[{"title":"Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state","status":"public","_id":"14402","date_created":"2023-10-08T22:01:15Z","oa":1,"abstract":[{"lang":"eng","text":"Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition)."}],"isi":1,"corr_author":"1","project":[{"grant_number":"M03318","name":"Functional Advantages of Critical Brain Dynamics","_id":"eb943429-77a9-11ec-83b8-9f471cdf5c67"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"pmid":1,"year":"2023","publication_status":"published","scopus_import":"1","oa_version":"Published Version","date_updated":"2026-07-06T12:48:55Z","publication_identifier":{"eissn":["2211-1247"]},"month":"10","quality_controlled":"1","article_type":"original","external_id":{"isi":["001086695500001"],"pmid":["37777965"]},"type":"journal_article","has_accepted_license":"1","volume":42,"doi":"10.1016/j.celrep.2023.113162","citation":{"mla":"Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>, vol. 42, no. 10, 113162, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>.","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. <i>Cell Reports</i>. 2023;42(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">10.1016/j.celrep.2023.113162</a>","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” <i>Cell Reports</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.celrep.2023.113162\">https://doi.org/10.1016/j.celrep.2023.113162</a>.","ieee":"F. Lombardi <i>et al.</i>, “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” <i>Cell Reports</i>, vol. 42, no. 10. Elsevier, 2023.","ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 42(10), 113162.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023)."},"publisher":"Elsevier","file":[{"relation":"main_file","checksum":"9c71eb2a03aa160415f01ad95f49ceb5","file_size":5599007,"access_level":"open_access","success":1,"date_updated":"2024-01-30T14:07:08Z","content_type":"application/pdf","file_id":"14914","file_name":"2023_CellReports_Lombardi.pdf","creator":"dernst","date_created":"2024-01-30T14:07:08Z"}],"intvolume":"        42","issue":"10","article_number":"113162","file_date_updated":"2024-01-30T14:07:08Z","article_processing_charge":"Yes","date_published":"2023-10-31T00:00:00Z","day":"31","ec_funded":1,"author":[{"last_name":"Lombardi","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","orcid":"0000-0003-2623-5249","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"full_name":"Herrmann, Hans J.","first_name":"Hans J.","last_name":"Herrmann"},{"first_name":"Liborio","last_name":"Parrino","full_name":"Parrino, Liborio"},{"first_name":"Dietmar","last_name":"Plenz","full_name":"Plenz, Dietmar"},{"full_name":"Scarpetta, Silvia","last_name":"Scarpetta","first_name":"Silvia"},{"last_name":"Vaudano","first_name":"Anna Elisabetta","full_name":"Vaudano, Anna Elisabetta"},{"last_name":"De Arcangelis","first_name":"Lucilla","full_name":"De Arcangelis, Lucilla"},{"last_name":"Shriki","first_name":"Oren","full_name":"Shriki, Oren"}],"department":[{"_id":"GaTk"}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10821"}]},"acknowledgement":"This research was funded in whole or in part by the Austrian Science Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP [brain criticality and information processing]). L.d.A. acknowledges support from the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU (NGEU) funded by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022). O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The work was supported in part by DIRP ZIAMH02797 (to D.P.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"ddc":["570"],"publication":"Cell Reports","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"oa":1,"date_created":"2023-07-23T22:01:13Z","abstract":[{"lang":"eng","text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","_id":"13267","status":"public","isi":1,"corr_author":"1","OA_type":"hybrid","publication_status":"published","page":"1256-1265","pmid":1,"project":[{"name":"Optical control of synaptic function via adhesion molecules","grant_number":"I03600","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Molecular Drug Targets","grant_number":"W1232","call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425"},{"_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Synaptic communication in neuronal microcircuits","grant_number":"Z00312"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","grant_number":"LS18-022","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration"}],"year":"2023","date_updated":"2026-07-06T12:49:46Z","scopus_import":"1","oa_version":"Published Version","month":"08","quality_controlled":"1","article_type":"original","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"has_accepted_license":"1","volume":20,"doi":"10.1038/s41592-023-01936-6","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"type":"journal_article","file_date_updated":"2025-02-26T08:01:57Z","article_processing_charge":"Yes (in subscription journal)","day":"01","date_published":"2023-08-01T00:00:00Z","citation":{"apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>"},"publisher":"Springer Nature","file":[{"date_created":"2025-02-26T08:01:57Z","file_name":"2023_NatureMethods_Velicky.pdf","creator":"dernst","file_id":"19088","success":1,"date_updated":"2025-02-26T08:01:57Z","content_type":"application/pdf","file_size":14103039,"access_level":"open_access","checksum":"a68e845780a82ea36d0d4d3212a87c10","relation":"main_file"}],"intvolume":"        20","ddc":["570"],"publication":"Nature Methods","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"OA_place":"publisher","author":[{"first_name":"Philipp","last_name":"Velicky","full_name":"Velicky, Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Miguel Villalba, Eder","first_name":"Eder","last_name":"Miguel Villalba","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5665-0430"},{"full_name":"Michalska, Julia M","last_name":"Michalska","first_name":"Julia M","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235"},{"first_name":"Julia","last_name":"Lyudchik","full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wei","first_name":"Donglai","full_name":"Wei, Donglai"},{"first_name":"Zudi","last_name":"Lin","full_name":"Lin, Zudi"},{"id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","full_name":"Watson, Jake","last_name":"Watson","first_name":"Jake"},{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"full_name":"Beyer, Johanna","last_name":"Beyer","first_name":"Johanna"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","last_name":"Ben Simon","first_name":"Yoav","full_name":"Ben Simon, Yoav"},{"full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105"},{"full_name":"Jahr, Wiebke","first_name":"Wiebke","last_name":"Jahr","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0201-2315"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","last_name":"Cenameri","first_name":"Alban"},{"last_name":"Broichhagen","first_name":"Johannes","full_name":"Broichhagen, Johannes"},{"full_name":"Grant, Seth G.N.","first_name":"Seth G.N.","last_name":"Grant"},{"orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","full_name":"Jonas, Peter M"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","first_name":"Gaia","last_name":"Novarino"},{"full_name":"Pfister, Hanspeter","last_name":"Pfister","first_name":"Hanspeter"},{"orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","last_name":"Bickel","full_name":"Bickel, Bernd"},{"last_name":"Danzl","first_name":"Johann G","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"ec_funded":1,"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}],"record":[{"relation":"research_data","status":"public","id":"12817"},{"status":"public","relation":"shorter_version","id":"14770"},{"id":"18674","status":"public","relation":"dissertation_contains"},{"relation":"earlier_version","status":"public","id":"11943"}]}},{"license":"https://choosealicense.com/licenses/agpl-3.0/","date_published":"2023-11-21T00:00:00Z","day":"21","file_date_updated":"2023-11-21T08:20:23Z","year":"2023","publisher":"Institute of Science and Technology Austria","file":[{"date_created":"2023-11-08T20:23:07Z","file_name":"Computational_Toolbox_v1.2.zip","creator":"fschur","file_id":"14503","date_updated":"2023-11-08T20:23:07Z","success":1,"content_type":"application/zip","access_level":"open_access","file_size":347641117,"relation":"main_file","checksum":"a8b9adeb53a4109dea4d5e39fa1acccf"},{"checksum":"14db2addbfca61a085ba301ed6f2900b","relation":"main_file","file_size":1522,"access_level":"open_access","date_updated":"2023-11-21T08:20:23Z","content_type":"text/plain","success":1,"file_id":"14586","creator":"dernst","file_name":"Readme.txt","date_created":"2023-11-21T08:20:23Z"}],"project":[{"name":"Structure and isoform diversity of the Arp2/3 complex","grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"}],"citation":{"mla":"Dimchev, Georgi A., et al. <i>Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., &#38; Schur, F. K. (2023). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2023. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">10.15479/AT:ISTA:14502</a>.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14502\">https://doi.org/10.15479/AT:ISTA:14502</a>.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data.” Institute of Science and Technology Austria, 2023.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, (2023)."