14933","publisher":"Springer Nature","alternative_title":["LNCS"],"department":[{"_id":"KrCh"}],"citation":{"mla":"Chatterjee, Krishnendu, et al. “Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs.” <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, vol. 14933, Springer Nature, 2024, pp. 600–19, doi:<a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">10.1007/978-3-031-71162-6_31</a>.","ieee":"K. Chatterjee, A. K. Goharshady, E. Goharshady, M. Karrabi, and D. Zikelic, “Sound and complete witnesses for template-based verification of LTL properties on polynomial programs,” in <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, Milan, Italy, 2024, vol. 14933, pp. 600–619.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Ehsan Goharshady, Mehrdad Karrabi, and Dorde Zikelic. “Sound and Complete Witnesses for Template-Based Verification of LTL Properties on Polynomial Programs.” In <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>, 14933:600–619. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">https://doi.org/10.1007/978-3-031-71162-6_31</a>.","apa":"Chatterjee, K., Goharshady, A. K., Goharshady, E., Karrabi, M., &#38; Zikelic, D. (2024). Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. In <i>Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i> (Vol. 14933, pp. 600–619). Milan, Italy: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">https://doi.org/10.1007/978-3-031-71162-6_31</a>","ista":"Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. 2024. Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). FM: Formal Methods, LNCS, vol. 14933, 600–619.","ama":"Chatterjee K, Goharshady AK, Goharshady E, Karrabi M, Zikelic D. Sound and complete witnesses for template-based verification of LTL properties on polynomial programs. In: <i>Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)</i>. Vol 14933. Springer Nature; 2024:600-619. doi:<a href=\"https://doi.org/10.1007/978-3-031-71162-6_31\">10.1007/978-3-031-71162-6_31</a>","short":"K. Chatterjee, A.K. Goharshady, E. Goharshady, M. Karrabi, D. Zikelic, in:, Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer Nature, 2024, pp. 600–619."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031711619"]},"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-09-29T22:01:37Z","external_id":{"isi":["001336893300031"],"arxiv":["2403.05386"]},"oa_version":"Published Version","abstract":[{"text":"We study the classical problem of verifying programs with respect to formal specifications given in the linear temporal logic (LTL). We first present novel sound and complete witnesses for LTL verification over imperative programs. Our witnesses are applicable to both verification (proving) and refutation (finding bugs) settings. We then consider LTL formulas in which atomic propositions can be polynomial constraints and turn our focus to polynomial arithmetic programs, i.e. programs in which every assignment and guard consists only of polynomial expressions. For this setting, we provide an efficient algorithm to automatically synthesize such LTL witnesses. Our synthesis procedure is both sound and semi-complete. Finally, we present experimental results demonstrating the effectiveness of our approach and that it can handle programs which were beyond the reach of previous state-of-the-art tools.","lang":"eng"}],"ec_funded":1,"page":"600-619","year":"2024","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"volume":14933,"isi":1,"ddc":["000"],"publication_status":"published","date_updated":"2025-09-08T09:51:34Z","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"},{"first_name":"Ehsan","full_name":"Goharshady, Ehsan","last_name":"Goharshady"},{"first_name":"Mehrdad","full_name":"Karrabi, Mehrdad","id":"67638922-f394-11eb-9cf6-f20423e08757","last_name":"Karrabi"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"month":"09","_id":"18155","language":[{"iso":"eng"}],"publication":"Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)","file":[{"date_updated":"2024-10-01T09:56:54Z","success":1,"date_created":"2024-10-01T09:56:54Z","file_size":650495,"checksum":"223845be9e754681ee218866827c95e7","file_name":"2024_LNCS_Chatterjee.