[{"month":"03","department":[{"_id":"TiVo"}],"external_id":{"isi":["001190689800001"],"pmid":["38484020"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":20,"citation":{"apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., &#38; Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">https://doi.org/10.1371/journal.pcbi.1011941</a>","ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. <i>PLoS Computational Biology</i>. 2024;20(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">10.1371/journal.pcbi.1011941</a>","chicago":"Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">https://doi.org/10.1371/journal.pcbi.1011941</a>.","ieee":"C. Chintaluri <i>et al.</i>, “kCSD-python, reliable current source density estimation with quality control,” <i>PLoS Computational Biology</i>, vol. 20, no. 3. Public Library of Science, 2024.","ista":"Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941.","mla":"Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” <i>PLoS Computational Biology</i>, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011941\">10.1371/journal.pcbi.1011941</a>.","short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024)."},"status":"public","publisher":"Public Library of Science","file":[{"success":1,"relation":"main_file","file_name":"2024_PLoSCompBio_Chintaluri.pdf","creator":"dernst","access_level":"open_access","file_size":2540277,"file_id":"19897","checksum":"c09718d0d09614642d877d0716ce32e8","date_created":"2025-06-25T05:47:36Z","content_type":"application/pdf","date_updated":"2025-06-25T05:47:36Z"}],"scopus_import":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"link":[{"url":"https://github.com/Neuroinflab/kCSD-python","relation":"software"}]},"has_accepted_license":"1","article_type":"original","day":"14","quality_controlled":"1","OA_type":"gold","year":"2024","article_number":"e1011941","oa_version":"Published Version","file_date_updated":"2025-06-25T05:47:36Z","isi":1,"author":[{"full_name":"Chintaluri, Chaitanya","id":"BA06AFEE-A4BA-11EA-AE5C-14673DDC885E","last_name":"Chintaluri","orcid":"0000-0003-4252-1608","first_name":"Chaitanya"},{"full_name":"Bejtka, Marta","last_name":"Bejtka","first_name":"Marta"},{"first_name":"Wladyslaw","last_name":"Sredniawa","full_name":"Sredniawa, Wladyslaw"},{"full_name":"Czerwinski, Michal","first_name":"Michal","last_name":"Czerwinski"},{"full_name":"Dzik, Jakub M.","last_name":"Dzik","first_name":"Jakub M."},{"full_name":"Jedrzejewska-Szmek, Joanna","last_name":"Jedrzejewska-Szmek","first_name":"Joanna"},{"full_name":"Wojciki, Daniel K.","last_name":"Wojciki","first_name":"Daniel K."}],"acknowledgement":"The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ","pmid":1,"oa":1,"publication_status":"published","DOAJ_listed":"1","publication":"PLoS Computational Biology","OA_place":"publisher","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"doi":"10.1371/journal.pcbi.1011941","date_updated":"2026-07-13T12:30:33Z","title":"kCSD-python, reliable current source density estimation with quality control","date_published":"2024-03-14T00:00:00Z","abstract":[{"text":"Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results.","lang":"eng"}],"corr_author":"1","intvolume":"        20","issue":"3","date_created":"2024-03-24T23:00:59Z","type":"journal_article","article_processing_charge":"Yes","das_tickbox":"1","_id":"15169","ddc":["000","570"]},{"title":"Inference of genetic effects via approximate message passing","date_published":"2024-04-19T00:00:00Z","abstract":[{"text":"Efficient utilization of large-scale biobank data is crucial for inferring the genetic basis of disease and predicting health outcomes from the DNA. Yet we lack efficient, accurate methods that scale to data where electronic health records are linked to whole genome sequence information. To address this issue, our paper develops a new algorithmic paradigm based on Approximate Message Passing (AMP), which is specifically tailored for genomic prediction and association testing. Our method yields comparable out-of-sample prediction accuracy to the state of the art on UK Biobank traits, whilst dramatically improving computational complexity, with a 8x-speed up in the run time. In addition, AMP theory provides a joint association testing framework, which outperforms the currently used REGENIE method, in roughly a third of the compute time. This first, truly large-scale application of the AMP framework lays the foundations for a far wider range of statistical analyses for hundreds of millions of variables measured on millions of people.","lang":"eng"}],"publication_identifier":{"isbn":["9798350344851"],"issn":["1520-6149"]},"doi":"10.1109/ICASSP48485.2024.10447198","date_updated":"2026-07-13T14:57:55Z","oa":1,"publication_status":"published","publication":"2024 IEEE International Conference on Acoustics, Speech, and Signal Processing","OA_place":"repository","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by a Lopez-Loreta Prize to MM, an SNSF Eccellenza Grant to MRR (PCEGP3-181181), and core funding from ISTA. The authors thank Philip Schniter, Matthew Stephens and Pragya Sur for valuable suggestions on an early version of the work. The authors acknowledge the participants and investigators of the UK Biobank study. High-performance\r\ncomputing was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp).","main_file_link":[{"open_access":"1","url":"https://openreview.net/forum?id=aQYCDxfZV0"}],"article_processing_charge":"No","_id":"17147","page":"13151-13155","date_created":"2024-06-16T22:01:07Z","type":"conference","corr_author":"1","day":"19","publisher":"IEEE","scopus_import":"1","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"ista":"Depope A, Mondelli M, Robinson MR. 2024. Inference of genetic effects via approximate message passing. 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing. ICASSP: International Conference on Acoustics, Speech and Signal Processing, 13151–13155.","ama":"Depope A, Mondelli M, Robinson MR. Inference of genetic effects via approximate message passing. In: <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>. IEEE; 2024:13151-13155. doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>","chicago":"Depope, Al, Marco Mondelli, and Matthew Richard Robinson. “Inference of Genetic Effects via Approximate Message Passing.” In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, 13151–55. IEEE, 2024. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>.","ieee":"A. Depope, M. Mondelli, and M. R. Robinson, “Inference of genetic effects via approximate message passing,” in <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, Seoul, Korea, 2024, pp. 13151–13155.","apa":"Depope, A., Mondelli, M., &#38; Robinson, M. R. (2024). Inference of genetic effects via approximate message passing. In <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i> (pp. 13151–13155). Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">https://doi.org/10.1109/ICASSP48485.2024.10447198</a>","short":"A. Depope, M. Mondelli, M.R. Robinson, in:, 2024 IEEE International Conference on Acoustics, Speech, and Signal Processing, IEEE, 2024, pp. 13151–13155.","mla":"Depope, Al, et al. “Inference of Genetic Effects via Approximate Message Passing.” <i>2024 IEEE International Conference on Acoustics, Speech, and Signal Processing</i>, IEEE, 2024, pp. 13151–55, doi:<a href=\"https://doi.org/10.1109/ICASSP48485.2024.10447198\">10.1109/ICASSP48485.2024.10447198</a>."},"month":"04","department":[{"_id":"MaMo"},{"_id":"MaRo"}],"conference":{"location":"Seoul, Korea","name":"ICASSP: International Conference on Acoustics, Speech and Signal Processing","end_date":"2024-04-19","start_date":"2024-04-14"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001396233806078"]},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"},{"_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A","name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181"}],"author":[{"first_name":"Al","last_name":"Depope","id":"0b77531d-dbcd-11ea-9d1d-a8eee0bf3830","full_name":"Depope, Al"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli"},{"last_name":"Robinson","orcid":"0000-0001-8982-8813","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"}],"isi":1,"OA_type":"green","year":"2024","oa_version":"Submitted Version","quality_controlled":"1"},{"issue":"22","corr_author":"1","intvolume":"        14","article_processing_charge":"Yes (via OA deal)","ddc":["530"],"_id":"15182","date_created":"2024-03-25T08:57:40Z","type":"journal_article","oa":1,"publication_status":"published","publication":"Advanced Energy Materials","language":[{"iso":"eng"}],"acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","date_published":"2024-06-12T00:00:00Z","abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["1614-6832"],"eissn":["1614-6840"]},"doi":"10.1002/aenm.202400408","date_updated":"2026-07-17T07:09:41Z","year":"2024","article_number":"2400408","oa_version":"Published Version","file_date_updated":"2024-07-22T12:07:56Z","quality_controlled":"1","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","full_name":"Kleinhanns, Tobias","orcid":"0000-0003-1537-7436","first_name":"Tobias","last_name":"Kleinhanns"},{"full_name":"Milillo, Francesco","id":"38b830db-ea88-11ee-bf9b-929beaf79054","last_name":"Milillo","first_name":"Francesco"},{"orcid":"0000-0003-4566-5877","first_name":"Mariano","last_name":"Calcabrini","id":"45D7531A-F248-11E8-B48F-1D18A9856A87","full_name":"Calcabrini, Mariano"},{"id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine","first_name":"Christine","last_name":"Fiedler"},{"full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","last_name":"Horta","first_name":"Sharona"},{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","orcid":"0000-0001-7597-043X","first_name":"Daniel"},{"first_name":"Marissa J.","last_name":"Strumolo","full_name":"Strumolo, Marissa J."},{"last_name":"Hasler","first_name":"Roger","full_name":"Hasler, Roger"},{"full_name":"Llorca, Jordi","first_name":"Jordi","last_name":"Llorca"},{"full_name":"Tkadletz, Michael","last_name":"Tkadletz","first_name":"Michael"},{"full_name":"Brutchey, Richard L.","last_name":"Brutchey","first_name":"Richard L."},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","first_name":"Maria","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"}],"isi":1,"citation":{"mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>, vol. 14, no. 22, 2400408, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials 14 (2024).","ieee":"T. Kleinhanns <i>et al.</i>, “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” <i>Advanced Energy Materials</i>, vol. 14, no. 22. Wiley, 2024.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” <i>Advanced Energy Materials</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>.","ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. 2024;14(22). doi:<a href=\"https://doi.org/10.1002/aenm.202400408\">10.1002/aenm.202400408</a>","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. <i>Advanced Energy Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/aenm.202400408\">https://doi.org/10.1002/aenm.202400408</a>","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 14(22), 2400408."