},"keyword":["cryo-electron tomography","actin cytoskeleton","toolbox"],"tmp":{"name":"GNU Affero General Public License v3.0","short":"GNU AGPLv3  ","legal_code_url":"https://www.gnu.org/licenses/agpl-3.0.html"},"date_updated":"2026-07-06T12:57:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"related_material":{"record":[{"id":"10290","status":"public","relation":"used_for_analysis_in"}]},"department":[{"_id":"FlSc"}],"author":[{"full_name":"Dimchev, Georgi A","last_name":"Dimchev","first_name":"Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161"},{"first_name":"Behnam","last_name":"Amiri","full_name":"Amiri, Behnam"},{"first_name":"Florian","last_name":"Fäßler","full_name":"Fäßler, Florian","orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4790-8078"}],"abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized fila- mentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"oa":1,"month":"11","date_created":"2023-11-08T19:40:54Z","status":"public","_id":"14502","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","doi":"10.15479/AT:ISTA:14502","corr_author":"1","has_accepted_license":"1","type":"software"},{"date_created":"2023-07-12T07:32:46Z","oa":1,"abstract":[{"text":"Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast.","lang":"eng"}],"status":"public","_id":"13212","title":"Distinct functions of TIR1 and AFB1 receptors in auxin signalling.","das_tickbox":"1","isi":1,"corr_author":"1","publication_status":"published","page":"1117-1119","year":"2023","project":[{"call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"pmid":1,"date_updated":"2026-07-06T12:58:58Z","oa_version":"Published Version","scopus_import":"1","article_type":"letter_note","month":"07","quality_controlled":"1","publication_identifier":{"issn":["1752-9867"],"eissn":["1674-2052"]},"has_accepted_license":"1","volume":16,"doi":"10.1016/j.molp.2023.06.007","external_id":{"pmid":["37393433"],"isi":["001044410900001"]},"type":"journal_article","article_processing_charge":"Yes (via OA deal)","date_published":"2023-07-01T00:00:00Z","day":"01","file_date_updated":"2024-01-29T10:37:05Z","intvolume":"        16","issue":"7","citation":{"apa":"Chen, H., Li, L., Zou, M., Qi, L., &#38; Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">https://doi.org/10.1016/j.molp.2023.06.007</a>","mla":"Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” <i>Molecular Plant</i>, vol. 16, no. 7, Elsevier, 2023, pp. 1117–19, doi:<a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">10.1016/j.molp.2023.06.007</a>.","short":"H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119.","ieee":"H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” <i>Molecular Plant</i>, vol. 16, no. 7. Elsevier, pp. 1117–1119, 2023.","chicago":"Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” <i>Molecular Plant</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">https://doi.org/10.1016/j.molp.2023.06.007</a>.","ista":"Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119.","ama":"Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. <i>Molecular Plant</i>. 2023;16(7):1117-1119. doi:<a href=\"https://doi.org/10.1016/j.molp.2023.06.007\">10.1016/j.molp.2023.06.007</a>"},"publisher":"Elsevier","file":[{"file_id":"14894","file_name":"2023_MolecularPlant_Chen.pdf","creator":"dernst","date_created":"2024-01-29T10:37:05Z","relation":"main_file","checksum":"6012b7e4a2f680ee6c1f84001e2b945f","success":1,"date_updated":"2024-01-29T10:37:05Z","content_type":"application/pdf","access_level":"open_access","file_size":1000871}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"ddc":["580"],"publication":"Molecular Plant","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"19478"}]},"acknowledgement":"We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985).","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"author":[{"id":"83c96512-15b2-11ec-abd3-b7eede36184f","last_name":"Chen","first_name":"Huihuang","full_name":"Chen, Huihuang"},{"id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","first_name":"Lanxin","last_name":"Li"},{"full_name":"Zou, Minxia","last_name":"Zou","first_name":"Minxia","id":"5c243f41-03f3-11ec-841c-96faf48a7ef9"},{"id":"44B04502-A9ED-11E9-B6FC-583AE6697425","orcid":"0000-0001-5187-8401","full_name":"Qi, Linlin","first_name":"Linlin","last_name":"Qi"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","first_name":"Jiří","last_name":"Friml"}],"ec_funded":1},{"volume":4,"has_accepted_license":"1","doi":"10.1016/j.xplc.2023.100632","external_id":{"pmid":["37254481"],"isi":["001113003000001"]},"type":"journal_article","month":"11","quality_controlled":"1","article_type":"original","publication_identifier":{"eissn":["2590-3462"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"Plant Communications","ddc":["580"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"author":[{"last_name":"Xia","first_name":"Jing","full_name":"Xia, Jing"},{"full_name":"Kong, Mengjuan","last_name":"Kong","first_name":"Mengjuan"},{"full_name":"Yang, Zhisen","last_name":"Yang","first_name":"Zhisen"},{"full_name":"Sun, Lianghanxiao","last_name":"Sun","first_name":"Lianghanxiao"},{"full_name":"Peng, Yakun","last_name":"Peng","first_name":"Yakun"},{"first_name":"Yanbo","last_name":"Mao","full_name":"Mao, Yanbo"},{"first_name":"Hong","last_name":"Wei","full_name":"Wei, Hong"},{"full_name":"Ying, Wei","last_name":"Ying","first_name":"Wei"},{"full_name":"Gao, Yongxiao","last_name":"Gao","first_name":"Yongxiao"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"last_name":"Weng","first_name":"Jianping","full_name":"Weng, Jianping"},{"full_name":"Liu, Xin","last_name":"Liu","first_name":"Xin"},{"first_name":"Linfeng","last_name":"Sun","full_name":"Sun, Linfeng"},{"first_name":"Shutang","last_name":"Tan","full_name":"Tan, Shutang"}],"department":[{"_id":"JiFr"}],"acknowledgement":"This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China (QYPY20220012 to S.T.); start-up funding from the University of Science and Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051, and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885 to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun); and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing published materials (Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We are grateful to Y. Gao and all other staff members for their technical support on cryo-EM data collection. ","article_number":"100632","file_date_updated":"2024-01-30T10:54:40Z","article_processing_charge":"Yes","day":"13","date_published":"2023-11-13T00:00:00Z","citation":{"ama":"Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. <i>Plant Communications</i>. 2023;4(6). doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">10.1016/j.xplc.2023.100632</a>","ista":"Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J, Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 4(6), 100632.","chicago":"Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” <i>Plant Communications</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">https://doi.org/10.1016/j.xplc.2023.100632</a>.","ieee":"J. Xia <i>et al.</i>, “Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen,” <i>Plant Communications</i>, vol. 4, no. 6. Elsevier, 2023.","short":"J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao, J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023).","mla":"Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” <i>Plant Communications</i>, vol. 4, no. 6, 100632, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">10.1016/j.xplc.2023.100632</a>.","apa":"Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023). Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. <i>Plant Communications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xplc.2023.100632\">https://doi.org/10.1016/j.xplc.2023.100632</a>"},"publisher":"Elsevier","file":[{"date_created":"2024-01-30T10:54:40Z","file_name":"2023_PlantCommunications_Xia.pdf","creator":"dernst","file_id":"14900","access_level":"open_access","file_size":1434862,"success":1,"content_type":"application/pdf","date_updated":"2024-01-30T10:54:40Z","relation":"main_file","checksum":"f8ef92af6096834f91ce38587fb1db9f"}],"intvolume":"         4","issue":"6","isi":1,"das_tickbox":"1","date_created":"2023-07-12T07:32:00Z","oa":1,"abstract":[{"lang":"eng","text":"The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture."}],"title":"Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen","status":"public","_id":"13209","date_updated":"2026-07-06T12:59:25Z","scopus_import":"1","oa_version":"Published Version","publication_status":"published","pmid":1,"year":"2023"},{"corr_author":"1","status":"public","_id":"13162","title":"Cryo-EM software packages: A sys-admins point of view","date_created":"2023-06-23T11:03:18Z","oa":1,"oa_version":"Submitted Version","conference":{"start_date":"2023-06-12","location":"Maribor, Slovenia","name":"ASHPC: Austrian-Slovenian HPC Meeting","end_date":"2023-06-15"},"date_updated":"2026-07-06T13:01:58Z","year":"2023","publication_status":"published","page":"42-42","type":"conference_abstract","has_accepted_license":"1","month":"07","quality_controlled":"1","department":[{"_id":"ScienComp"}],"author":[{"full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano","id":"490F40CE-F248-11E8-B48F-1D18A9856A87"},{"id":"4D0BC184-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan","last_name":"Stadlbauer","full_name":"Stadlbauer, Stephan"},{"last_name":"Alexander","first_name":"Michael F","full_name":"Alexander, Michael F","id":"3A02A8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Schlögl, Alois","last_name":"Schlögl","first_name":"Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","language":[{"iso":"eng"}],"citation":{"apa":"Elefante, S., Stadlbauer, S., Alexander, M. F., &#38; Schlögl, A. (2023). Cryo-EM software packages: A sys-admins point of view. In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i> (pp. 42–42). Maribor, Slovenia: EuroCC Austria.","mla":"Elefante, Stefano, et al. “Cryo-EM Software Packages: A Sys-Admins Point of View.” <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, EuroCC Austria, 2023, pp. 42–42.","short":"S. Elefante, S. Stadlbauer, M.F. Alexander, A. Schlögl, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 42–42.","ieee":"S. Elefante, S. Stadlbauer, M. F. Alexander, and A. Schlögl, “Cryo-EM software packages: A sys-admins point of view,” in <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, Maribor, Slovenia, 2023, pp. 42–42.","chicago":"Elefante, Stefano, Stephan Stadlbauer, Michael F Alexander, and Alois Schlögl. “Cryo-EM Software Packages: A Sys-Admins Point of View.” In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, 42–42. EuroCC Austria, 2023.","ista":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. 2023. Cryo-EM software packages: A sys-admins point of view. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 42–42.","ama":"Elefante S, Stadlbauer S, Alexander MF, Schlögl A. Cryo-EM software packages: A sys-admins point of view. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC Austria; 2023:42-42."