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18165","creator":"dernst"}],"status":"public","scopus_import":"1","title":"Sound and complete witnesses for template-based verification of LTL properties on polynomial programs"},{"publication_identifier":{"isbn":["9783959773485"],"issn":["1868-8969"]},"article_processing_charge":"No","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["LIPIcs"],"citation":{"ama":"Henzinger M, Sricharan AR, Steiner TA. Private counting of distinct elements in the turnstile model and extensions. In: <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>. Vol 317. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>","short":"M. Henzinger, A.R. Sricharan, T.A. Steiner, in:, International Conference on Approximation Algorithms for Combinatorial Optimization Problems , Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Henzinger, Monika, et al. “Private Counting of Distinct Elements in the Turnstile Model and Extensions.” <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>, vol. 317, 40, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>.","ieee":"M. Henzinger, A. R. Sricharan, and T. A. Steiner, “Private counting of distinct elements in the turnstile model and extensions,” in <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>, London, United Kingdom, 2024, vol. 317.","chicago":"Henzinger, Monika, A. R. Sricharan, and Teresa Anna Steiner. “Private Counting of Distinct Elements in the Turnstile Model and Extensions.” In <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i>, Vol. 317. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>.","apa":"Henzinger, M., Sricharan, A. R., &#38; Steiner, T. A. (2024). Private counting of distinct elements in the turnstile model and extensions. In <i>International Conference on Approximation Algorithms for Combinatorial Optimization Problems </i> (Vol. 317). London, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40\">https://doi.org/10.4230/LIPIcs.APPROX/RANDOM.2024.40</a>","ista":"Henzinger M, Sricharan AR, Steiner TA. 2024. Private counting of distinct elements in the turnstile model and extensions. International Conference on Approximation Algorithms for Combinatorial Optimization Problems . APPROX: Conference on Approximation Algorithms for Combinatorial Optimization Problems, LIPIcs, vol. 317, 40."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MoHe"}],"date_published":"2024-09-16T00:00:00Z","intvolume":"       317","arxiv":1,"day":"16","quality_controlled":"1","oa":1,"doi":"10.4230/LIPIcs.APPROX/RANDOM.2024.40","conference":{"name":"APPROX: Conference on Approximation Algorithms for Combinatorial Optimization Problems","start_date":"2024-08-27","location":"London, United Kingdom","end_date":"2024-08-30"},"type":"conference","file_date_updated":"2024-10-01T10:07:14Z","corr_author":"1","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (MoDynStruct,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\nTeresa Anna Steiner: Supported by a research grant (VIL51463) from VILLUM FONDEN.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"40","file":[{"file_name":"2024_LIPICs_HenzingerM.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"18166","date_updated":"2024-10-01T10:07:14Z","success":1,"date_created":"2024-10-01T10:07:14Z","checksum":"c08b41c896e4d8c69570044808b40e0b","file_size":973917}],"status":"public","scopus_import":"1","title":"Private counting of distinct elements in the turnstile model and extensions","_id":"18156","language":[{"iso":"eng"}],"publication":"International Conference on Approximation Algorithms for Combinatorial Optimization Problems ","month":"09","author":[{"first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger"},{"last_name":"Sricharan","full_name":"Sricharan, A. R.","first_name":"A. R."},{"last_name":"Steiner","full_name":"Steiner, Teresa Anna","first_name":"Teresa Anna"}],"ddc":["000"],"publication_status":"published","date_updated":"2025-12-02T13:47:16Z","year":"2024","isi":1,"volume":317,"project":[{"name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"name":"Efficient algorithms","_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"},{"_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Privately counting distinct elements in a stream is a fundamental data analysis problem with many applications in machine learning. In the turnstile model, Jain et al. [NeurIPS2023] initiated the study of this problem parameterized by the maximum flippancy of any element, i.e., the number of times that the