},"month":"06","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"external_id":{"isi":["001184300200001"]},"volume":14,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","day":"12","article_type":"original","scopus_import":"1","publisher":"Wiley","file":[{"date_updated":"2024-07-22T12:07:56Z","date_created":"2024-07-22T12:07:56Z","content_type":"application/pdf","access_level":"open_access","file_size":8824301,"file_id":"17314","checksum":"86b26430e00d5f43ea19e9b610692ab7","file_name":"2024_AdvancedEnergyMaterials_Kleinhanns.pdf","creator":"dernst","success":1,"relation":"main_file"}],"status":"public","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"related_material":{"record":[{"id":"22017","relation":"dissertation_contains","status":"public"}]},"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"has_accepted_license":"1"},{"article_processing_charge":"Yes","arxiv":1,"_id":"18951","das_tickbox":"1","date_created":"2025-01-29T10:57:09Z","type":"journal_article","title":"Local dimer dynamics in higher dimensions","date_published":"2024-08-26T00:00:00Z","abstract":[{"text":"We consider local dynamics of the dimer model (perfect matchings) on hypercubic boxes [n] \r\nd . These consist of successively switching the dimers along alternating cycles of prescribed (small) lengths. We study the connectivity properties of the dimer configuration space equipped with these transitions. Answering a question of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any configuration admits an alternating cycle of length at most 6. We further establish that any configuration on [n] d  features order n d−2  alternating cycles of length at most 4d−2. We also prove that the dynamics of dimer configurations on the unit hypercube of dimension d is ergodic when switching alternating cycles of length at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped boxes in the triangular lattice are ergodic for switching alternating cycles of lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also uses 8-cycles. None of our proofs make reference to height functions.","lang":"eng"}],"publication_identifier":{"eissn":["2308-5835"],"issn":["2308-5827"]},"doi":"10.4171/aihpd/200","date_updated":"2026-07-23T05:41:50Z","oa":1,"publication_status":"epub_ahead","publication":"Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions","DOAJ_listed":"1","OA_place":"repository","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2304.10930","open_access":"1"}],"author":[{"last_name":"Hartarsky","first_name":"Ivailo","full_name":"Hartarsky, Ivailo"},{"full_name":"Lichev, Lyuben","id":"9aa8388e-d003-11ee-8458-c4c1d7447977","last_name":"Lichev","first_name":"Lyuben"},{"full_name":"Toninelli, Fabio Lucio","first_name":"Fabio Lucio","last_name":"Toninelli"}],"OA_type":"gold","year":"2024","oa_version":"Preprint","quality_controlled":"1","day":"26","article_type":"original","status":"public","publisher":"EMS Press","scopus_import":"1","citation":{"mla":"Hartarsky, Ivailo, et al. “Local Dimer Dynamics in Higher Dimensions.” <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions</i>, EMS Press, 2024, doi:<a href=\"https://doi.org/10.4171/aihpd/200\">10.4171/aihpd/200</a>.","short":"I. Hartarsky, L. Lichev, F.L. Toninelli, Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions (2024).","ama":"Hartarsky I, Lichev L, Toninelli FL. Local dimer dynamics in higher dimensions. <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions</i>. 2024. doi:<a href=\"https://doi.org/10.4171/aihpd/200\">10.4171/aihpd/200</a>","chicago":"Hartarsky, Ivailo, Lyuben Lichev, and Fabio Lucio Toninelli. “Local Dimer Dynamics in Higher Dimensions.” <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions</i>. EMS Press, 2024. <a href=\"https://doi.org/10.4171/aihpd/200\">https://doi.org/10.4171/aihpd/200</a>.","ieee":"I. Hartarsky, L. Lichev, and F. L. Toninelli, “Local dimer dynamics in higher dimensions,” <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions</i>. EMS Press, 2024.","apa":"Hartarsky, I., Lichev, L., &#38; Toninelli, F. L. (2024). Local dimer dynamics in higher dimensions. <i>Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions</i>. EMS Press. <a href=\"https://doi.org/10.4171/aihpd/200\">https://doi.org/10.4171/aihpd/200</a>","ista":"Hartarsky I, Lichev L, Toninelli FL. 2024. Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions."},"mathsc":["05B50","05C70","82C20"],"month":"08","department":[{"_id":"MaKw"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2304.10930"]}},{"title":"Eight-partitioning points in 3D, and efficiently too","date_published":"2024-06-06T00:00:00Z","abstract":[{"lang":"eng","text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in ℝ³ consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument.\r\nWe prove the following variant of this result: Any mass distribution (or point set) in ℝ³ admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction.\r\nMoreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2})."}],"publication_identifier":{"isbn":["9783959773164"]},"doi":"10.4230/LIPIcs.SoCG.2024.8","date_updated":"2026-07-23T11:14:45Z","oa":1,"publication":"40th International Symposium on Computational Geometry","publication_status":"published","OA_place":"publisher","language":[{"iso":"eng"}],"acknowledgement":"Aronov, Boris: Work has been supported by NSF grants CCF 15-40656 and CCF 20-08551, and by grant 2014/170 from the US-Israel Binational Science Foundation. Part of this research was conducted while BA was visiting ISTA in the summers of 2022 and 2023. The visit of BA to ISTA in the summer of 2022 was supported by an ISTA Visiting Professorship.\r\nBasit, Abdul: Work has been supported by Australian Research Council grant DP220102212.\r\nRamesh, Indu: Work supported by a Tandon School of Engineering Fellowship and by NSF Grant CCF-20-08551.\r\nBA and AB would like to thank William Steiger for insightful initial discussions of the problems addressed in this work.","article_processing_charge":"Yes","arxiv":1,"_id":"18917","ddc":["510"],"page":"8:1-8:15","date_created":"2025-01-27T14:19:17Z","type":"conference","corr_author":"1","intvolume":"       293","day":"06","scopus_import":"1","status":"public","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","file":[{"date_created":"2025-01-27T14:17:37Z","content_type":"application/pdf","date_updated":"2025-01-27T14:17:37Z","file_name":"2024_LIPICs_Aronov.pdf","creator":"dernst","access_level":"open_access","file_size":880725,"checksum":"443aa29ea5d948e917cfccd681dcf176","file_id":"18918","success":1,"relation":"main_file"}],"related_material":{"record":[{"status":"public","id":"19860","relation":"later_version"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"has_accepted_license":"1","citation":{"ista":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. 2024. Eight-partitioning points in 3D, and efficiently too. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry vol. 293, 8:1-8:15.","apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2024). Eight-partitioning points in 3D, and efficiently too. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 8:1-8:15). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">https://doi.org/10.4230/LIPIcs.SoCG.2024.8</a>","ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 8:1-8:15.","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:8:1-8:15. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">10.4230/LIPIcs.SoCG.2024.8</a>","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” In <i>40th International Symposium on Computational Geometry</i>, 293:8:1-8:15. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">https://doi.org/10.4230/LIPIcs.SoCG.2024.8</a>.","short":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, U. Wagner, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15.","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">10.4230/LIPIcs.SoCG.2024.8</a>."},"month":"06","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Athens, Greece","start_date":"2024-06-11","end_date":"2024-06-14"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2403.02627"]},"volume":293,"author":[{"full_name":"Aronov, Boris","first_name":"Boris","last_name":"Aronov"},{"last_name":"Basit","first_name":"Abdul","full_name":"Basit, Abdul"},{"first_name":"Indu","last_name":"Ramesh","full_name":"Ramesh, Indu"},{"first_name":"Gianluca","last_name":"Tasinato","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca"},{"last_name":"Wagner","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"gold","year":"2024","oa_version":"Published Version","file_date_updated":"2025-01-27T14:17:37Z","quality_controlled":"1"},{"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"id":"22281","relation":"dissertation_contains","status":"public"}]},"ec_funded":1,"file":[{"date_created":"2024-11-18T08:02:45Z","content_type":"application/pdf","date_updated":"2024-11-18T08:02:45Z","creator":"dernst","file_name":"2024_LIPIcs_ElHayek.pdf","access_level":"open_access","file_size":809666,"file_id":"18561","checksum":"d6c8277331cafa188c33ba1717206cf4","success":1,"relation":"main_file"}],"scopus_import":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","status":"public","day":"24","external_id":{"arxiv":["2302.11988"],"isi":["001542467600021"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":319,"conference":{"end_date":"2024-11-01","start_date":"2024-10-28","location":"Madrid, Spain","name":"DISC: Symposium on Distributed Computing"},"department":[{"_id":"MoHe"}],"month":"10","citation":{"ista":"El-Hayek A, Henzinger M, Schmid S. 2024. Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges. 38th International Symposium on Distributed Computing. DISC: Symposium on Distributed Computing, LIPIcs, vol. 319, 21.","chicago":"El-Hayek, Antoine, Monika Henzinger, and Stefan Schmid. “Broadcast and Consensus in Stochastic Dynamic Networks with Byzantine Nodes and Adversarial Edges.” In <i>38th International Symposium on Distributed Computing</i>, Vol. 319. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">https://doi.org/10.4230/LIPIcs.DISC.2024.21</a>.","ama":"El-Hayek A, Henzinger M, Schmid S. Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges. In: <i>38th International Symposium on Distributed Computing</i>. Vol 319. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">10.4230/LIPIcs.DISC.2024.21</a>","ieee":"A. El-Hayek, M. Henzinger, and S. Schmid, “Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges,” in <i>38th International Symposium on Distributed Computing</i>, Madrid, Spain, 2024, vol. 319.","apa":"El-Hayek, A., Henzinger, M., &#38; Schmid, S. (2024). Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges. In <i>38th International Symposium on Distributed Computing</i> (Vol. 319). Madrid, Spain: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">https://doi.org/10.4230/LIPIcs.DISC.2024.21</a>","short":"A. El-Hayek, M. Henzinger, S. Schmid, in:, 38th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"El-Hayek, Antoine, et al. “Broadcast and Consensus in Stochastic Dynamic Networks with Byzantine Nodes and Adversarial Edges.” <i>38th International Symposium on Distributed Computing</i>, vol. 319, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2024.21\">10.4230/LIPIcs.DISC.2024.21</a>."