},"publisher":"EuroCC Austria","file":[{"access_level":"open_access","file_size":380354,"success":1,"date_updated":"2023-07-18T09:28:30Z","content_type":"application/pdf","checksum":"0ab6173cd5c5634ed773cd37ff012681","relation":"main_file","date_created":"2023-07-18T09:28:30Z","creator":"dernst","file_name":"2023_ASHPC_Elefante.pdf","file_id":"13250"}],"article_processing_charge":"No","day":"01","date_published":"2023-07-01T00:00:00Z","file_date_updated":"2023-07-18T09:28:30Z"},{"department":[{"_id":"ScienComp"},{"_id":"EM-Fac"}],"acknowledgement":"Thanks to Jesse Hansen for his suggestions on improving the abstract.","author":[{"full_name":"Schlögl, Alois","first_name":"Alois","last_name":"Schlögl","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100"},{"id":"490F40CE-F248-11E8-B48F-1D18A9856A87","full_name":"Elefante, Stefano","last_name":"Elefante","first_name":"Stefano"},{"id":"3661B498-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3904-947X","full_name":"Hodirnau, Victor-Valentin","last_name":"Hodirnau","first_name":"Victor-Valentin"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"ASHPC23 - Austrian-Slovenian HPC Meeting 2023","ddc":["000"],"citation":{"short":"A. Schlögl, S. Elefante, V.-V. Hodirnau, in:, ASHPC23 - Austrian-Slovenian HPC Meeting 2023, EuroCC Austria, 2023, pp. 59–59.","ama":"Schlögl A, Elefante S, Hodirnau V-V. Running Windows-applications on a Linux HPC cluster using WINE. In: <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>. EuroCC Austria; 2023:59-59.","ista":"Schlögl A, Elefante S, Hodirnau V-V. 2023. Running Windows-applications on a Linux HPC cluster using WINE. ASHPC23 - Austrian-Slovenian HPC Meeting 2023. ASHPC: Austrian-Slovenian HPC Meeting, 59–59.","ieee":"A. Schlögl, S. Elefante, and V.-V. Hodirnau, “Running Windows-applications on a Linux HPC cluster using WINE,” in <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, Maribor, Slovenia, 2023, pp. 59–59.","chicago":"Schlögl, Alois, Stefano Elefante, and Victor-Valentin Hodirnau. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, 59–59. EuroCC Austria, 2023.","mla":"Schlögl, Alois, et al. “Running Windows-Applications on a Linux HPC Cluster Using WINE.” <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i>, EuroCC Austria, 2023, pp. 59–59.","apa":"Schlögl, A., Elefante, S., &#38; Hodirnau, V.-V. (2023). Running Windows-applications on a Linux HPC cluster using WINE. In <i>ASHPC23 - Austrian-Slovenian HPC Meeting 2023</i> (pp. 59–59). Maribor, Slovenia: EuroCC Austria."},"publisher":"EuroCC Austria","file":[{"date_created":"2023-07-18T09:18:55Z","file_id":"13249","file_name":"2023_ASHPC_Schloegl.pdf","creator":"dernst","file_size":316959,"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2023-07-18T09:18:55Z","relation":"main_file","checksum":"ec8e4295d54171032cdd1b01423eb4a6"}],"article_processing_charge":"No","day":"01","date_published":"2023-07-01T00:00:00Z","file_date_updated":"2023-07-18T09:18:55Z","type":"conference_abstract","has_accepted_license":"1","month":"07","quality_controlled":"1","oa_version":"Submitted Version","conference":{"end_date":"2023-06-15","name":"ASHPC: Austrian-Slovenian HPC Meeting","location":"Maribor, Slovenia","start_date":"2023-06-13"},"date_updated":"2026-07-06T13:01:46Z","year":"2023","page":"59-59","publication_status":"published","corr_author":"1","_id":"13161","status":"public","title":"Running Windows-applications on a Linux HPC cluster using WINE","date_created":"2023-06-23T11:01:23Z","oa":1},{"date_updated":"2026-07-06T13:37:53Z","scopus_import":"1","oa_version":"Preprint","publication_status":"published","page":"125-141","year":"2023","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"das_tickbox":"1","corr_author":"1","isi":1,"abstract":[{"text":"We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations.","lang":"eng"}],"date_created":"2023-07-23T22:01:14Z","oa":1,"_id":"13268","status":"public","title":"On type II degenerations of hyperkähler manifolds","publication":"Mathematical Research Letters","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"acknowledgement":"The first author is supported by the ERC Synergy Grant HyperK. The second author is supported by the Max Planck Institute for Mathematics and the Institute of Science and Technology Austria. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413.","department":[{"_id":"TaHa"}],"ec_funded":1,"author":[{"full_name":"Huybrechts, D.","last_name":"Huybrechts","first_name":"D."},{"id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","full_name":"Mauri, Mirko","last_name":"Mauri","first_name":"Mirko"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2108.01587"}],"date_published":"2023-06-21T00:00:00Z","day":"21","article_processing_charge":"No","issue":"1","intvolume":"        30","publisher":"International Press of Boston","citation":{"mla":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>, vol. 30, no. 1, International Press of Boston, 2023, pp. 125–41, doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>.","apa":"Huybrechts, D., &#38; Mauri, M. (2023). On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. International Press of Boston. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>","ama":"Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. <i>Mathematical Research Letters</i>. 2023;30(1):125-141. doi:<a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">10.4310/mrl.2023.v30.n1.a6</a>","ieee":"D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,” <i>Mathematical Research Letters</i>, vol. 30, no. 1. International Press of Boston, pp. 125–141, 2023.","ista":"Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141.","chicago":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” <i>Mathematical Research Letters</i>. International Press of Boston, 2023. <a href=\"https://doi.org/10.4310/mrl.2023.v30.n1.a6\">https://doi.org/10.4310/mrl.2023.v30.n1.a6</a>.","short":"D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141."},"doi":"10.4310/mrl.2023.v30.n1.a6","volume":30,"type":"journal_article","external_id":{"isi":["001027656000006"],"arxiv":["2108.01587"]},"article_type":"original","quality_controlled":"1","month":"06","publication_identifier":{"eissn":["1945-001X"],"issn":["1073-2780"]}},{"abstract":[{"lang":"eng","text":"Distributed Key Generation (DKG) is a technique to bootstrap threshold cryptosystems without a trusted party. DKG is an essential building block to many decentralized protocols such as randomness beacons, threshold signatures, Byzantine consensus, and multiparty computation. While significant progress has been made recently, existing asynchronous DKG constructions are inefficient when the reconstruction threshold is larger than one-third of the total nodes. In this paper, we present a simple and concretely efficient asynchronous DKG (ADKG) protocol among n = 3t + 1 nodes that can tolerate up to t malicious nodes and support any reconstruction threshold ℓ ≥ t. Our protocol has an expected O(κn3) communication cost, where κ is the security parameter, and only assumes the hardness of the Discrete Logarithm. The\r\ncore ingredient of our ADKG protocol is an asynchronous protocol to secret share a random polynomial of degree ℓ ≥ t, which has other applications, such as asynchronous proactive secret sharing and asynchronous multiparty computation. We implement our high-threshold ADKG protocol and evaluate it using a network of up to 128 geographically distributed nodes. Our evaluation shows that our high-threshold ADKG protocol reduces the running time by 90% and bandwidth usage by 80% over the state-of-the-art."}],"oa":1,"date_created":"2023-11-26T23:00:55Z","title":"Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling","_id":"14609","status":"public","corr_author":"1","das_tickbox":"1","page":"5359-5376","publication_status":"published","project":[{"name":"Security and Privacy by Design for Complex Systems","grant_number":"F8512","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f"}],"year":"2023","date_updated":"2026-07-07T06:02:32Z","conference":{"start_date":"2023-08-09","location":"Anaheim, CA, United States","end_date":"2023-08-11","name":"USENIX Security Symposium"},"oa_version":"Published Version","scopus_import":"1","quality_controlled":"1","month":"08","cryptoeprintid":1,"publication_identifier":{"isbn":["9781713879497"]},"has_accepted_license":"1","volume":8,"type":"conference","external_id":{"cryptoeprintid":["2022/1389"]},"file_date_updated":"2023-11-28T09:14:34Z","day":"15","main_file_link":[{"url":"https://eprint.iacr.org/2022/1389","open_access":"1"}],"date_published":"2023-08-15T00:00:00Z","article_processing_charge":"No","publisher":"Usenix Association","file":[{"file_name":"2023_USENIX_Das.pdf","creator":"dernst","file_id":"14621","date_created":"2023-11-28T09:14:34Z","checksum":"1a730765930138e23c6efd2575872641","relation":"main_file","success":1,"content_type":"application/pdf","date_updated":"2023-11-28T09:14:34Z","access_level":"open_access","file_size":704331}],"citation":{"short":"S. Das, Z. Xiang, E. Kokoris Kogias, L. Ren, in:, 32nd USENIX Security Symposium, Usenix Association, 2023, pp. 5359–5376.","ama":"Das S, Xiang Z, Kokoris Kogias E, Ren L. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In: <i>32nd USENIX Security Symposium</i>. Vol 8. Usenix Association; 2023:5359-5376.","ista":"Das S, Xiang Z, Kokoris Kogias E, Ren L. 2023. Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. 32nd USENIX Security Symposium. USENIX Security Symposium vol. 8, 5359–5376.","ieee":"S. Das, Z. Xiang, E. Kokoris Kogias, and L. Ren, “Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling,” in <i>32nd USENIX Security Symposium</i>, Anaheim, CA, United States, 2023, vol. 8, pp. 5359–5376.","chicago":"Das, Sourav, Zhuolun Xiang, Eleftherios Kokoris Kogias, and Ling Ren. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” In <i>32nd USENIX Security Symposium</i>, 8:5359–76. Usenix Association, 2023.","mla":"Das, Sourav, et al. “Practical Asynchronous High-Threshold Distributed Key Generation and Distributed Polynomial Sampling.” <i>32nd USENIX Security Symposium</i>, vol. 8, Usenix Association, 2023, pp. 5359–76.","apa":"Das, S., Xiang, Z., Kokoris Kogias, E., &#38; Ren, L. (2023). Practical asynchronous high-threshold distributed key generation and distributed polynomial sampling. In <i>32nd USENIX Security Symposium</i> (Vol. 8, pp. 5359–5376). Anaheim, CA, United States: Usenix Association."