count of an element changes from 0 to above 0 or vice versa. They give an item-level (ε,δ)-differentially private algorithm whose additive error is tight with respect to that parameterization. In this work, we show that a very simple algorithm based on the sparse vector technique achieves a tight additive error for item-level (ε,δ)-differential privacy and item-level ε-differential privacy with regards to a different parameterization, namely the sum of all flippancies. Our second result is a bound which shows that for a large class of algorithms, including all existing differentially private algorithms for this problem, the lower bound from item-level differential privacy extends to event-level differential privacy. This partially answers an open question by Jain et al. [NeurIPS2023]."}],"oa_version":"Published Version","external_id":{"isi":["001545634500040"],"arxiv":["2408.11637"]},"date_created":"2024-09-29T22:01:38Z"},{"department":[{"_id":"JaMa"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","citation":{"mla":"Dello Schiavo, Lorenzo, et al. “Wasserstein Geometry and Ricci Curvature Bounds for Poisson Spaces.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 11, Ecole Polytechnique, 2024, pp. 957–1010, doi:<a href=\"https://doi.org/10.5802/jep.270\">10.5802/jep.270</a>.","chicago":"Dello Schiavo, Lorenzo, Ronan Herry, and Kohei Suzuki. “Wasserstein Geometry and Ricci Curvature Bounds for Poisson Spaces.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2024. <a href=\"https://doi.org/10.5802/jep.270\">https://doi.org/10.5802/jep.270</a>.","apa":"Dello Schiavo, L., Herry, R., &#38; Suzuki, K. (2024). Wasserstein geometry and Ricci curvature bounds for Poisson spaces. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.270\">https://doi.org/10.5802/jep.270</a>","ieee":"L. Dello Schiavo, R. Herry, and K. Suzuki, “Wasserstein geometry and Ricci curvature bounds for Poisson spaces,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 11. Ecole Polytechnique, pp. 957–1010, 2024.","ista":"Dello Schiavo L, Herry R, Suzuki K. 2024. Wasserstein geometry and Ricci curvature bounds for Poisson spaces. Journal de l’Ecole Polytechnique - Mathematiques. 11, 957–1010.","ama":"Dello Schiavo L, Herry R, Suzuki K. Wasserstein geometry and Ricci curvature bounds for Poisson spaces. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2024;11:957-1010. doi:<a href=\"https://doi.org/10.5802/jep.270\">10.5802/jep.270</a>","short":"L. Dello Schiavo, R. Herry, K. Suzuki, Journal de l’Ecole Polytechnique - Mathematiques 11 (2024) 957–1010."},"publisher":"Ecole Polytechnique","article_processing_charge":"Yes","publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"quality_controlled":"1","day":"01","arxiv":1,"intvolume":"        11","date_published":"2024-01-01T00:00:00Z","file_date_updated":"2024-10-01T07:31:56Z","type":"journal_article","doi":"10.5802/jep.270","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","corr_author":"1","language":[{"iso":"eng"}],"publication":"Journal de l'Ecole Polytechnique - Mathematiques","_id":"18158","title":"Wasserstein geometry and Ricci curvature bounds for Poisson spaces","status":"public","file":[{"date_updated":"2024-10-01T07:31:56Z","date_created":"2024-10-01T07:31:56Z","success":1,"file_size":1250553,"checksum":"5a51da5fb5f7fcaada378d43444cced8","file_name":"2024_JourEcolePolytechniqueMath_DelloSchiavo.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"18164"}],"scopus_import":"1","article_type":"original","date_updated":"2025-09-08T09:50:50Z","publication_status":"published","ddc":["510"],"author":[{"full_name":"Dello Schiavo, Lorenzo","orcid":"0000-0002-9881-6870","first_name":"Lorenzo","last_name":"Dello Schiavo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E"},{"last_name":"Herry","first_name":"Ronan","full_name":"Herry, Ronan"},{"last_name":"Suzuki","first_name":"Kohei","full_name":"Suzuki, Kohei"}],"month":"01","page":"957-1010","abstract":[{"lang":"eng","text":"We study the geometry of Poisson point processes from the point of view of optimal transport and Ricci lower bounds. We construct a Riemannian structure on the space of point processes and the associated distance W that corresponds to the Benamou–Brenier variational formula. Our main tool is a non-local continuity equation formulated with the difference operator. The closure of the domain of the relative entropy is a complete geodesic space, when endowed with \r\nW. The geometry of this non-local infinite-dimensional space is analogous to that of spaces with positive Ricci curvature. Among others: (a) the Ornstein–Uhlenbeck semi-group is the gradient flow of the relative entropy; (b) the Poisson space has an entropic Ricci curvature bounded from below by 1; (c) W satisfies an HWI inequality."