},"isi":1,"author":[{"id":"888a098e-fcac-11ee-aff7-d347be57b725","full_name":"El-Hayek, Antoine","first_name":"Antoine","orcid":"0000-0003-4268-7368","last_name":"El-Hayek"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Stefan","last_name":"Schmid","full_name":"Schmid, Stefan"}],"project":[{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"},{"_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","call_identifier":"H2020"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","name":"Efficient algorithms","grant_number":"Z00422"},{"_id":"bda196b2-d553-11ed-ba76-8e8ee6c21103","name":"Static and Dynamic Hierarchical Graph Decompositions","grant_number":"I05982"}],"quality_controlled":"1","file_date_updated":"2024-11-18T08:02:45Z","article_number":"21","oa_version":"Published Version","year":"2024","OA_type":"gold","date_updated":"2026-07-24T12:48:28Z","doi":"10.4230/LIPIcs.DISC.2024.21","publication_identifier":{"issn":["1868-8969"],"isbn":["9783959773522"]},"abstract":[{"lang":"eng","text":"Broadcast and Consensus are most fundamental tasks in distributed computing. These tasks are particularly challenging in dynamic networks where communication across the network links may be unreliable, e.g., due to mobility or failures. Over the last years, researchers have derived several impossibility results and high time complexity lower bounds for these tasks. Specifically for the setting where in each round of communication the adversary is allowed to choose one rooted tree along which the information is disseminated, there is a lower as well as an upper bound that is linear in the number n of nodes for Broadcast and for n ≥ 3 the adversary can guarantee that Consensus never happens. This setting is called the oblivious message adversary for rooted trees. Also note that if the adversary is allowed to choose a graph that does not contain a rooted tree, then it can guarantee that Broadcast and Consensus will never happen. However, such deterministic adversarial models may be overly pessimistic, as many processes in real-world settings are stochastic in nature rather than worst-case. This paper studies Broadcast on stochastic dynamic networks and shows that the situation is very different to the deterministic case. In particular, we show that if information dissemination occurs along random rooted trees and directed Erdős–Rényi graphs, Broadcast completes in O(log n) rounds of communication with high probability. The fundamental insight in our analysis is that key variables are mutually independent. We then study two adversarial models, (a) one with Byzantine nodes and (b) one where an adversary controls the edges. (a) Our techniques without Byzantine nodes are general enough so that they can be extended to Byzantine nodes. (b) In the spirit of smoothed analysis, we introduce the notion of randomized oblivious message adversary, where in each round, an adversary picks k ≤ 2n/3 edges to appear in the communication network, and then a graph (e.g. rooted tree or directed Erdős–Rényi graph) is chosen uniformly at random among the set of all such graphs that include these edges. We show that Broadcast completes in a finite number of rounds, which is, e.g., O(k+log n) rounds in rooted trees. We then extend these results to All-to-All Broadcast, and Consensus, and give lower bounds that show that most of our upper bounds are tight."}],"date_published":"2024-10-24T00:00:00Z","title":"Broadcast and Consensus in stochastic dynamic networks with Byzantine nodes and adversarial edges","acknowledgement":"Antoine El-Hayek: This project has received funding from the Austrian Science Fund\r\n(FWF) grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE Stiftung,\r\n2020–2024.\r\nMonika Henzinger: This project has received funding from the European Research Council (ERC)\r\nunder the European Union’s Horizon 2020 research and innovation programme (MoDynStruct,\r\nNo. 101019564) and the Austrian Science Fund (FWF) grant DOI 10.55776/Z422, grant DOI\r\n10.55776/I5982, and grant DOI 10.55776/P33775 with additional funding from the netidee SCIENCE\r\nStiftung, 2020–2024.\r\nStefan Schmid: This project has received funding from the German Research Foundation (DFG),\r\nSPP 2378 (project ReNO), 2023-2027.","language":[{"iso":"eng"}],"OA_place":"publisher","publication_status":"published","publication":"38th International Symposium on Distributed Computing","alternative_title":["LIPIcs"],"oa":1,"type":"conference","date_created":"2024-11-17T23:01:47Z","ddc":["000"],"_id":"18557","arxiv":1,"article_processing_charge":"Yes","intvolume":"       319","corr_author":"1"},{"day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","scopus_import":"1","ec_funded":1,"file":[{"date_created":"2024-06-17T08:46:33Z","content_type":"application/pdf","date_updated":"2024-06-17T08:46:33Z","creator":"dernst","file_name":"2024_LIPICS_Edelsbrunner.pdf","file_size":766562,"access_level":"open_access","file_id":"17152","checksum":"5442d44fb89d77477a87668d6e61aac9","success":1,"relation":"main_file"}],"status":"public","related_material":{"record":[{"relation":"later_version","id":"20657","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"has_accepted_license":"1","citation":{"short":"H. Edelsbrunner, J. Pach, in:, 40th International Symposium on Computational Geometry, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","mla":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, 53, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">10.4230/LIPIcs.SoCG.2024.53</a>.","ista":"Edelsbrunner H, Pach J. 2024. Maximum Betti numbers of Čech complexes. 40th International Symposium on Computational Geometry. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 293, 53.","apa":"Edelsbrunner, H., &#38; Pach, J. (2024). Maximum Betti numbers of Čech complexes. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">https://doi.org/10.4230/LIPIcs.SoCG.2024.53</a>","ama":"Edelsbrunner H, Pach J. Maximum Betti numbers of Čech complexes. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">10.4230/LIPIcs.SoCG.2024.53</a>","chicago":"Edelsbrunner, Herbert, and János Pach. “Maximum Betti Numbers of Čech Complexes.” In <i>40th International Symposium on Computational Geometry</i>, Vol. 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.53\">https://doi.org/10.4230/LIPIcs.SoCG.2024.53</a>.","ieee":"H. Edelsbrunner and J. Pach, “Maximum Betti numbers of Čech complexes,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293."},"month":"06","department":[{"_id":"HeEd"}],"conference":{"start_date":"2024-06-11","end_date":"2024-06-14","name":"SoCG: Symposium on Computational Geometry","location":"Athens, Greece"},"volume":293,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2310.14801"]},"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes"},{"name":"Mathematics, Computer Science","grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"},{"full_name":"Pach, János","id":"E62E3130-B088-11EA-B919-BF823C25FEA4","last_name":"Pach","first_name":"János"}],"year":"2024","article_number":"53","oa_version":"Published Version","file_date_updated":"2024-06-17T08:46:33Z","quality_controlled":"1","title":"Maximum Betti numbers of Čech complexes","date_published":"2024-06-01T00:00:00Z","abstract":[{"text":"The Upper Bound Theorem for convex polytopes implies that the p-th Betti number of the Čech complex of any set of N points in ℝ^d and any radius satisfies β_p = O(N^m), with m = min{p+1, ⌈d/2⌉}. We construct sets in even and odd dimensions, which prove that this upper bound is asymptotically tight. For example, we describe a set of N = 2(n+1) points in ℝ³ and two radii such that the first Betti number of the Čech complex at one radius is (n+1)² - 1, and the second Betti number of the Čech complex at the other radius is n². In particular, there is an arrangement of n contruent balls in ℝ³ that enclose a quadratic number of voids, which answers a long-standing open question in computational geometry.","lang":"eng"}],"publication_identifier":{"isbn":["9783959773164"],"issn":["1868-8969"]},"doi":"10.4230/LIPIcs.SoCG.2024.53","date_updated":"2026-07-27T08:15:58Z","alternative_title":["LIPIcs"],"oa":1,"publication_status":"published","publication":"40th International Symposium on Computational Geometry","language":[{"iso":"eng"}],"acknowledgement":"The first author is supported by the European Research Council (ERC), grant no. 788183, and by the DFG Collaborative Research Center TRR 109, Austrian Science Fund (FWF), grant no. {I 02979-N35.} The second author is supported by the European Research Council (ERC), grant \"GeoScape\" and by the Hungarian Science Foundation (NKFIH), grant K-131529. Both authors are supported by the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.\r\nThe authors thank Matt Kahle for communicating the question about extremal Čech complexes, Ben Schweinhart for early discussions on the linked circles construction in three dimensions, and Gábor Tardos for helpful remarks and suggestions.","article_processing_charge":"No","arxiv":1,"ddc":["510"],"_id":"17146","date_created":"2024-06-16T22:01:06Z","type":"conference","intvolume":"       293"},{"language":[{"iso":"eng"}],"OA_place":"repository","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","publication_status":"published","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.16833","open_access":"1"}],"acknowledgement":"This work was partially supported by project SERICS (PE00000014) under the MUR National Recovery and Resilience Plan funded by the European Union - NextGenerationEU.\r\n","abstract":[{"lang":"eng","text":"The robustness of neural networks against input perturbations with bounded\r\nmagnitude represents a serious concern in the deployment of deep learning\r\nmodels in safety-critical systems. Recently, the scientific community has\r\nfocused on enhancing certifiable robustness guarantees by crafting 1-Lipschitz\r\nneural networks that leverage Lipschitz bounded dense and convolutional layers.\r\nAlthough different methods have been proposed in the literature to achieve this\r\ngoal, understanding the performance of such methods is not straightforward,\r\nsince different metrics can be relevant (e.g., training time, memory usage,\r\naccuracy, certifiable robustness) for different applications. For this reason,\r\nthis work provides a thorough theoretical and empirical comparison between\r\nmethods by evaluating them in terms of memory usage, speed, and certifiable\r\nrobust accuracy. The paper also provides some guidelines and recommendations to\r\nsupport the user in selecting the methods that work best depending on the\r\navailable resources. We provide code at\r\nhttps://github.com/berndprach/1LipschitzLayersCompared."}],"date_published":"2024-06-01T00:00:00Z","title":"1-Lipschitz layers compared: Memory, speed, and certifiable robustness","date_updated":"2026-07-27T12:47:43Z","doi":"10.1109/CVPR52733.2024.02320","corr_author":"1","_id":"17426","arxiv":1,"article_processing_charge":"No","type":"conference","date_created":"2024-08-14T08:42:32Z","page":"24574-24583","citation":{"mla":"Prach, Bernd, et al. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Computer Vision Foundation, 2024, pp. 24574–83, doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>.","short":"B. Prach, F. Brau, G. Buttazzo, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Computer Vision Foundation, 2024, pp. 24574–24583.","ieee":"B. Prach, F. Brau, G. Buttazzo, and C. Lampert, “1-Lipschitz layers compared: Memory, speed, and certifiable robustness,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Seattle, WA, United States, 2024, pp. 24574–24583.","chicago":"Prach, Bernd, Fabio Brau, Giorgio Buttazzo, and Christoph Lampert. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24574–83. Computer Vision Foundation, 2024. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>.","ama":"Prach B, Brau F, Buttazzo G, Lampert C. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. Computer Vision Foundation; 2024:24574-24583. doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>","apa":"Prach, B., Brau, F., Buttazzo, G., &#38; Lampert, C. (2024). 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24574–24583). Seattle, WA, United States: Computer Vision Foundation. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>","ista":"Prach B, Brau F, Buttazzo G, Lampert C. 2024. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24574–24583."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"arxiv":["2311.16833"],"isi":["001344387500055"]},"conference":{"start_date":"2024-06-16","end_date":"2024-06-22","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Seattle, WA, United States"},"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"month":"06","day":"01","has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"19759","status":"public"}],"link":[{"url":"https://github.com/berndprach/1LipschitzLayersCompared","relation":"software"}]},"status":"public","publisher":"Computer Vision Foundation","oa_version":"Preprint","year":"2024","OA_type":"green","quality_controlled":"1","author":[{"full_name":"Prach, Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach","first_name":"Bernd"},{"full_name":"Brau, Fabio","first_name":"Fabio","last_name":"Brau"},{"full_name":"Buttazzo, Giorgio","first_name":"Giorgio","last_name":"Buttazzo"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","first_name":"Christoph","orcid":"0000-0001-8622-7887"}],"isi":1},{"OA_place":"repository","language":[{"iso":"eng"}],"oa":1,"citation":{"mla":"Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” <i>ArXiv</i>, 2412.04245, doi:<a href=\"https://doi.org/10.48550/arXiv.2412.04245\">10.48550/arXiv.2412.04245</a>.","short":"B. Prach, C. Lampert, ArXiv (n.d.).","ama":"Prach B, Lampert C. Intriguing properties of robust classification. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2412.04245\">10.48550/arXiv.2412.04245</a>","chicago":"Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2412.04245\">https://doi.org/10.48550/arXiv.2412.04245</a>.","ieee":"B. Prach and C. Lampert, “Intriguing properties of robust classification,” <i>arXiv</i>. .","apa":"Prach, B., &#38; Lampert, C. (n.d.). Intriguing properties of robust classification. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2412.04245\">https://doi.org/10.48550/arXiv.2412.04245</a>","ista":"Prach B, Lampert C. Intriguing properties of robust classification. arXiv, 2412.04245."},"publication_status":"draft","publication":"arXiv","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","external_id":{"arxiv":["2412.04245"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2412.04245"}],"month":"12","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"abstract":[{"text":"Despite extensive research since the community learned about adversarial\r\nexamples 10 years ago, we still do not know how to train high-accuracy\r\nclassifiers that are guaranteed to be robust to small perturbations of their\r\ninputs. Previous works often argued that this might be because no classifier\r\nexists that is robust and accurate at the same time. However, in computer\r\nvision this assumption does not match reality where humans are usually accurate\r\nand robust on most tasks of interest. We offer an alternative explanation and\r\nshow that in certain settings robust generalization is only possible with\r\nunrealistically large amounts of data. More precisely we find a setting where a\r\nrobust classifier exists, it is easy to learn an accurate classifier, yet it\r\nrequires an exponential amount of data to learn a robust classifier. Based on\r\nthis theoretical result, we explore how well robust classifiers generalize on\r\ndatasets such as CIFAR-10. We come to the conclusion that on this datasets, the\r\nlimitation of current robust models also lies in the generalization, and that\r\nthey require a lot of data to do well on the test set. We also show that the\r\nproblem is not in the expressiveness or generalization capabilities of current\r\narchitectures, and that there are low magnitude features in the data which are\r\nuseful for non-robust generalization but are not available for robust\r\nclassifiers.","lang":"eng"}],"title":"Intriguing properties of robust classification","day":"05","date_published":"2024-12-05T00:00:00Z","date_updated":"2026-07-27T12:47:43Z","status":"public","doi":"10.48550/arXiv.2412.04245","related_material":{"record":[{"status":"public","relation":"later_version","id":"20455"},{"status":"public","relation":"dissertation_contains","id":"19759"}]},"article_number":"2412.04245","oa_version":"Preprint","year":"2024","corr_author":"1","_id":"18874","article_processing_charge":"No","arxiv":1,"author":[{"id":"2D561D42-C427-11E9-89B4-9C1AE6697425","full_name":"Prach, Bernd","first_name":"Bernd","last_name":"Prach"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"}],"type":"preprint","date_created":"2025-01-24T16:57:29Z"},{"quality_controlled":"1","file_date_updated":"2025-01-21T14:39:49Z","oa_version":"Published Version","year":"2024","OA_type":"hybrid","isi":1,"project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","name":"Vigilant Algorithmic Monitoring of Software","grant_number":"101020093","call_identifier":"H2020"}],"author":[{"last_name":"Chalupa","first_name":"Marek","full_name":"Chalupa, Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000-0002-2985-7724","last_name":"Henzinger"},{"last_name":"Mazzocchi","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien","id":"b26baa86-3308-11ec-87b0-8990f34baa85"},{"first_name":"Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425","full_name":"Sarac, Naci E"}],"external_id":{"arxiv":["2409.03569"],"isi":["001419008700001"]},"volume":15222,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","conference":{"end_date":"2024-10-31","start_date":"2024-10-27","location":"Crete, Greece","name":"ISoLA: International Symposium on Leveraging Applications"},"department":[{"_id":"GradSch"},{"_id":"ToHe"}],"month":"10","citation":{"mla":"Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, vol. 15222, Springer Nature, 2024, pp. 3–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">10.1007/978-3-031-75387-9_1</a>.","short":"M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Springer Nature, 2024, pp. 3–20.","apa":"Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2024). QuAK: Quantitative Automata Kit. In <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i> (Vol. 15222, pp. 3–20). Crete, Greece: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">https://doi.org/10.1007/978-3-031-75387-9_1</a>","chicago":"Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “QuAK: Quantitative Automata Kit.” In <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, 15222:3–20. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">https://doi.org/10.1007/978-3-031-75387-9_1</a>.","ieee":"M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative Automata Kit,” in <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, Crete, Greece, 2024, vol. 15222, pp. 3–20.","ama":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata Kit. In: <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>. Vol 15222. Springer Nature; 2024:3-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">10.1007/978-3-031-75387-9_1</a>","ista":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative Automata Kit. 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. ISoLA: International Symposium on Leveraging Applications, LNCS, vol. 15222, 3–20."},"has_accepted_license":"1","related_material":{"record":[{"relation":"dissertation_contains","id":"20147","status":"public"}]},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"publisher":"Springer Nature","scopus_import":"1","status":"public","file":[{"success":1,"relation":"main_file","file_name":"isola24.pdf","creator":"esarac","file_size":847422,"access_level":"open_access","file_id":"17635","checksum":"43e432f82be376434b358f3dd7a94b71","date_created":"2024-09-05T14:26:02Z","content_type":"application/pdf","date_updated":"2024-09-05T14:26:02Z"},{"checksum":"6bc04f07bb5612c0e7ea00ac121a69b6","file_id":"18865","access_level":"open_access","file_size":1358706,"file_name":"2024_LNCS_Chalupa.pdf","creator":"dernst","date_updated":"2025-01-21T14:39:49Z","content_type":"application/pdf","date_created":"2025-01-21T14:39:49Z","relation":"main_file","success":1}],"ec_funded":1,"day":"26","intvolume":"     15222","corr_author":"1","type":"conference","date_created":"2024-09-05T14:27:08Z","page":"3-20","_id":"17634","ddc":["000"],"arxiv":1,"article_processing_charge":"Yes (in subscription journal)","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when his collaboration started.","language":[{"iso":"eng"}],"OA_place":"publisher","publication":"12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation","publication_status":"published","oa":1,"alternative_title":["LNCS"],"date_updated":"2026-07-27T12:48:18Z","doi":"10.1007/978-3-031-75387-9_1","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031753862"],"eissn":["1611-3349"]},"abstract":[{"lang":"eng","text":"System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems."}],"APC_amount":"2748 EUR","date_published":"2024-10-26T00:00:00Z","title":"QuAK: Quantitative Automata Kit"},{"article_processing_charge":"No","arxiv":1,"_id":"18121","page":"45955-45987","date_created":"2024-09-22T22:01:46Z","type":"conference","corr_author":"1","intvolume":"       235","title":"SPADE: Sparsity-guided debugging for deep neural networks","date_published":"2024-09-01T00:00:00Z","abstract":[{"text":"It is known that sparsity can improve interpretability for deep neural networks. However, existing methods in the area either require networks that are pre-trained with sparsity constraints, or impose sparsity after the fact, altering the network’s general behavior. In this paper, we demonstrate, for the first time, that sparsity can instead be incorporated into the interpretation process itself, as a sample-specific preprocessing step. Unlike previous work, this approach, which we call SPADE, does not place constraints on the trained model and does not affect its behavior during inference on the sample. Given a trained model and a target sample, SPADE uses sample-targeted pruning to provide a \"trace\" of the network’s execution on the sample, reducing the network to the most important connections prior to computing an interpretation. We demonstrate that preprocessing with SPADE significantly increases the accuracy of image saliency maps across several interpretability methods. Additionally, SPADE improves the usefulness of neuron visualizations, aiding humans in reasoning about network behavior. Our code is available at https://github.com/IST-DASLab/SPADE.","lang":"eng"}],"publication_identifier":{"eissn":["2640-3498"]},"date_updated":"2026-07-27T12:50:03Z","alternative_title":["PMLR"],"oa":1,"publication_status":"published","publication":"Proceedings of the 41st International Conference on Machine Learning","language":[{"iso":"eng"}],"acknowledgement":"The authors would like to thank Stephen Casper and Tony Wang for their feedback on this work, and Eldar Kurtic for his advice on aspects of the project. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific Computing (SciComp). EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.04519"}],"author":[{"full_name":"Moakhar, Arshia Soltani","first_name":"Arshia Soltani","last_name":"Moakhar"},{"last_name":"Iofinova","first_name":"Eugenia B","orcid":"0000-0002-7778-3221","full_name":"Iofinova, Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117"},{"full_name":"Frantar, Elias","id":"09a8f98d-ec99-11ea-ae11-c063a7b7fe5f","last_name":"Frantar","first_name":"Elias"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"project":[{"grant_number":"W1260-N35","name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"year":"2024","oa_version":"Preprint","quality_controlled":"1","day":"01","publisher":"ML Research Press","scopus_import":"1","status":"public","related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/SPADE"}],"record":[{"relation":"dissertation_contains","id":"21854","status":"public"}]},"acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"apa":"Moakhar, A. S., Iofinova, E. B., Frantar, E., &#38; Alistarh, D.-A. (2024). SPADE: Sparsity-guided debugging for deep neural networks. In <i>Proceedings of the 41st International Conference on Machine Learning</i> (Vol. 235, pp. 45955–45987). Vienna, Austria: ML Research Press.","chicago":"Moakhar, Arshia Soltani, Eugenia B Iofinova, Elias Frantar, and Dan-Adrian Alistarh. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” In <i>Proceedings of the 41st International Conference on Machine Learning</i>, 235:45955–87. ML Research Press, 2024.","ama":"Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. SPADE: Sparsity-guided debugging for deep neural networks. In: <i>Proceedings of the 41st International Conference on Machine Learning</i>. Vol 235. ML Research Press; 2024:45955-45987.","ieee":"A. S. Moakhar, E. B. Iofinova, E. Frantar, and D.-A. Alistarh, “SPADE: Sparsity-guided debugging for deep neural networks,” in <i>Proceedings of the 41st International Conference on Machine Learning</i>, Vienna, Austria, 2024, vol. 235, pp. 45955–45987.","ista":"Moakhar AS, Iofinova EB, Frantar E, Alistarh D-A. 2024. SPADE: Sparsity-guided debugging for deep neural networks. Proceedings of the 41st International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 235, 45955–45987.","mla":"Moakhar, Arshia Soltani, et al. “SPADE: Sparsity-Guided Debugging for Deep Neural Networks.” <i>Proceedings of the 41st International Conference on Machine Learning</i>, vol. 235, ML Research Press, 2024, pp. 45955–87.","short":"A.S. Moakhar, E.B. Iofinova, E. Frantar, D.-A. Alistarh, in:, Proceedings of the 41st International Conference on Machine Learning, ML Research Press, 2024, pp. 45955–45987."},"month":"09","department":[{"_id":"DaAl"}],"conference":{"end_date":"2024-07-27","start_date":"2024-07-21","location":"Vienna, Austria","name":"ICML: International Conference on Machine Learning"},"external_id":{"arxiv":["2310.04519"]},"volume":235,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"03","department":[{"_id":"KrCh"}],"volume":20,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001194482400002"],"arxiv":["2401.14914"]},"citation":{"ama":"Svoboda J, Joshi SS, Tkadlec J, Chatterjee K. Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. <i>PLoS Computational Biology</i>. 2024;20(3). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012008\">10.1371/journal.pcbi.1012008</a>","ieee":"J. Svoboda, S. S. Joshi, J. Tkadlec, and K. Chatterjee, “Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating,” <i>PLoS Computational Biology</i>, vol. 20, no. 3. Public Library of Science, 2024.","chicago":"Svoboda, Jakub, Soham Shrikant Joshi, Josef Tkadlec, and Krishnendu Chatterjee. “Amplifiers of Selection for the Moran Process with Both Birth-Death and Death-Birth Updating.” <i>PLoS Computational Biology</i>. Public Library of Science, 2024. <a href=\"https://doi.org/10.1371/journal.pcbi.1012008\">https://doi.org/10.1371/journal.pcbi.1012008</a>.","apa":"Svoboda, J., Joshi, S. S., Tkadlec, J., &#38; Chatterjee, K. (2024). Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1012008\">https://doi.org/10.1371/journal.pcbi.1012008</a>","ista":"Svoboda J, Joshi SS, Tkadlec J, Chatterjee K. 2024. Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating. PLoS Computational Biology. 20(3), e1012008.","mla":"Svoboda, Jakub, et al. “Amplifiers of Selection for the Moran Process with Both Birth-Death and Death-Birth Updating.” <i>PLoS Computational Biology</i>, vol. 20, no. 3, e1012008, Public Library of Science, 2024, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1012008\">10.1371/journal.pcbi.1012008</a>.","short":"J. Svoboda, S.S. Joshi, J. Tkadlec, K. Chatterjee, PLoS Computational Biology 20 (2024)."},"file":[{"creator":"dernst","file_name":"2024_PloSComBio_Svoboda.pdf","file_id":"17450","checksum":"a511cf369d9172beb123fe73f291b5cc","file_size":1425292,"access_level":"open_access","content_type":"application/pdf","date_created":"2024-08-20T10:52:28Z","date_updated":"2024-08-20T10:52:28Z","relation":"main_file","success":1}],"publisher":"Public Library of Science","ec_funded":1,"scopus_import":"1","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"status":"public","id":"20138","relation":"dissertation_contains"}]},"has_accepted_license":"1","day":"29","article_type":"original","quality_controlled":"1","OA_type":"gold","year":"2024","article_number":"e1012008","oa_version":"Published Version","file_date_updated":"2024-08-20T10:52:28Z","isi":1,"author":[{"id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","full_name":"Svoboda, Jakub","first_name":"Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda"},{"last_name":"Joshi","first_name":"Soham Shrikant","full_name":"Joshi, Soham Shrikant","id":"f97aac0e-f57c-11ee-93d0-a5a82d8df168"},{"last_name":"Tkadlec","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"acknowledgement":"We thank Gavin Rees for helpful discussions. J.S., S.J., and K.C were supported by\r\nEuropean Research Council (ERC) CoG 863818 (ForM-SMArt). J.T was supported by Center for Foundations of Modern Computer Science (Charles University project UNCE/SCI/004) and by the project PRIMUS/24/SCI/012 from Charles University. ","oa":1,"DOAJ_listed":"1","publication_status":"published","publication":"PLoS Computational Biology","OA_place":"publisher","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1553-7358"],"issn":["1553-734X"]},"doi":"10.1371/journal.pcbi.1012008","date_updated":"2026-07-27T12:52:03Z","title":"Amplifiers of selection for the Moran process with both Birth-death and death-Birth updating","APC_amount":"3149,96 EUR","date_published":"2024-03-29T00:00:00Z","abstract":[{"text":"Populations evolve by accumulating advantageous mutations. Every population has some spatial structure that can be modeled by an underlying network. The network then influences the probability that new advantageous mutations fixate. Amplifiers of selection are networks that increase the fixation probability of advantageous mutants, as compared to the unstructured fully-connected network. Whether or not a network is an amplifier depends on the choice of the random process that governs the evolutionary dynamics. Two popular choices are Moran process with Birth-death updating and Moran process with death-Birth updating. Interestingly, while some networks are amplifiers under Birth-death updating and other networks are amplifiers under death-Birth updating, so far no spatial structures have been found that function as an amplifier under both types of updating simultaneously. In this work, we identify networks that act as amplifiers of selection under both versions of the Moran process. The amplifiers are robust, modular, and increase fixation probability for any mutant fitness advantage in a range r ∈ (1, 1.2). To complement this positive result, we also prove that for certain quantities closely related to fixation probability, it is impossible to improve them simultaneously for both versions of the Moran process. Together, our results highlight how the two versions of the Moran process differ and what they have in common.","lang":"eng"}],"corr_author":"1","intvolume":"        20","issue":"3","date_created":"2024-04-07T22:00:55Z","type":"journal_article","article_processing_charge":"Yes","arxiv":1,"_id":"15297","ddc":["000"]},{"publication_status":"published","publication":"Proceedings of the National Academy of Sciences of the United States of America","oa":1,"language":[{"iso":"eng"}],"OA_place":"publisher","acknowledgement":"J.S. and K.C. were supported by the European Research Council CoG 863818 (ForM-SMArt) and Austrian Science Fund 10.55776/COE12.","pmid":1,"APC_amount":"3143,76 EUR","date_published":"2024-12-10T00:00:00Z","title":"Density amplifiers of cooperation for spatial games","abstract":[{"lang":"eng","text":"Spatial games provide a simple and elegant mathematical model to study the evolution of cooperation in networks. In spatial games, individuals reside in vertices, adopt simple strategies, and interact with neighbors to receive a payoff. Depending on their own and neighbors’ payoffs, individuals can change their strategy. The payoff is determined by the Prisoners’ Dilemma, a classical matrix game, where players cooperate or defect. While cooperation is the desired behavior, defection provides a higher payoff for a selfish individual. There are many theoretical and empirical studies related to the role of the network in the evolution of cooperation. However, the fundamental question of whether there exist networks that for low initial cooperation rate ensure a high chance of fixation, i.e., cooperation spreads across the whole population, has remained elusive for spatial games with strong selection. In this work, we answer this fundamental question in the affirmative by presenting network structures that ensure high fixation probability for cooperators in the strong selection regime. Besides, our structures have many desirable properties: (a) they ensure the spread of cooperation even for a low initial density of cooperation and high temptation of defection, (b) they have constant degrees, and (c) the number of steps, until cooperation spreads, is at most quadratic in the size of the network."