},"intvolume":"         8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"32nd USENIX Security Symposium","language":[{"iso":"eng"}],"author":[{"first_name":"Sourav","last_name":"Das","full_name":"Das, Sourav"},{"full_name":"Xiang, Zhuolun","first_name":"Zhuolun","last_name":"Xiang"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","orcid":"0000-0002-8827-3382","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"last_name":"Ren","first_name":"Ling","full_name":"Ren, Ling"}],"acknowledgement":"The authors would like to thank Amit Agarwal, Andrew Miller, and Tom Yurek for the helpful discussions related to the paper. This work is funded in part by a VMware early career faculty grant, a Chainlink Labs Ph.D. fellowship, the National Science Foundation, and the Austrian Science Fund (FWF) F8512-N.","department":[{"_id":"ElKo"}]},{"month":"10","quality_controlled":"1","publication_identifier":{"isbn":["9783854480600"]},"has_accepted_license":"1","doi":"10.34727/2023/isbn.978-3-85448-060-0_20","external_id":{"isi":["001504402400020"]},"type":"conference","article_processing_charge":"No","date_published":"2023-10-01T00:00:00Z","day":"01","file_date_updated":"2024-01-02T08:14:23Z","citation":{"mla":"Pastva, Samuel, and Thomas A. Henzinger. “Binary Decision Diagrams on Modern Hardware.” <i>Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design</i>, TU Wien Academic Press, 2023, pp. 122–31, doi:<a href=\"https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20\">10.34727/2023/isbn.978-3-85448-060-0_20</a>.","apa":"Pastva, S., &#38; Henzinger, T. A. (2023). Binary decision diagrams on modern hardware. In <i>Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design</i> (pp. 122–131). Ames, IA, United States: TU Wien Academic Press. <a href=\"https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20\">https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20</a>","ama":"Pastva S, Henzinger TA. Binary decision diagrams on modern hardware. In: <i>Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design</i>. TU Wien Academic Press; 2023:122-131. doi:<a href=\"https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20\">10.34727/2023/isbn.978-3-85448-060-0_20</a>","ista":"Pastva S, Henzinger TA. 2023. Binary decision diagrams on modern hardware. Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design. FMCAD: Formal Methods in Computer-Aided Design, 122–131.","chicago":"Pastva, Samuel, and Thomas A Henzinger. “Binary Decision Diagrams on Modern Hardware.” In <i>Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design</i>, 122–31. TU Wien Academic Press, 2023. <a href=\"https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20\">https://doi.org/10.34727/2023/isbn.978-3-85448-060-0_20</a>.","ieee":"S. Pastva and T. A. Henzinger, “Binary decision diagrams on modern hardware,” in <i>Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design</i>, Ames, IA, United States, 2023, pp. 122–131.","short":"S. Pastva, T.A. Henzinger, in:, Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design, TU Wien Academic Press, 2023, pp. 122–131."},"file":[{"checksum":"818d6e13dd508f3a04f0941081022e5d","relation":"main_file","file_size":524321,"access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2024-01-02T08:14:23Z","creator":"dernst","file_name":"2023_FMCAD_Pastva.pdf","file_id":"14721","date_created":"2024-01-02T08:14:23Z"}],"publisher":"TU Wien Academic Press","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"Proceedings of the 23rd Conference on Formal Methods in Computer-Aided Design","language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"acknowledgement":"This work was supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413 and the\r\n“VAMOS” grant ERC-2020-AdG 101020093.","ec_funded":1,"author":[{"orcid":"0000-0003-1993-0331","id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","first_name":"Samuel","full_name":"Pastva, Samuel"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A"}],"date_created":"2023-12-31T23:01:03Z","oa":1,"abstract":[{"text":"Binary decision diagrams (BDDs) are one of the fundamental data structures in formal methods and computer science in general. However, the performance of BDD-based algorithms greatly depends on memory latency due to the reliance on large hash tables and thus, by extension, on the speed of random memory access. This hinders the full utilisation of resources available on modern CPUs, since the absolute memory latency has not improved significantly for at least a decade. In this paper, we explore several implementation techniques that improve the performance of BDD manipulation either through enhanced memory locality or by partially eliminating random memory access. On a benchmark suite of 600+ BDDs derived from real-world applications, we demonstrate runtime that is comparable or better than parallelising the same operations on eight CPU cores. ","lang":"eng"}],"_id":"14718","status":"public","title":"Binary decision diagrams on modern hardware","das_tickbox":"1","isi":1,"corr_author":"1","page":"122-131","publication_status":"published","year":"2023","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093"}],"conference":{"name":"FMCAD: Formal Methods in Computer-Aided Design","end_date":"2023-10-27","location":"Ames, IA, United States","start_date":"2023-10-25"},"date_updated":"2026-07-07T05:58:51Z","scopus_import":"1","oa_version":"Published Version"},{"year":"2023","publication_status":"published","page":"1618-1629","scopus_import":"1","oa_version":"Published Version","date_updated":"2026-07-07T06:18:55Z","title":"The human factor: Results of a small-angle scattering data analysis round robin","_id":"14799","status":"public","abstract":[{"lang":"eng","text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed."}],"date_created":"2024-01-14T23:00:57Z","oa":1,"isi":1,"das_tickbox":"1","file":[{"date_updated":"2024-01-17T07:47:35Z","content_type":"application/pdf","success":1,"access_level":"open_access","file_size":2165864,"relation":"main_file","checksum":"dab30d4556360f2cecf99f4b7efb0ee9","date_created":"2024-01-17T07:47:35Z","file_id":"14822","creator":"dernst","file_name":"2023_JourApplCrystallography_Pauw.pdf"}],"publisher":"International Union of Crystallography","citation":{"ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. 2023;56(6):1618-1629. doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>","ieee":"B. R. Pauw <i>et al.</i>, “The human factor: Results of a small-angle scattering data analysis round robin,” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6. International Union of Crystallography, pp. 1618–1629, 2023.","ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>. International Union of Crystallography, 2023. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>.","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6, International Union of Crystallography, 2023, pp. 1618–29, doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>.","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. International Union of Crystallography. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>"},"issue":"6","intvolume":"        56","file_date_updated":"2024-01-17T07:47:35Z","day":"01","date_published":"2023-12-01T00:00:00Z","article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Pauw","first_name":"Brian R.","full_name":"Pauw, Brian R."},{"first_name":"Glen J.","last_name":"Smales","full_name":"Smales, Glen J."},{"full_name":"Anker, Andy S.","first_name":"Andy S.","last_name":"Anker"},{"first_name":"Venkatasamy","last_name":"Annadurai","full_name":"Annadurai, Venkatasamy"},{"full_name":"Balazs, Daniel","first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X"},{"last_name":"Bienert","first_name":"Ralf","full_name":"Bienert, Ralf"},{"full_name":"Bouwman, Wim G.","first_name":"Wim G.","last_name":"Bouwman"},{"full_name":"Breßler, Ingo","first_name":"Ingo","last_name":"Breßler"},{"full_name":"Breternitz, Joachim","first_name":"Joachim","last_name":"Breternitz"},{"last_name":"Brok","first_name":"Erik S.","full_name":"Brok, Erik S."},{"full_name":"Bryant, Gary","last_name":"Bryant","first_name":"Gary"},{"full_name":"Clulow, Andrew J.","last_name":"Clulow","first_name":"Andrew J."},{"full_name":"Crater, Erin R.","last_name":"Crater","first_name":"Erin R."},{"first_name":"Frédéric","last_name":"De Geuser","full_name":"De Geuser, Frédéric"},{"full_name":"Giudice, Alessandra Del","first_name":"Alessandra Del","last_name":"Giudice"},{"first_name":"Jérôme","last_name":"Deumer","full_name":"Deumer, Jérôme"},{"full_name":"Disch, Sabrina","first_name":"Sabrina","last_name":"Disch"},{"full_name":"Dutt, Shankar","first_name":"Shankar","last_name":"Dutt"},{"last_name":"Frank","first_name":"Kilian","full_name":"Frank, Kilian"},{"full_name":"Fratini, Emiliano","first_name":"Emiliano","last_name":"Fratini"},{"first_name":"Paulo R.A.F.","last_name":"Garcia","full_name":"Garcia, Paulo R.A.F."},{"full_name":"Gilbert, Elliot P.","first_name":"Elliot P.","last_name":"Gilbert"},{"last_name":"Hahn","first_name":"Marc B.","full_name":"Hahn, Marc B."},{"first_name":"James","last_name":"Hallett","full_name":"Hallett, James"},{"full_name":"Hohenschutz, Max","first_name":"Max","last_name":"Hohenschutz"},{"first_name":"Martin","last_name":"Hollamby","full_name":"Hollamby, Martin"},{"full_name":"Huband, Steven","last_name":"Huband","first_name":"Steven"},{"last_name":"Ilavsky","first_name":"Jan","full_name":"Ilavsky, Jan"},{"first_name":"Johanna K.","last_name":"Jochum","full_name":"Jochum, Johanna K."},{"full_name":"Juelsholt, Mikkel","first_name":"Mikkel","last_name":"Juelsholt"},{"full_name":"Mansel, Bradley W.","last_name":"Mansel","first_name":"Bradley W."},{"last_name":"Penttilä","first_name":"Paavo","full_name":"Penttilä, Paavo"},{"first_name":"Rebecca K.","last_name":"Pittkowski","full_name":"Pittkowski, Rebecca K."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"},{"full_name":"Pozzo, Lilo D.","last_name":"Pozzo","first_name":"Lilo D."},{"last_name":"Rochels","first_name":"Leonhard","full_name":"Rochels, Leonhard"},{"last_name":"Rosalie","first_name":"Julian M.","full_name":"Rosalie, Julian M."},{"full_name":"Saloga, Patrick E.J.","last_name":"Saloga","first_name":"Patrick E.J."