},{"lang":"fre","text":"Nous étudions la géométrie des processus ponctuels de Poisson à travers le prisme du transport optimal et de la minoration de la courbure de Ricci. Nous construisons une structure\r\nriemannienne sur l’espace des processus ponctuels et la distance associée W qui concorde avec la formulation variationnelle de Benamou–Brenier. Notre analyse repose sur une équation de continuité non locale définie à l’aide de l’opérateur de différence. La fermeture du domaine de l’entropie relative, équipé de W, est un espace géodésique complet. La géométrie de cet espace non local et de dimension infinie est analogue à celle des espaces à courbure de Ricci strictement positive. Entre autres : (a) le semi-groupe d’Ornstein–Uhlenbeck est le flot du gradient de l’entropie relative ; (b) l’espace de Poisson a une courbure de Ricci entropique minorée par 1 ; (c) W satisfait une inégalité HWI."}],"isi":1,"volume":11,"year":"2024","date_created":"2024-09-29T22:01:38Z","external_id":{"isi":["001367254000003"],"arxiv":["2303.00398"]},"oa_version":"Published Version"},{"page":"3-12","abstract":[{"lang":"eng","text":"Markov Decision Processes (MDPs) are a classical model for decision making in the presence of uncertainty. Often they are viewed as state transformers with planning objectives defned with respect to paths over MDP states. An increasingly\r\npopular alternative is to view them as distribution transformers, giving rise to a sequence of probability distributions over MDP states. For instance, reachability and safety properties in modeling robot swarms or chemical reaction networks are naturally defned in terms of probability distributions over states. Verifying such distributional properties is known to be hard and often beyond the reach of classical state-based verifcation techniques. In this work, we consider the problems of certifed policy (i.e. controller) verifcation and synthesis in MDPs under distributional reach-avoidance specifcations. By certifed we mean that, along with a policy, we also aim to synthesize a (checkable) certifcate ensuring that the MDP indeed satisfes the property. Thus, given the target set of distributions and an unsafe set of distributions over MDP states, our goal is to either synthesize a certifcate for a given policy or synthesize a policy along with a certifcate, proving that the target distribution can be reached while avoiding unsafe distributions. To solve this problem, we introduce the novel notion of distributional reach-avoid certifcates and present automated procedures for (1) synthesizing a certifcate for a given policy, and (2) synthesizing a policy together with the certifcate, both providing formal guarantees on certifcate correctness. Our experimental evaluation demonstrates the ability of our method to solve several non-trivial examples, including a multi-agent robot-swarm model, to synthesize certifed policies and to certify existing policies. "}],"ec_funded":1,"year":"2024","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"date_created":"2024-09-29T22:01:38Z","external_id":{"arxiv":["2405.04015"]},"oa_version":"Preprint","publication":"Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence","language":[{"iso":"eng"}],"_id":"18159","status":"public","scopus_import":"1","title":"Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties","publication_status":"published","date_updated":"2025-04-14T07:52:46Z","month":"09","author":[{"last_name":"Akshay","first_name":"S","full_name":"Akshay, S"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias"},{"first_name":"Dorde","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic"}],"type":"conference","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.04015"}],"conference":{"start_date":"2024-08-03","name":"IJCAI: International Joint Conference on Artificial Intelligence","end_date":"2024-08-09","location":"Jeju, Korea"},"doi":"10.24963/ijcai.2024/1","oa":1,"acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt), the