}],"doi":"10.1073/pnas.2405605121","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"date_updated":"2026-07-27T12:52:03Z","issue":"50","corr_author":"1","intvolume":"       121","article_processing_charge":"Yes","ddc":["000"],"_id":"18703","date_created":"2024-12-22T23:01:47Z","type":"journal_article","citation":{"short":"J. Svoboda, K. Chatterjee, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50, e2405605121, National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>.","ista":"Svoboda J, Chatterjee K. 2024. Density amplifiers of cooperation for spatial games. Proceedings of the National Academy of Sciences of the United States of America. 121(50), e2405605121.","apa":"Svoboda, J., &#38; Chatterjee, K. (2024). Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>","ieee":"J. Svoboda and K. Chatterjee, “Density amplifiers of cooperation for spatial games,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 50. National Academy of Sciences, 2024.","chicago":"Svoboda, Jakub, and Krishnendu Chatterjee. “Density Amplifiers of Cooperation for Spatial Games.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2405605121\">https://doi.org/10.1073/pnas.2405605121</a>.","ama":"Svoboda J, Chatterjee K. Density amplifiers of cooperation for spatial games. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(50). doi:<a href=\"https://doi.org/10.1073/pnas.2405605121\">10.1073/pnas.2405605121</a>"},"department":[{"_id":"KrCh"}],"month":"12","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":121,"external_id":{"isi":["001379596100014"],"pmid":["39642209"]},"article_type":"original","day":"10","tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"related_material":{"record":[{"status":"public","id":"20138","relation":"dissertation_contains"}]},"publisher":"National Academy of Sciences","status":"public","ec_funded":1,"scopus_import":"1","file":[{"success":1,"relation":"main_file","file_size":2491151,"access_level":"open_access","checksum":"0115e9090b478e0644308c6dab58605b","file_id":"18721","file_name":"2024_PNAS_Svoboda.pdf","creator":"dernst","date_updated":"2025-01-02T12:14:15Z","date_created":"2025-01-02T12:14:15Z","content_type":"application/pdf"}],"has_accepted_license":"1","year":"2024","OA_type":"hybrid","file_date_updated":"2025-01-02T12:14:15Z","article_number":"e2405605121","oa_version":"Published Version","quality_controlled":"1","author":[{"last_name":"Svoboda","orcid":"0000-0002-1419-3267","first_name":"Jakub","full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"isi":1},{"citation":{"mla":"Gallei, Michelle C., et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>.","short":"M.C. Gallei, S.M. Truckenbrodt, C. Kreuzinger, S. Inumella, V. Vistunou, C.M. Sommer, M. Tavakoli, N. Agudelo Duenas, J. Vorlaufer, W. Jahr, M. Randuch, A.J. Johnson, E. Benková, J. Friml, J.G. Danzl, BioRxiv (n.d.).","ieee":"M. C. Gallei <i>et al.</i>, “Super-resolution expansion microscopy in plant roots,” <i>bioRxiv</i>. .","chicago":"Gallei, Michelle C, Sven M Truckenbrodt, Caroline Kreuzinger, Syamala Inumella, Vitali Vistunou, Christoph M Sommer, Mojtaba Tavakoli, et al. “Super-Resolution Expansion Microscopy in Plant Roots.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>.","ama":"Gallei MC, Truckenbrodt SM, Kreuzinger C, et al. Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>","apa":"Gallei, M. C., Truckenbrodt, S. M., Kreuzinger, C., Inumella, S., Vistunou, V., Sommer, C. M., … Danzl, J. G. (n.d.). Super-resolution expansion microscopy in plant roots. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.02.21.581330\">https://doi.org/10.1101/2024.02.21.581330</a>","ista":"Gallei MC, Truckenbrodt SM, Kreuzinger C, Inumella S, Vistunou V, Sommer CM, Tavakoli M, Agudelo Duenas N, Vorlaufer J, Jahr W, Randuch M, Johnson AJ, Benková E, Friml J, Danzl JG. Super-resolution expansion microscopy in plant roots. bioRxiv, <a href=\"https://doi.org/10.1101/2024.02.21.581330\">10.1101/2024.02.21.581330</a>."},"department":[{"_id":"EvBe"},{"_id":"JoDa"},{"_id":"JiFr"}],"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"21","related_material":{"record":[{"id":"19003","relation":"later_version","status":"public"},{"relation":"dissertation_contains","id":"18681","status":"public"}]},"tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"status":"public","ec_funded":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"year":"2024","oa_version":"Preprint","project":[{"call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"ALTF 679-2018","name":"UltraX - achieving sub-nanometer resolution in light microscopy using iterative X10 microscopy in combination with nanobodies and STED","_id":"269B5B22-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Gallei","orcid":"0000-0003-1286-7368","first_name":"Michelle C","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Truckenbrodt","first_name":"Sven M","full_name":"Truckenbrodt, Sven M","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline","first_name":"Caroline","last_name":"Kreuzinger"},{"last_name":"Inumella","orcid":"0009-0002-5890-120X","first_name":"Syamala","full_name":"Inumella, Syamala","id":"F8660870-D756-11E9-98C5-34DFE5697425"},{"full_name":"Vistunou, Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","first_name":"Vitali"},{"orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M"},{"full_name":"Tavakoli, Mojtaba","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","last_name":"Tavakoli","orcid":"0000-0002-7667-6854","first_name":"Mojtaba"},{"full_name":"Agudelo Duenas, Nathalie","id":"40E7F008-F248-11E8-B48F-1D18A9856A87","last_name":"Agudelo Duenas","first_name":"Nathalie"},{"orcid":"0009-0000-7590-3501","first_name":"Jakob","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob"},{"full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","last_name":"Jahr","orcid":"0000-0003-0201-2315","first_name":"Wiebke"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","full_name":"Randuch, Marek","first_name":"Marek","last_name":"Randuch"},{"full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","first_name":"Eva","last_name":"Benková"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"draft","publication":"bioRxiv","oa":1,"language":[{"iso":"eng"}],"OA_place":"repository","acknowledgement":"We gratefully acknowledge support by the Scientific Service Units at ISTA, including the Imaging and Optics and Lab Support facilities and the mechanical workshop and Library. We thank Philipp Velicky for STED microscope alignment.\r\n\r\nThis project has received funding from the Austrian Science Fund (FWF): I 3630-B25 (J.G.D) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 742985, J.F.). It has also received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385. S.T. has received funding as an ISTplus Fellow from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie grant agreement no. 754411 and from an EMBO Long-Term Fellowship (grant number ALTF 679-2018). It has further received funding from the Austrian Science Fund (FWF) grant DK W1232 (M.T, N.A-D., J.G.D). W.J. received funding via a Human Frontier Science Program postdoctoral fellowship LT000557/2018.\r\n\r\nThe funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.02.21.581330"}],"date_published":"2024-02-21T00:00:00Z","title":"Super-resolution expansion microscopy in plant roots","license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"text":"Multiplexed fluorescence microscopy imaging is widely used in biomedical applications. However, simultaneous imaging of multiple fluorophores can result in spectral leaks and overlapping, which greatly degrades image quality and subsequent analysis. Existing popular spectral unmixing methods are mainly based on computational intensive linear models and the performance is heavily dependent on the reference spectra, which may greatly preclude its further applications. In this paper, we propose a deep learning-based blindly spectral unmixing method, termed AutoUnmix, to imitate the physical spectral mixing process. A tranfer learning framework is further devised to allow our AutoUnmix adapting to a variety of imaging systems without retraining the network. Our proposed method has demonstrated real-time unmixing capabilities, surpassing existing methods by up to 100-fold in terms of unmixing speed. We further validate the reconstruction performance on both synthetic datasets and biological samples. The unmixing results of AutoUnmix achieve a highest SSIM of 0.99 in both three- and four-color imaging, with nearly up to 20% higher than other popular unmixing methods. Due to the desirable property of data independency and superior blind unmixing performance, we believe AutoUnmix is a powerful tool to study the interaction process of different organelles labeled by multiple fluorophores.","lang":"eng"}],"doi":"10.1101/2024.02.21.581330","date_updated":"2026-07-28T08:33:52Z","corr_author":"1","article_processing_charge":"No","_id":"18689","date_created":"2024-12-19T12:28:00Z","type":"preprint"},{"title":"Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory","day":"02","date_published":"2024-05-02T00:00:00Z","abstract":[{"lang":"eng","text":"The human brain has remarkable computational power. It generates sophisticated behavioral sequences, stores engrams over an individual’s lifetime, and produces higher cognitive functions up to the level of consciousness. However, so little of our neuroscience knowledge covers the human brain, and it remains unknown whether this organ is truly unique, or is a scaled version of the extensively studied rodent brain. To address this fundamental question, we determined the cellular, synaptic, and connectivity rules of the hippocampal CA3 recurrent circuit using multicellular patch clamp-recording. This circuit is the largest autoassociative network in the brain, and plays a key role in memory and higher-order computations such as pattern separation and pattern completion. We demonstrate that human hippocampal CA3 employs sparse connectivity, in stark contrast to neocortical recurrent networks. Connectivity sparsifies from rodents to humans, providing a circuit architecture that maximizes associational power. Unitary synaptic events at human CA3–CA3 synapses showed both distinct species-specific and circuit-dependent properties, with high reliability, unique amplitude precision, and long integration times. We also identify differential scaling rules between hippocampal pathways from rodents to humans, with a moderate increase in the convergence of CA3 inputs per cell, but a marked increase in human mossy fiber innervation. Anatomically guided full-scale modeling suggests that the human brain’s sparse connectivity, expanded neuronal number, and reliable synaptic signaling combine to enhance the associative memory storage capacity of CA3. Together, our results reveal unique rules of connectivity and synaptic signaling in the human hippocampus, demonstrating the absolute necessity of human brain research and beginning to unravel the remarkable performance of our autoassociative memory circuits."}],"status":"public","ec_funded":1,"doi":"10.1101/2024.05.02.592169","related_material":{"record":[{"id":"18879","relation":"later_version","status":"public"},{"id":"18681","relation":"dissertation_contains","status":"public"}]},"date_updated":"2026-07-28T08:33:51Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"PreCl"},{"_id":"ScienComp"}],"oa":1,"citation":{"ista":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, Navas-Olive A, Tavakoli M, Danzl JG, Tomschik M, Rössler K, Jonas PM. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. bioRxiv, <a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>.","chicago":"Watson, Jake F., Victor Vargas-Barroso, Rebecca J. Morse-Mora, Andrea Navas-Olive, Mojtaba Tavakoli, Johann G Danzl, Matthias Tomschik, Karl Rössler, and Peter M Jonas. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>.","ama":"Watson JF, Vargas-Barroso V, Morse-Mora RJ, et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>","ieee":"J. F. Watson <i>et al.</i>, “Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory,” <i>bioRxiv</i>. .","apa":"Watson, J. F., Vargas-Barroso, V., Morse-Mora, R. J., Navas-Olive, A., Tavakoli, M., Danzl, J. G., … Jonas, P. M. (n.d.). Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.05.02.592169\">https://doi.org/10.1101/2024.05.02.592169</a>","short":"J.F. Watson, V. Vargas-Barroso, R.J. Morse-Mora, A. Navas-Olive, M. Tavakoli, J.G. Danzl, M. Tomschik, K. Rössler, P.M. Jonas, BioRxiv (n.d.).","mla":"Watson, Jake F., et al. “Human Hippocampal CA3 Uses Specific Functional Connectivity Rules for Efficient Associative Memory.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.05.02.592169\">10.1101/2024.05.02.592169</a>."},"publication_status":"draft","publication":"bioRxiv","OA_place":"repository","language":[{"iso":"eng"}],"month":"05","acknowledgement":"We thank Florian Marr for excellent technical assistance, Christina Altmutter and Julia Flor for technical support, Alois Schlögl for programming, Todor Asenov for development of the transportation box for human brain tissue, Tim Vogels for guidance on simulations, Marcus Huber for mathematical advice, and Eleftheria Kralli-Beller for manuscript editing. This research was supported by the Scientific Services Units (SSUs) of ISTA, and we are particularly grateful for assistance from Christoph Sommer and the Imaging and Optics Facility, Preclinical Facility, Life Science Facility, Miba Machine Shop, and Scientific Computing. We also acknowledge the excellent support of the Medical University of Vienna Department of Neurosurgery staff, Romana Hoeftberger and the Division of Neuropathology and Neurochemistry, and Gregor Kasprian and the Division of Neuroradiology and Musculoskeletal Radiology. The project received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 to J.F.W.), the Austrian Science Fund (FWF; grant PAT 4178023 to P.J.; grant DK W1232 to M.R.T. and J.G.D.) and the Austrian Academy of Sciences (DOC fellowship 26137 to M.R.T.).","department":[{"_id":"JoDa"},{"_id":"PeJo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2024.05.02.592169","open_access":"1"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"call_identifier":"FWF","name":"Molecular Drug Targets","grant_number":"W1232-B24","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"},{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"}],"author":[{"full_name":"Watson, Jake F.","first_name":"Jake F.","last_name":"Watson"},{"full_name":"Vargas-Barroso, Victor","first_name":"Victor","last_name":"Vargas-Barroso"},{"full_name":"Morse-Mora, Rebecca J.","last_name":"Morse-Mora","first_name":"Rebecca J."},{"full_name":"Navas-Olive, Andrea","first_name":"Andrea","last_name":"Navas-Olive"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","first_name":"Mojtaba","last_name":"Tavakoli"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","first_name":"Johann G","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Tomschik, Matthias","first_name":"Matthias","last_name":"Tomschik"},{"full_name":"Rössler, Karl","first_name":"Karl","last_name":"Rössler"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas","first_name":"Peter M","orcid":"0000-0001-5001-4804"}],"_id":"18688","date_created":"2024-12-19T11:35:08Z","type":"preprint","year":"2024","oa_version":"Preprint","corr_author":"1"},{"type":"dissertation","date_created":"2024-12-19T02:30:39Z","page":"230","_id":"18681","das_tickbox":"1","ddc":["600","570"],"article_processing_charge":"No","corr_author":"1","doi_confirm":"1","OA_embargo":"20","date_updated":"2026-07-28T08:33:52Z","doi":"10.15479/at:ista:18681","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-048-0"]},"date_published":"2024-12-20T00:00:00Z","title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","language":[{"iso":"eng"}],"OA_place":"publisher","publication_status":"published","alternative_title":["ISTA Thesis"],"project":[{"grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","_id":"6285a163-2b32-11ec-9570-8e204ca2dba5"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"author":[{"orcid":"0000-0002-7667-6854","first_name":"Mojtaba","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba"}],"supervisor":[{"first_name":"Johann G","orcid":"0000-0001-8559-3973","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G"}],"file_date_updated":"2026-07-28T08:33:51Z","oa_version":"Published Version","year":"2024","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"has_accepted_license":"1","related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"id":"18688","relation":"part_of_dissertation","status":"public"},{"relation":"part_of_dissertation","id":"18677","status":"public"},{"status":"public","id":"18689","relation":"part_of_dissertation"}]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"status":"public","publisher":"Institute of Science and Technology Austria","file":[{"relation":"source_file","date_created":"2024-12-20T10:23:17Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2024-12-20T10:31:37Z","file_name":"Thesis_Mojtaba Tavakoli_.docx","creator":"mtavakol","access_level":"closed","file_size":118593521,"checksum":"b61651d417cafddd740a8528f46068c5","file_id":"18699"},{"relation":"main_file","file_id":"18700","checksum":"c80bcfd1a34c23afc3538052325283e5","access_level":"closed","file_size":63885521,"file_name":"Thesis_Mojtaba Tavakoli_.pdf","embargo_to":"open_access","creator":"mtavakol","date_updated":"2026-07-28T08:33:51Z","embargo":"2027-08-01","content_type":"application/pdf","date_created":"2024-12-20T10:25:12Z"}],"day":"20","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"month":"12","degree_awarded":"PhD","citation":{"apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>.","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>","ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024."}},{"date_created":"2024-12-18T14:48:24Z","type":"preprint","article_processing_charge":"No","_id":"18677","corr_author":"1","doi":"10.1101/2024.03.01.582884","date_updated":"2026-07-28T08:33:51Z","title":"Light-microscopy based dense connectomic reconstruction of mammalian brain tissue","date_published":"2024-07-08T00:00:00Z","abstract":[{"lang":"eng","text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labeling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner."}],"acknowledgement":"We thank Sven Dorkenwald and Peter Li for critical reading of the\r\nmanuscript. We acknowledge expert support by ISTA’s scientific service units: Imaging and\r\nOptics, Lab Support, Scientific Computing, Preclinical Facility, Miba Machine Shop, and Library.\r\nWe gratefully acknowledge funding by the following sources:\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, MRT)\r\nAustrian Academy of Sciences DOC fellowship 26137 (MRT)\r\nEU Horizon 2020 program, Marie Skłodowska-Curie Actions Fellowship 665385 (JL)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research\r\nCouncil (ERC) grant 101044865 “SecretAutism.”\r\n","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2024.03.01.582884"}],"oa":1,"publication_status":"draft","publication":"bioRxiv","OA_place":"repository","language":[{"iso":"eng"}],"project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy","grant_number":"26137"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program"},{"_id":"34ba8964-11ca-11ed-8bc3-e15864e7e9a6","grant_number":"101044865","name":"Toward an understanding of the brain interstitial system and the extracellular proteome in health and autism spectrum disorders"},{"call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"26AA4EF2-B435-11E9-9278-68D0E5697425"}],"author":[{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","full_name":"Tavakoli, Mojtaba","first_name":"Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli"},{"full_name":"Lyudchik, Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","first_name":"Julia"},{"full_name":"Januszewski, Michał","first_name":"Michał","last_name":"Januszewski"},{"full_name":"Vistunou, Vitali","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81","last_name":"Vistunou","first_name":"Vitali"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","full_name":"Agudelo Duenas, Nathalie","first_name":"Nathalie","last_name":"Agudelo Duenas"},{"first_name":"Jakob","orcid":"0009-0000-7590-3501","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425","full_name":"Vorlaufer, Jakob"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","first_name":"Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer"},{"first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"},{"id":"3B03AA1A-F248-11E8-B48F-1D18A9856A87","full_name":"Oliveira, Bárbara","first_name":"Bárbara","last_name":"Oliveira"},{"last_name":"Cenameri","first_name":"Alban","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","first_name":"Gaia","last_name":"Novarino"},{"last_name":"Jain","first_name":"Viren","full_name":"Jain, Viren"},{"last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","oa_version":"Preprint","status":"public","ec_funded":1,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"related_material":{"record":[{"status":"public","id":"18674","relation":"dissertation_contains"},{"relation":"later_version","id":"19704","status":"public"},{"id":"18681","relation":"dissertation_contains","status":"public"}]},"acknowledged_ssus":[{"_id":"E-Lib"},{"_id":"M-Shop"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"ScienComp"}],"day":"08","month":"07","department":[{"_id":"GaNo"},{"_id":"JoDa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"M. Tavakoli, J. Lyudchik, M. Januszewski, V. Vistunou, N. Agudelo Duenas, J. Vorlaufer, C.M. Sommer, C. Kreuzinger, B. Oliveira, A. Cenameri, G. Novarino, V. Jain, J.G. Danzl, BioRxiv (n.d.).","mla":"Tavakoli, Mojtaba, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","ista":"Tavakoli M, Lyudchik J, Januszewski M, Vistunou V, Agudelo Duenas N, Vorlaufer J, Sommer CM, Kreuzinger C, Oliveira B, Cenameri A, Novarino G, Jain V, Danzl JG. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. bioRxiv, <a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>.","ieee":"M. Tavakoli <i>et al.</i>, “Light-microscopy based dense connectomic reconstruction of mammalian brain tissue,” <i>bioRxiv</i>. .","chicago":"Tavakoli, Mojtaba, Julia Lyudchik, Michał Januszewski, Vitali Vistunou, Nathalie Agudelo Duenas, Jakob Vorlaufer, Christoph M Sommer, et al. “Light-Microscopy Based Dense Connectomic Reconstruction of Mammalian Brain Tissue.