},{"full_name":"Seibt, Susanne","first_name":"Susanne","last_name":"Seibt"},{"full_name":"Smith, Andrew J.","last_name":"Smith","first_name":"Andrew J."},{"full_name":"Smith, Gregory N.","last_name":"Smith","first_name":"Gregory N."},{"full_name":"Spiering, Glenn A.","first_name":"Glenn A.","last_name":"Spiering"},{"last_name":"Stawski","first_name":"Tomasz M.","full_name":"Stawski, Tomasz M."},{"last_name":"Taché","first_name":"Olivier","full_name":"Taché, Olivier"},{"first_name":"Andreas F.","last_name":"Thünemann","full_name":"Thünemann, Andreas F."},{"full_name":"Toth, Kristof","last_name":"Toth","first_name":"Kristof"},{"full_name":"Whitten, Andrew E.","first_name":"Andrew E.","last_name":"Whitten"},{"last_name":"Wuttke","first_name":"Joachim","full_name":"Wuttke, Joachim"}],"acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","department":[{"_id":"LifeSc"}],"publication":"Journal of Applied Crystallography","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["540"],"language":[{"iso":"eng"}],"arxiv":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"quality_controlled":"1","month":"12","article_type":"original","type":"journal_article","external_id":{"isi":["001120776200002"],"arxiv":["2303.03772"]},"doi":"10.1107/S1600576723008324","volume":56,"has_accepted_license":"1"},{"intvolume":"        37","issue":"5","citation":{"ista":"Avni G, Jecker IR, Zikelic D. 2023. Bidding graph games with partially-observable budgets. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 5464–5471.","chicago":"Avni, Guy, Ismael R Jecker, and Dorde Zikelic. “Bidding Graph Games with Partially-Observable Budgets.” In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, 37:5464–71. AAAI Press, 2023. <a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">https://doi.org/10.1609/aaai.v37i5.25679</a>.","ieee":"G. Avni, I. R. Jecker, and D. Zikelic, “Bidding graph games with partially-observable budgets,” in <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, Washington, DC, United States, 2023, vol. 37, no. 5, pp. 5464–5471.","ama":"Avni G, Jecker IR, Zikelic D. Bidding graph games with partially-observable budgets. In: <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>. Vol 37. AAAI Press; 2023:5464-5471. doi:<a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">10.1609/aaai.v37i5.25679</a>","short":"G. Avni, I.R. Jecker, D. Zikelic, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, AAAI Press, 2023, pp. 5464–5471.","apa":"Avni, G., Jecker, I. R., &#38; Zikelic, D. (2023). Bidding graph games with partially-observable budgets. In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i> (Vol. 37, pp. 5464–5471). Washington, DC, United States: AAAI Press. <a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">https://doi.org/10.1609/aaai.v37i5.25679</a>","mla":"Avni, Guy, et al. “Bidding Graph Games with Partially-Observable Budgets.” <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, vol. 37, no. 5, AAAI Press, 2023, pp. 5464–71, doi:<a href=\"https://doi.org/10.1609/aaai.v37i5.25679\">10.1609/aaai.v37i5.25679</a>."},"publisher":"AAAI Press","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1609/aaai.v37i5.25679"}],"day":"27","date_published":"2023-06-27T00:00:00Z","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"This research was supported in part by ISF grant no.1679/21, by the ERC CoG 863818 (ForM-SMArt), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","author":[{"orcid":"0000-0001-5588-8287","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy","last_name":"Avni","full_name":"Avni, Guy"},{"first_name":"Ismael R","last_name":"Jecker","full_name":"Jecker, Ismael R","id":"85D7C63E-7D5D-11E9-9C0F-98C4E5697425"},{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde"}],"ec_funded":1,"arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","ddc":["000"],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781577358800"]},"month":"06","quality_controlled":"1","external_id":{"arxiv":["2211.13626"]},"type":"conference","volume":37,"doi":"10.1609/aaai.v37i5.25679","year":"2023","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"publication_status":"published","page":"5464-5471","scopus_import":"1","oa_version":"Published Version","conference":{"start_date":"2023-02-07","location":"Washington, DC, United States","name":"AAAI: Conference on Artificial Intelligence","end_date":"2023-02-14"},"date_updated":"2026-07-07T06:24:15Z","status":"public","_id":"14243","title":"Bidding graph games with partially-observable budgets","date_created":"2023-08-27T22:01:18Z","oa":1,"abstract":[{"lang":"eng","text":"Two-player zero-sum \"graph games\" are central in logic, verification, and multi-agent systems. The game proceeds by placing a token on a vertex of a graph, and allowing the players to move it to produce an infinite path, which determines the winner or payoff of the game. Traditionally, the players alternate turns in moving the token. In \"bidding games\", however, the players have budgets and in each turn, an auction (bidding) determines which player moves the token. So far, bidding games have only been studied as full-information games. In this work we initiate the study of partial-information bidding games: we study bidding games in which a player's initial budget is drawn from a known probability distribution. We show that while for some bidding mechanisms and objectives, it is straightforward to adapt the results from the full-information setting to the partial-information setting, for others, the analysis is significantly more challenging, requires new techniques, and gives rise to interesting results. Specifically, we study games with \"mean-payoff\" objectives in combination with \"poorman\" bidding. We construct optimal strategies for a partially-informed player who plays against a fully-informed adversary. We show that, somewhat surprisingly, the \"value\" under pure strategies does not necessarily exist in such games."}],"das_tickbox":"1"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"37th Conference on Neural Information Processing Systems","language":[{"iso":"eng"}],"arxiv":1,"acknowledgement":"Moses Charikar was supported by a Simons Investigator award. Lunjia Hu was supported by Moses Charikar’s and Omer Reingold’s Simons Investigators awards, Omer Reingold’s NSF Award IIS-1908774, and the Simons Foundation Collaboration on the Theory of Algorithmic Fairness. Part of this work was done while Erik Waingarten was a postdoc at Stanford University, supported by an NSF postdoctoral fellowship and by Moses Charikar’s Simons\r\nInvestigator Award. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme\r\n(Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data\r\nStructures (MoDynStruct)” and the Austrian Science Fund (FWF) project Z 422-N, project “Static and Dynamic Hierarchical Graph Decompositions”, I 5982-N, and project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","department":[{"_id":"MoHe"}],"author":[{"full_name":"Charikar, Moses","last_name":"Charikar","first_name":"Moses"},{"last_name":"Hu","first_name":"Lunjia","full_name":"Hu, Lunjia"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H","last_name":"Henzinger","full_name":"Henzinger, Monika H"},{"last_name":"Vötsch","first_name":"Maximilian","full_name":"Vötsch, Maximilian"},{"first_name":"Erik","last_name":"Waingarten","full_name":"Waingarten, Erik"}],"ec_funded":1,"day":"15","date_published":"2023-12-15T00:00:00Z","article_processing_charge":"Yes","file_date_updated":"2024-05-22T07:34:00Z","intvolume":"        36","file":[{"checksum":"d169a147a2adf55878e0a99e36a9d468","relation":"main_file","file_size":1445159,"access_level":"open_access","content_type":"application/pdf","date_updated":"2024-05-22T07:34:00Z","success":1,"creator":"dernst","file_name":"2023_Neurips_Charikar.pdf","file_id":"15416","date_created":"2024-05-22T07:34:00Z"}],"publisher":"Neural Information Processing Systems Foundation","citation":{"apa":"Charikar, M., Hu, L., Henzinger, M., Vötsch, M., &#38; Waingarten, E. (2023). Simple, scalable and effective clustering via one-dimensional projections. In <i>37th Conference on Neural Information Processing Systems</i> (Vol. 36). New Orleans, LA, United States: Neural Information Processing Systems Foundation.","mla":"Charikar, Moses, et al. “Simple, Scalable and Effective Clustering via One-Dimensional Projections.” <i>37th Conference on Neural Information Processing Systems</i>, vol. 36, Neural Information Processing Systems Foundation, 2023.","ieee":"M. Charikar, L. Hu, M. Henzinger, M. Vötsch, and E. Waingarten, “Simple, scalable and effective clustering via one-dimensional projections,” in <i>37th Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States, 2023, vol. 36.","chicago":"Charikar, Moses, Lunjia Hu, Monika Henzinger, Maximilian Vötsch, and Erik Waingarten. “Simple, Scalable and Effective Clustering via One-Dimensional Projections.” In <i>37th Conference on Neural Information Processing Systems</i>, Vol. 36. Neural Information Processing Systems Foundation, 2023.","ista":"Charikar M, Hu L, Henzinger M, Vötsch M, Waingarten E. 2023. Simple, scalable and effective clustering via one-dimensional projections. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36.","ama":"Charikar M, Hu L, Henzinger M, Vötsch M, Waingarten E. Simple, scalable and effective clustering via one-dimensional projections. In: <i>37th Conference on Neural Information Processing Systems</i>. Vol 36. Neural Information Processing Systems Foundation; 2023.","short":"M. Charikar, L. Hu, M. Henzinger, M. Vötsch, E. Waingarten, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023."