Singapore Ministry of Education (MOE) Academic Research Fund (AcRF) Tier 1 grant, Google Research Award 2023 and the SBI Foundation Hub for Data and Analytics.","corr_author":"1","publisher":"International Joint Conferences on Artificial Intelligence","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. In: <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2024:3-12. doi:<a href=\"https://doi.org/10.24963/ijcai.2024/1\">10.24963/ijcai.2024/1</a>","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2024, pp. 3–12.","mla":"Akshay, S., et al. “Certified Policy Verification and Synthesis for MDPs under Distributional Reach-Avoidance Properties.” <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2024, pp. 3–12, doi:<a href=\"https://doi.org/10.24963/ijcai.2024/1\">10.24963/ijcai.2024/1</a>.","chicago":"Akshay, S, Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “Certified Policy Verification and Synthesis for MDPs under Distributional Reach-Avoidance Properties.” In <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, 3–12. International Joint Conferences on Artificial Intelligence, 2024. <a href=\"https://doi.org/10.24963/ijcai.2024/1\">https://doi.org/10.24963/ijcai.2024/1</a>.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties,” in <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i>, Jeju, Korea, 2024, pp. 3–12.","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2024). Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. In <i>Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence</i> (pp. 3–12). Jeju, Korea: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2024/1\">https://doi.org/10.24963/ijcai.2024/1</a>","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2024. Certified policy verification and synthesis for MDPs under distributional reach-avoidance properties. Proceedings of the Thirty-Third International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 3–12."},"article_processing_charge":"No","publication_identifier":{"issn":["1045-0823"],"isbn":["9781956792041"]},"quality_controlled":"1","day":"01","arxiv":1,"date_published":"2024-09-01T00:00:00Z"},{"OA_type":"green","publication_status":"published","date_updated":"2025-04-14T07:52:46Z","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Kafshdar Goharshadi","id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","full_name":"Kafshdar Goharshadi, Ehsan","orcid":"0000-0002-8595-0587","first_name":"Ehsan"},{"last_name":"Karrabi","id":"67638922-f394-11eb-9cf6-f20423e08757","first_name":"Mehrdad","full_name":"Karrabi, Mehrdad"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","first_name":"Petr","full_name":"Novotný, Petr"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"month":"09","_id":"18160","publication":"33rd International Joint Conference on Artificial Intelligence","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","title":"Solving long-run average reward robust MDPs via stochastic games","date_created":"2024-09-29T22:01:39Z","external_id":{"arxiv":["2312.13912"]},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Markov decision processes (MDPs) provide a standard framework for sequential decision making under uncertainty. However, MDPs do not take uncertainty in transition probabilities into account. Robust Markov decision processes (RMDPs) address this shortcoming of MDPs by assigning to each transition an uncertainty set rather than a single probability value. In this work, we consider polytopic RMDPs in which all uncertainty sets are polytopes and study the problem of solving long-run average reward polytopic RMDPs. We present a novel perspective on this problem and show that it can be reduced to solving long-run average reward turn-based stochastic games with finite state and action spaces. This reduction allows us to derive several important consequences that were hitherto not known to hold for polytopic RMDPs. First, we derive new computational complexity bounds for solving long-run average reward polytopic RMDPs, showing for the first time that the threshold decision problem for them is in NP∩CONP and that they admit a randomized algorithm with sub-exponential expected runtime. Second, we present Robust Polytopic Policy Iteration (RPPI), a novel policy iteration algorithm for solving long-run average reward polytopic RMDPs. Our experimental evaluation shows that RPPI is much more efficient in solving long-run average reward polytopic RMDPs compared to state-of-the-art methods based on value iteration. "}],"ec_funded":1,"page":"6707-6715","year":"2024","project":[{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"arxiv":1,"day":"01","quality_controlled":"1","date_published":"2024-09-01T00:00:00Z","OA_place":"repository","publisher":"International Joint Conferences on Artificial Intelligence","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Chatterjee, Krishnendu, et al. “Solving Long-Run Average Reward Robust MDPs via Stochastic Games.” <i>33rd International Joint Conference on Artificial Intelligence</i>, International Joint Conferences on Artificial Intelligence, 2024, pp. 6707–15, doi:<a href=\"https://doi.org/10.24963/ijcai.2024/741\">10.24963/ijcai.2024/741</a>.","ieee":"K. Chatterjee, E. Goharshady, M. Karrabi, P. Novotný, and D. Zikelic, “Solving long-run average reward robust MDPs via stochastic games,” in <i>33rd International Joint Conference on Artificial Intelligence</i>, Jeju, South Korea, 2024, pp. 6707–6715.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Mehrdad Karrabi, Petr Novotný, and Dorde Zikelic. “Solving Long-Run Average Reward Robust MDPs via Stochastic Games.” In <i>33rd International Joint Conference on Artificial Intelligence</i>, 6707–15. International Joint Conferences on Artificial Intelligence, 2024. <a href=\"https://doi.org/10.24963/ijcai.2024/741\">https://doi.org/10.24963/ijcai.2024/741</a>.","apa":"Chatterjee, K., Goharshady, E., Karrabi, M., Novotný, P., &#38; Zikelic, D. (2024). Solving long-run average reward robust MDPs via stochastic games. In <i>33rd International Joint Conference on Artificial Intelligence</i> (pp. 6707–6715). Jeju, South Korea: International Joint Conferences on Artificial Intelligence. <a href=\"https://doi.org/10.24963/ijcai.2024/741\">https://doi.org/10.24963/ijcai.2024/741</a>","ista":"Chatterjee K, Goharshady E, Karrabi M, Novotný P, Zikelic D. 2024. Solving long-run average reward robust MDPs via stochastic games. 33rd International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence, 6707–6715.","ama":"Chatterjee K, Goharshady E, Karrabi M, Novotný P, Zikelic D. Solving long-run average reward robust MDPs via stochastic games. In: <i>33rd International Joint Conference on Artificial Intelligence</i>. International Joint Conferences on Artificial Intelligence; 2024:6707-6715. doi:<a href=\"https://doi.org/10.24963/ijcai.2024/741\">10.24963/ijcai.2024/741</a>","short":"K. Chatterjee, E. Goharshady, M. Karrabi, P. Novotný, D. Zikelic, in:, 33rd International Joint Conference on Artificial Intelligence, International Joint Conferences on Artificial Intelligence, 2024, pp. 6707–6715."},"publication_identifier":{"issn":["1045-0823"],"isbn":["9781956792041"]},"article_processing_charge":"No","acknowledgement":"This work was supported in part by the ERC-2020-CoG 863818 (FoRM-SMArt) and the Czech Science Foundation\r\ngrant no. GA23-06963S.","corr_author":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.13912","open_access":"1"}],"conference":{"location":"Jeju, South Korea","end_date":"2024-08-09","name":"IJCAI: International Joint Conference on Artificial Intelligence","start_date":"2024-08-03"},"type":"conference","oa":1,"doi":"10.24963/ijcai.2024/741"},{"page":"391-422","abstract":[{"lang":"eng","text":"Holdase chaperones are essential in the mitochondrial membrane-protein biogenesis as they stabilize preproteins and keep them in an import-competent state as they travel through the aqueous cytosol and intermembrane space. The small TIM chaperones of the mitochondrial intermembrane space function within a fine balance of client promiscuity and high affinity binding, while being also able to release their client proteins without significant energy barrier to the downstream insertases/translocases. The tendency of the preproteins to aggregate and the dynamic nature of the preprotein—chaperone complexes makes the preparation of these complexes challenging. Here we present two optimized methods for complex formation of highly hydrophobic precursor proteins and chaperones: a pull-down approach and an in-vitro translation strategy. In the former, attaching the client protein to an affinity resin keeps the individual client protein copies apart from each other and decreases the client self-aggregation probability, thereby favouring complex formation. In the latter approach, a purified chaperone, added to the cell-free protein synthesis, captures the nascent precursor protein. The choice of method will depend on the desired client-chaperone complex amount, or the need for specific labeling scheme."