},"volume":36,"has_accepted_license":"1","type":"conference","external_id":{"arxiv":["2310.16752"]},"quality_controlled":"1","month":"12","alternative_title":["Advances in Neural Information Processing Systems"],"publication_identifier":{"issn":["1049-5258"]},"conference":{"end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems","location":"New Orleans, LA, United States","start_date":"2023-12-10"},"date_updated":"2026-07-07T06:37:54Z","scopus_import":"1","oa_version":"Published Version","publication_status":"published","year":"2023","project":[{"name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"_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"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"das_tickbox":"1","abstract":[{"lang":"eng","text":"Clustering is a fundamental problem in unsupervised machine learning with many applications in data analysis. Popular clustering algorithms such as Lloyd's algorithm and k-means++ can make Ω(ndk) time when clustering n points in a d-dimensional space (represented by an n×d matrix X) into k clusters. On massive datasets with moderate to large k, the multiplicative \r\nk factor can become very expensive. We introduce a simple randomized clustering algorithm that provably runs in expected time O(nnz(X)+nlogn) for arbitrary k. Here nnz(X) is the total number of non-zero entries in the input dataset X, which is upper bounded by nd and can be significantly smaller for sparse datasets. We prove that our algorithm achieves approximation ratio ˜O(k4) on any input dataset for the k-means objective, and our experiments show that the quality of the clusters found by our algorithm is usually much better than this worst-case bound. We use our algorithm for k-means clustering and for coreset construction; our experiments show that it gives a new tradeoff between running time and cluster quality compared to previous state-of-the-art methods for these tasks. Our theoretical analysis is based on novel results of independent interest. We show that the approximation ratio achieved after a random one-dimensional projection can be lifted to the original points and that k-means++ seeding can be implemented in expected time O(nlogn) in one dimension."}],"date_created":"2024-05-05T22:01:05Z","oa":1,"status":"public","_id":"15364","title":"Simple, scalable and effective clustering via one-dimensional projections"},{"publication_status":"published","year":"2023","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"conference":{"end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems","location":"New Orleans, LA, United States","start_date":"2023-12-10"},"date_updated":"2026-07-07T06:37:28Z","oa_version":"Published Version","scopus_import":"1","abstract":[{"text":"Knowledge distillation is a popular approach for enhancing the performance of \"student\" models, with lower representational capacity, by taking advantage of more powerful \"teacher\" models. Despite its apparent simplicity, the underlying mechanics behind knowledge distillation (KD) are not yet fully understood. In this work, we shed new light on the inner workings of this method, by examining it from an optimization perspective. Specifically, we show that, in the context of linear and deep linear models, KD can be interpreted as a novel type of stochastic variance reduction mechanism. We provide a detailed convergence analysis of the resulting dynamics, which hold under standard assumptions for both strongly-convex and non-convex losses, showing that KD acts as a form of \\emph{partial variance reduction}, which can reduce the stochastic gradient noise, but may not eliminate it completely, depending on the properties of the teacher'' model. Our analysis puts further emphasis on the need for careful parametrization of KD, in particular w.r.t. the weighting of the distillation loss, and is validated empirically on both linear models and deep neural networks.","lang":"eng"}],"date_created":"2024-05-05T22:01:04Z","oa":1,"status":"public","_id":"15363","title":"Knowledge distillation performs partial variance reduction","das_tickbox":"1","corr_author":"1","day":"15","date_published":"2023-12-15T00:00:00Z","article_processing_charge":"Yes","file_date_updated":"2024-05-22T08:08:08Z","intvolume":"        36","file":[{"file_id":"15417","file_name":"2023_Neurips_Safaryan.pdf","creator":"dernst","date_created":"2024-05-22T08:08:08Z","checksum":"288c5148a85abf24ad5e22a6b1183655","relation":"main_file","date_updated":"2024-05-22T08:08:08Z","success":1,"content_type":"application/pdf","access_level":"open_access","file_size":672571}],"publisher":"Neural Information Processing Systems Foundation","citation":{"ama":"Safaryan M, Krumes A, Alistarh D-A. Knowledge distillation performs partial variance reduction. In: <i>36th Conference on Neural Information Processing Systems</i>. Vol 36. Neural Information Processing Systems Foundation; 2023.","ista":"Safaryan M, Krumes A, Alistarh D-A. 2023. Knowledge distillation performs partial variance reduction. 36th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 36.","ieee":"M. Safaryan, A. Krumes, and D.-A. Alistarh, “Knowledge distillation performs partial variance reduction,” in <i>36th Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States, 2023, vol. 36.","chicago":"Safaryan, Mher, Alexandra Krumes, and Dan-Adrian Alistarh. “Knowledge Distillation Performs Partial Variance Reduction.” In <i>36th Conference on Neural Information Processing Systems</i>, Vol. 36. Neural Information Processing Systems Foundation, 2023.","short":"M. Safaryan, A. Krumes, D.-A. Alistarh, in:, 36th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023.","mla":"Safaryan, Mher, et al. “Knowledge Distillation Performs Partial Variance Reduction.” <i>36th Conference on Neural Information Processing Systems</i>, vol. 36, Neural Information Processing Systems Foundation, 2023.","apa":"Safaryan, M., Krumes, A., &#38; Alistarh, D.-A. (2023). Knowledge distillation performs partial variance reduction. In <i>36th Conference on Neural Information Processing Systems</i> (Vol. 36). New Orleans, LA, United States: Neural Information Processing Systems Foundation."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"language":[{"iso":"eng"}],"publication":"36th Conference on Neural Information Processing Systems","arxiv":1,"acknowledgement":"MS has received funding from the European Union’s Horizon 2020 research and innovation programme\r\nunder the Marie Skłodowska-Curie grant agreement No 101034413.","department":[{"_id":"DaAl"}],"author":[{"last_name":"Safaryan","first_name":"Mher","full_name":"Safaryan, Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d"},{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","last_name":"Peste","first_name":"Elena-Alexandra"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"}],"ec_funded":1,"quality_controlled":"1","month":"12","alternative_title":["Advances in Neural Information Processing Systems"],"publication_identifier":{"issn":["1049-5258"]},"volume":36,"has_accepted_license":"1","type":"conference","external_id":{"arxiv":["2305.17581"]}},{"title":"Compositional policy learning in stochastic control systems with formal guarantees","_id":"15023","status":"public","oa":1,"date_created":"2024-02-25T09:23:24Z","abstract":[{"text":"Reinforcement learning has shown promising results in learning neural network policies for complicated control tasks. However, the lack of formal guarantees about the behavior of such policies remains an impediment to their deployment. We propose a novel method for learning a composition of neural network policies in stochastic environments, along with a formal certificate which guarantees that a specification over the policy's behavior is satisfied with the desired probability. Unlike prior work on verifiable RL, our approach leverages the compositional nature of logical specifications provided in SpectRL, to learn over graphs of probabilistic reach-avoid specifications. The formal guarantees are provided by learning neural network policies together with reach-avoid supermartingales (RASM) for the graph’s sub-tasks and then composing them into a global policy. We also derive a tighter lower bound compared to previous work on the probability of reach-avoidance implied by a RASM, which is required to find a compositional policy with an acceptable probabilistic threshold for complex tasks with multiple edge policies. We implement a prototype of our approach and evaluate it on a Stochastic Nine Rooms environment.","lang":"eng"}],"corr_author":"1","das_tickbox":"1","project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software"}],"year":"2023","publication_status":"published","oa_version":"Published Version","date_updated":"2026-07-07T06:36:54Z","conference":{"location":"New Orleans, LO, United States","start_date":"2023-12-10","end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems"},"alternative_title":["Advances in Neural Information Processing Systems"],"publication_identifier":{"eissn":["1049-5258"]},"month":"12","quality_controlled":"1","external_id":{"arxiv":["2312.01456"]},"type":"conference","has_accepted_license":"1","citation":{"apa":"Zikelic, D., Lechner, M., Verma, A., Chatterjee, K., &#38; Henzinger, T. A. (2023). Compositional policy learning in stochastic control systems with formal guarantees. In <i>37th Conference on Neural Information Processing Systems</i>. New Orleans, LO, United States: Neural Information Processing Systems Foundation.","mla":"Zikelic, Dorde, et al. “Compositional Policy Learning in Stochastic Control Systems with Formal Guarantees.” <i>37th Conference on Neural Information Processing Systems</i>, Neural Information Processing Systems Foundation, 2023.","ieee":"D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, and T. A. Henzinger, “Compositional policy learning in stochastic control systems with formal guarantees,” in <i>37th Conference on Neural Information Processing Systems</i>, New Orleans, LO, United States, 2023.","chicago":"Zikelic, Dorde, Mathias Lechner, Abhinav Verma, Krishnendu Chatterjee, and Thomas A Henzinger. “Compositional Policy Learning in Stochastic Control Systems with Formal Guarantees.” In <i>37th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation, 2023.","ista":"Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. 2023. Compositional policy learning in stochastic control systems with formal guarantees. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, .","ama":"Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. Compositional policy learning in stochastic control systems with formal guarantees. In: <i>37th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation; 2023.","short":"D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, T.A. Henzinger, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023."