}],"year":"2024","volume":707,"external_id":{"pmid":["39488384"]},"date_created":"2024-10-01T10:58:27Z","oa_version":"None","publication":"Methods in Enzymology","language":[{"iso":"eng"}],"_id":"18167","status":"public","scopus_import":"1","title":"Generation of TIM chaperone substrate complexes","publication_status":"published","date_updated":"2025-10-22T06:40:54Z","OA_type":"closed access","month":"09","author":[{"id":"bb74f472-ae54-11eb-9835-bc9c22fb1183","last_name":"Guillerm","full_name":"Guillerm, Undina","first_name":"Undina"},{"first_name":"Iva","full_name":"Sučec, Iva","last_name":"Sučec"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul"}],"type":"book_chapter","pmid":1,"doi":"10.1016/bs.mie.2024.07.051","corr_author":"1","publisher":"Elsevier","department":[{"_id":"PaSc"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Guillerm, Undina, et al. “Generation of TIM Chaperone Substrate Complexes.” <i>Methods in Enzymology</i>, vol. 707, Elsevier, 2024, pp. 391–422, doi:<a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">10.1016/bs.mie.2024.07.051</a>.","ista":"Guillerm U, Sučec I, Schanda P. 2024.Generation of TIM chaperone substrate complexes. In: Methods in Enzymology. vol. 707, 391–422.","ieee":"U. Guillerm, I. Sučec, and P. Schanda, “Generation of TIM chaperone substrate complexes,” in <i>Methods in Enzymology</i>, vol. 707, Elsevier, 2024, pp. 391–422.","chicago":"Guillerm, Undina, Iva Sučec, and Paul Schanda. “Generation of TIM Chaperone Substrate Complexes.” In <i>Methods in Enzymology</i>, 707:391–422. Elsevier, 2024. <a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">https://doi.org/10.1016/bs.mie.2024.07.051</a>.","apa":"Guillerm, U., Sučec, I., &#38; Schanda, P. (2024). Generation of TIM chaperone substrate complexes. In <i>Methods in Enzymology</i> (Vol. 707, pp. 391–422). Elsevier. <a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">https://doi.org/10.1016/bs.mie.2024.07.051</a>","ama":"Guillerm U, Sučec I, Schanda P. Generation of TIM chaperone substrate complexes. In: <i>Methods in Enzymology</i>. Vol 707. Elsevier; 2024:391-422. doi:<a href=\"https://doi.org/10.1016/bs.mie.2024.07.051\">10.1016/bs.mie.2024.07.051</a>","short":"U. Guillerm, I. Sučec, P. Schanda, in:, Methods in Enzymology, Elsevier, 2024, pp. 391–422."},"article_processing_charge":"No","publication_identifier":{"issn":["0076-6879"]},"quality_controlled":"1","day":"13","intvolume":"       707","date_published":"2024-09-13T00:00:00Z"},{"ddc":["540"],"publication_status":"published","date_updated":"2025-09-08T09:52:18Z","author":[{"last_name":"Wu","full_name":"Wu, Dongqing","first_name":"Dongqing"},{"last_name":"Koscic","full_name":"Koscic, Anamaria","first_name":"Anamaria"},{"last_name":"Schneider","full_name":"Schneider, Sonja","first_name":"Sonja"},{"last_name":"Dubini","first_name":"Romeo C. A.","full_name":"Dubini, Romeo C. A."},{"full_name":"Rodriguez Camargo, Diana C.","first_name":"Diana C.","last_name":"Rodriguez Camargo"},{"full_name":"Schneider, Sabine","first_name":"Sabine","last_name":"Schneider"},{"full_name":"Rovo, Petra","first_name":"Petra","orcid":"0000-0001-8729-7326","id":"c316e53f-b965-11eb-b128-bb26acc59c00","last_name":"Rovo"}],"month":"03","_id":"18168","language":[{"iso":"eng"}],"publication":"Biomacromolecules","article_type":"original","scopus_import":"1","file":[{"date_updated":"2024-10-07T08:33:35Z","success":1,"date_created":"2024-10-07T08:33:35Z","file_size":6597227,"checksum":"9552b6d52f1e8a350764849a535fc13e","file_name":"2024_BioMacromolecules_Wu.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"18180","creator":"dernst"}],"status":"public","title":"Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein","date_created":"2024-10-02T10:09:53Z","external_id":{"pmid":["38343096"],"isi":["001166501000001"]},"oa_version":"Published Version","abstract":[{"text":"Despite the considerable interest in the recombinant production of synthetic spider silk fibers that possess mechanical properties similar to those of native spider silks, such as the cost-effectiveness, tunability, and scalability realization, is still lacking. To address this long-standing challenge, we have constructed an artificial spider silk gene using Golden Gate assembly for the recombinant bacterial production of dragline-mimicking silk, incorporating all the essential components: the N-terminal domain, a 33-residue-long major-ampullate-spidroin-inspired segment repeated 16 times, and the C-terminal domain (N16C). This designed silk-like protein was successfully expressed in Escherichia coli, purified, and cast into films from formic acid. We produced uniformly 13C–15N-labeled N16C films and employed solid-state magic-angle spinning nuclear magnetic resonance (NMR) for characterization. Thus, we could demonstrate that our bioengineered silk-like protein self-assembles into a film where, when hydrated, the solvent-exposed layer of the rigid, β-nanocrystalline polyalanine core undergoes a transition to an α-helical structure, gaining mobility to the extent that it fully dissolves in water and transforms into a highly dynamic random coil. This hydration-induced behavior induces chain dynamics in the glycine-rich amorphous soft segments on the microsecond time scale, contributing to the elasticity of the solid material. Our findings not only reveal the presence of structurally and dynamically distinct segments within the film’s superstructure but also highlight the complexity of the self-organization responsible for the exceptional mechanical properties observed in proteins that mimic dragline silk.","lang":"eng"}],"page":"1759-1774","year":"2024","volume":25,"isi":1,"day":"11","quality_controlled":"1","date_published":"2024-03-11T00:00:00Z","intvolume":"        25","publisher":"American Chemical Society","issue":"3","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","department":[{"_id":"NMR"}],"citation":{"ama":"Wu D, Koscic A, Schneider S, et al. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. 2024;25(3):1759-1774. doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>","short":"D. Wu, A. Koscic, S. Schneider, R.C.A. Dubini, D.C. Rodriguez Camargo, S. Schneider, P. Rovo, Biomacromolecules 25 (2024) 1759–1774.","mla":"Wu, Dongqing, et al. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>, vol. 25, no. 3, American Chemical Society, 2024, pp. 1759–74, doi:<a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">10.1021/acs.biomac.3c01239</a>.","ieee":"D. Wu <i>et al.</i>, “Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein,” <i>Biomacromolecules</i>, vol. 25, no. 3. American Chemical Society, pp. 1759–1774, 2024.","apa":"Wu, D., Koscic, A., Schneider, S., Dubini, R. C. A., Rodriguez Camargo, D. C., Schneider, S., &#38; Rovo, P. (2024). Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. <i>Biomacromolecules</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>","chicago":"Wu, Dongqing, Anamaria Koscic, Sonja Schneider, Romeo C. A. Dubini, Diana C. Rodriguez Camargo, Sabine Schneider, and Petra Rovo. “Unveiling the Dynamic Self-Assembly of a Recombinant Dragline-Silk-Mimicking Protein.” <i>Biomacromolecules</i>. American Chemical Society, 2024. <a href=\"https://doi.org/10.1021/acs.biomac.3c01239\">https://doi.org/10.1021/acs.biomac.3c01239</a>.","ista":"Wu D, Koscic A, Schneider S, Dubini RCA, Rodriguez Camargo DC, Schneider S, Rovo P. 2024. Unveiling the dynamic self-assembly of a recombinant dragline-silk-mimicking protein. Biomacromolecules. 25(3), 1759–1774."},"publication_identifier":{"eissn":["1526-4602"],"issn":["1525-7797"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"We thank Dr. Pavel Kielkowski for performing the MS/MS measurement and providing feedback on the manuscript. We are grateful to Rodrigo Ledesma Amaro for introducing the Golden Gate Assembly technique in our lab. We acknowledge the support from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)─SFB 1309-325871075, the Center for NanoScience (CeNS), the Fonds der Chemischen Industrie, and Universitätsgesellschaft München.","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"corr_author":"1","type":"journal_article","pmid":1,"file_date_updated":"2024-10-07T08:33:35Z","oa":1,"doi":"10.1021/acs.biomac.3c01239"}]