},"publisher":"Neural Information Processing Systems Foundation","file":[{"access_level":"open_access","file_size":562008,"content_type":"application/pdf","date_updated":"2024-07-22T11:45:17Z","success":1,"relation":"main_file","checksum":"739c6d72506b778302d4e708723bf12c","date_created":"2024-07-22T11:45:17Z","file_id":"17309","creator":"dernst","file_name":"2023_NeurIPS_Zikelic.pdf"}],"file_date_updated":"2024-07-22T11:45:17Z","article_processing_charge":"No","day":"15","date_published":"2023-12-15T00:00:00Z","author":[{"orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic","full_name":"Zikelic, Dorde"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"full_name":"Verma, Abhinav","first_name":"Abhinav","last_name":"Verma","id":"a235593c-d7fa-11eb-a0c5-b22ca3c66ee6"},{"last_name":"Chatterjee","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger"}],"ec_funded":1,"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093 (VAMOS) and the ERC-2020-\r\nCoG 863818 (FoRM-SMArt).","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"publication":"37th Conference on Neural Information Processing Systems","ddc":["000"]},{"month":"12","quality_controlled":"1","alternative_title":["Advances in Neural Information Processing Systems"],"publication_identifier":{"eissn":["1049-5258"]},"external_id":{"arxiv":["2305.13165"]},"type":"conference","article_processing_charge":"No","day":"15","date_published":"2023-12-15T00:00:00Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2305.13165"}],"citation":{"mla":"Súkeník, Peter, et al. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” <i>37th Conference on Neural Information Processing Systems</i>, Neural Information Processing Systems Foundation, 2023.","apa":"Súkeník, P., Mondelli, M., &#38; Lampert, C. (2023). Deep neural collapse is provably optimal for the deep unconstrained features model. In <i>37th Conference on Neural Information Processing Systems</i>. New Orleans, LA, United States: Neural Information Processing Systems Foundation.","ama":"Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal for the deep unconstrained features model. In: <i>37th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation; 2023.","ista":"Súkeník P, Mondelli M, Lampert C. 2023. Deep neural collapse is provably optimal for the deep unconstrained features model. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, .","ieee":"P. Súkeník, M. Mondelli, and C. Lampert, “Deep neural collapse is provably optimal for the deep unconstrained features model,” in <i>37th Conference on Neural Information Processing Systems</i>, New Orleans, LA, United States, 2023.","chicago":"Súkeník, Peter, Marco Mondelli, and Christoph Lampert. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” In <i>37th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation, 2023.","short":"P. Súkeník, M. Mondelli, C. Lampert, in:, 37th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2023."},"publisher":"Neural Information Processing Systems Foundation","arxiv":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"37th Conference on Neural Information Processing Systems","language":[{"iso":"eng"}],"department":[{"_id":"MaMo"},{"_id":"ChLa"}],"acknowledgement":"M. M. is partially supported by the 2019 Lopez-Loreta Prize. The authors would like to thank Eugenia Iofinova, Bernd Prach and Simone Bombari for valuable feedback on the manuscript.","author":[{"id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","last_name":"Súkeník","first_name":"Peter","full_name":"Súkeník, Peter"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","first_name":"Marco"},{"first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2024-02-02T11:17:41Z","oa":1,"abstract":[{"lang":"eng","text":"Neural collapse (NC) refers to the surprising structure of the last layer of deep neural networks in the terminal phase of gradient descent training. Recently, an increasing amount of experimental evidence has pointed to the propagation of NC to earlier layers of neural networks. However, while the NC in the last layer is well studied theoretically, much less is known about its multi-layered counterpart - deep neural collapse (DNC). In particular, existing work focuses either on linear layers or only on the last two layers at the price of an extra assumption. Our paper fills this gap by generalizing the established analytical framework for NC - the unconstrained features model - to multiple non-linear layers. Our key technical contribution is to show that, in a deep unconstrained features model, the unique global optimum for binary classification exhibits all the properties typical of DNC. This explains the existing experimental evidence of DNC. We also empirically show that (i) by optimizing deep unconstrained features models via gradient descent, the resulting solution agrees well with our theory, and (ii) trained networks recover the unconstrained features suitable for the occurrence of DNC, thus supporting the validity of this modeling principle."}],"_id":"14921","status":"public","title":"Deep neural collapse is provably optimal for the deep unconstrained features model","das_tickbox":"1","corr_author":"1","publication_status":"published","year":"2023","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"}],"conference":{"end_date":"2023-12-16","name":"NeurIPS: Neural Information Processing Systems","start_date":"2023-12-10","location":"New Orleans, LA, United States"},"date_updated":"2026-07-07T06:35:57Z","oa_version":"Preprint"},{"month":"07","quality_controlled":"1","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"alternative_title":["LNCS"],"volume":13964,"has_accepted_license":"1","doi":"10.1007/978-3-031-37706-8_8","external_id":{"isi":["001310786500008"]},"type":"conference","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-07-17T00:00:00Z","day":"17","file_date_updated":"2023-09-06T08:16:25Z","intvolume":"     13964","citation":{"short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 156–169.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: <i>35th International Conference on Computer Aided Verification</i>. Vol 13964. Springer Nature; 2023:156-169. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in <i>35th International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13964, pp. 156–169.","ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In <i>35th International Conference on Computer Aided Verification</i>, 13964:156–69. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>.","mla":"Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” <i>35th International Conference on Computer Aided Verification</i>, vol. 13964, Springer Nature, 2023, pp. 156–69, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">10.1007/978-3-031-37706-8_8</a>.","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In <i>35th International Conference on Computer Aided Verification</i> (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_8\">https://doi.org/10.1007/978-3-031-37706-8_8</a>"},"file":[{"file_name":"2023_LNCS_Koval.pdf","creator":"dernst","file_id":"14275","date_created":"2023-09-06T08:16:25Z","checksum":"c346016393123a0a2338ad4d976f61bc","relation":"main_file","access_level":"open_access","file_size":421408,"success":1,"content_type":"application/pdf","date_updated":"2023-09-06T08:16:25Z"}],"publisher":"Springer Nature","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"publication":"35th International Conference on Computer Aided Verification","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"related_material":{"record":[{"id":"14995","status":"public","relation":"research_data"}]},"author":[{"first_name":"Nikita","last_name":"Koval","full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Alexander","last_name":"Fedorov","full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"first_name":"Maria","last_name":"Sokolova","full_name":"Sokolova, Maria"},{"full_name":"Tsitelov, Dmitry","first_name":"Dmitry","last_name":"Tsitelov"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"}],"oa":1,"date_created":"2023-09-03T22:01:16Z","abstract":[{"lang":"eng","text":"This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness."}],"status":"public","_id":"14260","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","das_tickbox":"1","isi":1,"page":"156-169","publication_status":"published","year":"2023","conference":{"location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22","name":"CAV: Computer Aided Verification"},"date_updated":"2026-07-07T13:39:36Z","scopus_import":"1","oa_version":"Published Version"},{"isi":1,"das_tickbox":"1","title":"Guessing winning policies in LTL synthesis by semantic learning","_id":"14259","status":"public","oa":1,"date_created":"2023-09-03T22:01:16Z","abstract":[{"text":"We provide a learning-based technique for guessing a winning strategy in a parity game originating from an LTL synthesis problem. A cheaply obtained guess can be useful in several applications. Not only can the guessed strategy be applied as best-effort in cases where the game’s huge size prohibits rigorous approaches, but it can also increase the scalability of rigorous LTL synthesis in several ways. Firstly, checking whether a guessed strategy is winning is easier than constructing one. Secondly, even if the guess is wrong in some places, it can be fixed by strategy iteration faster than constructing one from scratch. Thirdly, the guess can be used in on-the-fly approaches to prioritize exploration in the most fruitful directions.\r\nIn contrast to previous works, we (i) reflect the highly structured logical information in game’s states, the so-called semantic labelling, coming from the recent LTL-to-automata translations, and (ii) learn to reflect it properly by learning from previously solved games, bringing the solving process closer to human-like reasoning.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","date_updated":"2026-07-07T13:39:23Z","conference":{"location":"Paris, France","start_date":"2023-07-17","end_date":"2023-07-22","name":"CAV: Computer Aided Verification"},"year":"2023","publication_status":"published","page":"390-414","external_id":{"isi":["001310786500020"]},"type":"conference","has_accepted_license":"1","volume":13964,"doi":"10.1007/978-3-031-37706-8_20","alternative_title":["LNCS"],"publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031377051"]},"month":"07","quality_controlled":"1","author":[{"full_name":"Kretinsky, Jan","first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8122-2881"},{"first_name":"Tobias","last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1"},{"full_name":"Prokop, Maximilian","last_name":"Prokop","first_name":"Maximilian"},{"last_name":"Rieder","first_name":"Sabine","full_name":"Rieder, Sabine"}],"department":[{"_id":"KrCh"}],"acknowledgement":"This research was funded in part by the German Research Foundation (DFG) project 427755713 Group-By Objectives in Probabilistic Verification (GOPro).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"publication":"35th International Conference on Computer Aided Verification","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"apa":"Kretinsky, J., Meggendorfer, T., Prokop, M., &#38; Rieder, S. (2023). Guessing winning policies in LTL synthesis by semantic learning. In <i>35th International Conference on Computer Aided Verification</i> (Vol. 13964, pp. 390–414). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>","mla":"Kretinsky, Jan, et al. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” <i>35th International Conference on Computer Aided Verification</i>, vol. 13964, Springer Nature, 2023, pp. 390–414, doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>.","ieee":"J. Kretinsky, T. Meggendorfer, M. Prokop, and S. Rieder, “Guessing winning policies in LTL synthesis by semantic learning,” in <i>35th International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13964, pp. 390–414.","ista":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. 2023. Guessing winning policies in LTL synthesis by semantic learning. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13964, 390–414.","chicago":"Kretinsky, Jan, Tobias Meggendorfer, Maximilian Prokop, and Sabine Rieder. “Guessing Winning Policies in LTL Synthesis by Semantic Learning.” In <i>35th International Conference on Computer Aided Verification</i>, 13964:390–414. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">https://doi.org/10.1007/978-3-031-37706-8_20</a>.","ama":"Kretinsky J, Meggendorfer T, Prokop M, Rieder S. Guessing winning policies in LTL synthesis by semantic learning. In: <i>35th International Conference on Computer Aided Verification</i>. Vol 13964. Springer Nature; 2023:390-414. doi:<a href=\"https://doi.org/10.1007/978-3-031-37706-8_20\">10.1007/978-3-031-37706-8_20</a>","short":"J. Kretinsky, T. Meggendorfer, M. Prokop, S. Rieder, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 390–414."},"file":[{"access_level":"open_access","file_size":428354,"success":1,"content_type":"application/pdf","date_updated":"2023-09-06T08:25:50Z","checksum":"ed66278b61bb869e1baba3d9b9081271","relation":"main_file","date_created":"2023-09-06T08:25:50Z","file_id":"14276","file_name":"2023_LNCS_CAV_Kretinsky.pdf","creator":"dernst"}],"publisher":"Springer Nature","intvolume":"     13964","file_date_updated":"2023-09-06T08:25:50Z","article_processing_charge":"Yes (in subscription journal)","date_published":"2023-07-17T00:00:00Z","day":"17"},{"year":"2023","publisher":"Zenodo","citation":{"ista":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7877757\">10.5281/ZENODO.7877757</a>.","ieee":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM.” Zenodo, 2023.","chicago":"Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7877757\">https://doi.org/10.5281/ZENODO.7877757</a>.","ama":"Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7877757\">10.5281/ZENODO.7877757</a>","short":"N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023).","apa":"Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., &#38; Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7877757\">https://doi.org/10.5281/ZENODO.7877757</a>","mla":"Koval, Nikita, et al. <i>Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7877757\">10.5281/ZENODO.7877757</a>."},"day":"28","date_published":"2023-04-28T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7877757"}],"article_processing_charge":"No","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14260"}]},"department":[{"_id":"DaAl"}],"author":[{"full_name":"Koval, Nikita","last_name":"Koval","first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Fedorov, Alexander","first_name":"Alexander","last_name":"Fedorov","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6"},{"full_name":"Sokolova, Maria","last_name":"Sokolova","first_name":"Maria"},{"full_name":"Tsitelov, Dmitry","last_name":"Tsitelov","first_name":"Dmitry"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"}],"oa_version":"Published Version","date_updated":"2026-07-07T13:39:35Z","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14995","status":"public","title":"Lincheck: A practical framework for testing concurrent data structures on JVM","abstract":[{"text":"Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. \r\nThe artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation.","lang":"eng"}],"month":"04","date_created":"2024-02-14T15:14:13Z","oa":1,"type":"research_data_reference","doi":"10.5281/ZENODO.7877757"},{"publication_identifier":{"issn":["0097-5397"],"eissn":["1095-7111"]},"article_type":"original","month":"04","quality_controlled":"1","external_id":{"isi":["001013183000012"]},"type":"journal_article","volume":52,"doi":"10.1137/21M1412918","intvolume":"        52","issue":"2","citation":{"ieee":"J. D. Boissonnat, S. Kachanovich, and M. Wintraecken, “Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations,” <i>SIAM Journal on Computing</i>, vol. 52, no. 2. Society for Industrial and Applied Mathematics, pp. 452–486, 2023.","chicago":"Boissonnat, Jean Daniel, Siargey Kachanovich, and Mathijs Wintraecken. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics, 2023. <a href=\"https://doi.org/10.1137/21M1412918\">https://doi.org/10.1137/21M1412918</a>.","ista":"Boissonnat JD, Kachanovich S, Wintraecken M. 2023. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. SIAM Journal on Computing. 52(2), 452–486.","ama":"Boissonnat JD, Kachanovich S, Wintraecken M. Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. <i>SIAM Journal on Computing</i>. 2023;52(2):452-486. doi:<a href=\"https://doi.org/10.1137/21M1412918\">10.1137/21M1412918</a>","short":"J.D. Boissonnat, S. Kachanovich, M. Wintraecken, SIAM Journal on Computing 52 (2023) 452–486.","apa":"Boissonnat, J. D., Kachanovich, S., &#38; Wintraecken, M. (2023). Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations. <i>SIAM Journal on Computing</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/21M1412918\">https://doi.org/10.1137/21M1412918</a>","mla":"Boissonnat, Jean Daniel, et al. “Tracing Isomanifolds in Rd in Time Polynomial in d Using Coxeter–Freudenthal–Kuhn Triangulations.” <i>SIAM Journal on Computing</i>, vol. 52, no. 2, Society for Industrial and Applied Mathematics, 2023, pp. 452–86, doi:<a href=\"https://doi.org/10.1137/21M1412918\">10.1137/21M1412918</a>."},"publisher":"Society for Industrial and Applied Mathematics","article_processing_charge":"No","date_published":"2023-04-30T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://hal-emse.ccsd.cnrs.fr/3IA-COTEDAZUR/hal-04083489v1"}],"day":"30","department":[{"_id":"HeEd"}],"acknowledgement":"The authors have received funding from the European Research Council under the European Union's ERC grant greement 339025 GUDHI (Algorithmic Foundations of Geometric Un-derstanding  in  Higher  Dimensions).   The  first  author  was  supported  by  the  French  government,through the 3IA C\\^ote d'Azur Investments in the Future project managed by the National ResearchAgency (ANR) with the reference ANR-19-P3IA-0002.  The third author was supported by the Eu-ropean Union's Horizon 2020 research and innovation programme under the Marie Sk\\lodowska-Curiegrant agreement 754411 and the FWF (Austrian Science Fund) grant M 3073.","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"9441"}]},"ec_funded":1,"author":[{"full_name":"Boissonnat, Jean Daniel","last_name":"Boissonnat","first_name":"Jean Daniel"},{"full_name":"Kachanovich, Siargey","first_name":"Siargey","last_name":"Kachanovich"},{"full_name":"Wintraecken, Mathijs","first_name":"Mathijs","last_name":"Wintraecken","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220"}],"language":[{"iso":"eng"}],"publication":"SIAM Journal on Computing","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"12960","title":"Tracing isomanifolds in Rd in time polynomial in d using Coxeter–Freudenthal–Kuhn triangulations","date_created":"2023-05-14T22:01:00Z","oa":1,"abstract":[{"lang":"eng","text":"Isomanifolds are the generalization of isosurfaces to arbitrary dimension and codimension, i.e., submanifolds of Rd defined as the zero set of some multivariate multivalued smooth function f:Rd→Rd−n, where n is the intrinsic dimension of the manifold. A natural way to approximate a smooth isomanifold M=f−1(0) is to consider its piecewise linear (PL) approximation M^\r\n based on a triangulation T of the ambient space Rd. In this paper, we describe a simple algorithm to trace isomanifolds from a given starting point. The algorithm works for arbitrary dimensions n and d, and any precision D. Our main result is that, when f (or M) has bounded complexity, the complexity of the algorithm is polynomial in d and δ=1/D (and unavoidably exponential in n). Since it is known that for δ=Ω(d2.5), M^ is O(D2)-close and isotopic to M\r\n, our algorithm produces a faithful PL-approximation of isomanifolds of bounded complexity in time polynomial in d. Combining this algorithm with dimensionality reduction techniques, the dependency on d in the size of M^ can be completely removed with high probability. We also show that the algorithm can handle isomanifolds with boundary and, more generally, isostratifolds. The algorithm for isomanifolds with boundary has been implemented and experimental results are reported, showing that it is practical and can handle cases that are far ahead of the state-of-the-art. "}],"isi":1,"corr_author":"1","year":"2023","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Learning and triangulating manifolds via collapses","grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2"}],"publication_status":"published","page":"452-486","oa_version":"Submitted Version","scopus_import":"1","date_updated":"2026-07-07T13:43:40Z"}]