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>.","ama":"Tavakoli M, Lyudchik J, Januszewski M, et al. Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2024.03.01.582884\">10.1101/2024.03.01.582884</a>","apa":"Tavakoli, M., Lyudchik, J., Januszewski, M., Vistunou, V., Agudelo Duenas, N., Vorlaufer, J., … Danzl, J. G. (n.d.). Light-microscopy based dense connectomic reconstruction of mammalian brain tissue. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2024.03.01.582884\">https://doi.org/10.1101/2024.03.01.582884</a>"}},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"related_material":{"record":[{"relation":"earlier_version","id":"13312","status":"public"}]},"status":"public","scopus_import":"1","ec_funded":1,"publisher":"Springer Nature","file":[{"content_type":"application/pdf","date_created":"2024-01-17T11:03:00Z","date_updated":"2024-01-17T11:03:00Z","creator":"dernst","file_name":"2024_NatureComm_Valentini.pdf","checksum":"ef79173b45eeaf984ffa61ef2f8a52ab","file_id":"14825","access_level":"open_access","file_size":2336595,"relation":"main_file","success":1}],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"article_type":"original","day":"02","department":[{"_id":"GeKa"}],"month":"01","external_id":{"isi":["001142794000839"],"pmid":["38167818"]},"volume":15,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Valentini, M., Sagi, O., Baghumyan, L., de Gijsel, T., Jung, J., Calcaterra, S., … Katsaros, G. (2024). Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>","chicago":"Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1038/s41467-023-44114-0\">https://doi.org/10.1038/s41467-023-44114-0</a>.","ieee":"M. Valentini <i>et al.</i>, “Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium,” <i>Nature Communications</i>, vol. 15. Springer Nature, 2024.","ama":"Valentini M, Sagi O, Baghumyan L, et al. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. <i>Nature Communications</i>. 2024;15. doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>","ista":"Valentini M, Sagi O, Baghumyan L, de Gijsel T, Jung J, Calcaterra S, Ballabio A, Aguilera Servin JL, Aggarwal K, Janik M, Adletzberger T, Seoane Souto R, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. 2024. Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium. Nature Communications. 15, 169.","mla":"Valentini, Marco, et al. “Parity-Conserving Cooper-Pair Transport and Ideal Superconducting Diode in Planar Germanium.” <i>Nature Communications</i>, vol. 15, 169, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1038/s41467-023-44114-0\">10.1038/s41467-023-44114-0</a>.","short":"M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.L. Aguilera Servin, K. Aggarwal, M. Janik, T. Adletzberger, R. Seoane Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024)."},"isi":1,"project":[{"call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"_id":"34c0acea-11ca-11ed-8bc3-8775e10fd452","grant_number":"101069515","name":"Integrated Germanium Quantum Technology"},{"_id":"bdc2ca30-d553-11ed-ba76-cf164a5bb811","name":"Quantum bits with Kitaev Transmons","grant_number":"101115315"},{"call_identifier":"FWF","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235","name":"Towards scalable hut wire quantum devices"},{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"name":"Center for Correlated Quantum Materials and Solid State Quantum Systems: Conventional  and unconventional topological superconductors","grant_number":"F8606","_id":"34a66131-11ca-11ed-8bc3-a31681c6b03e"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"author":[{"full_name":"Valentini, Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425","last_name":"Valentini","first_name":"Marco"},{"id":"71616374-A8E9-11E9-A7CA-09ECE5697425","full_name":"Sagi, Oliver","first_name":"Oliver","last_name":"Sagi"},{"id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","full_name":"Baghumyan, Levon","first_name":"Levon","last_name":"Baghumyan"},{"full_name":"de Gijsel, Thijs","id":"a0ece13c-b527-11ee-929d-bad130106eee","last_name":"de Gijsel","first_name":"Thijs"},{"last_name":"Jung","first_name":"Jason","full_name":"Jung, Jason","id":"4C9ACE7A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcaterra, Stefano","first_name":"Stefano","last_name":"Calcaterra"},{"first_name":"Andrea","last_name":"Ballabio","full_name":"Ballabio, Andrea"},{"full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87","last_name":"Aguilera Servin","first_name":"Juan L","orcid":"0000-0002-2862-8372"},{"first_name":"Kushagra","orcid":"0000-0001-9985-9293","last_name":"Aggarwal","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","full_name":"Aggarwal, Kushagra"},{"last_name":"Janik","first_name":"Marian","orcid":"0009-0003-9037-8831","full_name":"Janik, Marian","id":"396A1950-F248-11E8-B48F-1D18A9856A87"},{"id":"38756BB2-F248-11E8-B48F-1D18A9856A87","full_name":"Adletzberger, Thomas","first_name":"Thomas","last_name":"Adletzberger"},{"full_name":"Seoane Souto, Rubén","first_name":"Rubén","last_name":"Seoane Souto"},{"first_name":"Martin","last_name":"Leijnse","full_name":"Leijnse, Martin"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"},{"full_name":"Schrade, Constantin","last_name":"Schrade","first_name":"Constantin"},{"full_name":"Bakkers, Erik","last_name":"Bakkers","first_name":"Erik"},{"full_name":"Chrastina, Daniel","first_name":"Daniel","last_name":"Chrastina"},{"last_name":"Isella","first_name":"Giovanni","full_name":"Isella, Giovanni"},{"last_name":"Katsaros","first_name":"Georgios","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"quality_controlled":"1","year":"2024","OA_type":"gold","file_date_updated":"2024-01-17T11:03:00Z","article_number":"169","oa_version":"Published Version","doi":"10.1038/s41467-023-44114-0","publication_identifier":{"eissn":["2041-1723"]},"date_updated":"2026-07-29T07:04:56Z","date_published":"2024-01-02T00:00:00Z","APC_amount":"6468 EUR","title":"Parity-conserving Cooper-pair transport and ideal superconducting diode in planar germanium","abstract":[{"text":"Superconductor/semiconductor hybrid devices have attracted increasing interest in the past years. Superconducting electronics aims to complement semiconductor technology, while hybrid architectures are at the forefront of new ideas such as topological superconductivity and protected qubits. In this work, we engineer the induced superconductivity in two-dimensional germanium hole gas by varying the distance between the quantum well and the aluminum. We demonstrate a hard superconducting gap and realize an electrically and flux tunable superconducting diode using a superconducting quantum interference device (SQUID). This allows to tune the current phase relation (CPR), to a regime where single Cooper pair tunneling is suppressed, creating a sin(2y) CPR. Shapiro experiments complement this interpretation and the microwave drive allows to create a diode with ≈ 100% efficiency. The reported results open up the path towards integration of spin qubit devices, microwave resonators and (protected) superconducting qubits on  the same silicon technology compatible platform.","lang":"eng"}],"acknowledgement":"We acknowledge Alexander Brinkmann, Alessandro Crippa, Francesco Giazotto, Andrew Higginbotham, Andrea Iorio, Giordano Scappucci, Christian Schonenberger, and Lukas Splitthoff for helpful discussions. We thank Marcel Verheijen for the support in the TEM analysis. This research and related results were made possible with the support of the NOMIS\r\nFoundation. It was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union’s Horizon 2020 research andinnovation programme under Grant Agreement No 862046, the HORIZONRIA\r\n101069515 project, the European Innovation Council Pathfinder grant no. 101115315 (QuKiT), and the FWF Projects #P-32235, #P-36507 and #F-8606. For the purpose of open access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. R.S.S. acknowledges Spanish CM “Talento Program\"\r\nProject No. 2022-T1/IND-24070. J.J. acknowledges European Research Council TOCINA 834290.","pmid":1,"publication_status":"published","DOAJ_listed":"1","publication":"Nature Communications","oa":1,"language":[{"iso":"eng"}],"OA_place":"publisher","date_created":"2024-01-14T23:00:56Z","type":"journal_article","article_processing_charge":"Yes","ddc":["530"],"_id":"14793","corr_author":"1","intvolume":"        15"},{"publication_identifier":{"issn":["1022-1824"],"eissn":["1420-9020"]},"doi":"10.1007/s00029-023-00908-0","date_updated":"2026-07-29T09:53:10Z","title":"On the local-global principle for isogenies of abelian surfaces","date_published":"2024-01-26T00:00:00Z","abstract":[{"lang":"eng","text":"Let $\\ell$ be a prime number. We classify the subgroups $G$ of $\\operatorname{Sp}_4(\\mathbb{F}_\\ell)$ and $\\operatorname{GSp}_4(\\mathbb{F}_\\ell)$ that act irreducibly on $\\mathbb{F}_\\ell^4$, but such that every element of $G$ fixes an $\\mathbb{F}_\\ell$-vector subspace of dimension 1. We use this classification to prove that the local-global principle for isogenies of degree $\\ell$ between abelian surfaces over number fields holds in many cases -- in particular, whenever the abelian surface has non-trivial endomorphisms and $\\ell$ is large enough with respect to the field of definition. Finally, we prove that there exist arbitrarily large primes $\\ell$ for which some abelian surface\r\n$A/\\mathbb{Q}$ fails the local-global principle for isogenies of degree $\\ell$."}],"acknowledgement":"It is a pleasure to thank Samuele Anni for his interest in this project and for several discussions on the topic of this paper, which led in particular to Remark 6.30 and to a better understanding of the difficulties with [6]. We also thank John Cullinan for correspondence about [6] and Barinder Banwait for his many insightful comments on the first version of this paper. Finally, we thank the referee for their thorough reading of the manuscript.\r\nOpen access funding provided by Università di Pisa within the CRUI-CARE Agreement. The authors have been partially supported by MIUR (Italy) through PRIN 2017 “Geometric, algebraic and analytic methods in arithmetic\" and PRIN 2022 “Semiabelian varieties, Galois representations and related Diophantine problems\", and by the University of Pisa through PRA 2018-19 and 2022 “Spazi di moduli, rappresentazioni e strutture combinatorie\". The first author is a member of the INdAM group GNSAGA.","oa":1,"publication":"Selecta Mathematica","publication_status":"published","language":[{"iso":"eng"}],"date_created":"2023-01-16T11:45:53Z","supplementarymaterial":"no","type":"journal_article","article_processing_charge":"Yes (via OA deal)","arxiv":1,"_id":"12312","das_tickbox":"0","ddc":["510"],"corr_author":"1","intvolume":"        30","researchdata_availability":"no","issue":"2","file":[{"access_level":"open_access","file_size":1301415,"checksum":"ae75441420aabd80c5828bce38272ba1","file_id":"17298","file_name":"2024_SelectaMath_Lombardo.pdf","creator":"dernst","date_updated":"2024-07-22T09:33:58Z","date_created":"2024-07-22T09:33:58Z","content_type":"application/pdf","success":1,"relation":"main_file"}],"scopus_import":"1","publisher":"Springer Nature","status":"public","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"has_accepted_license":"1","article_type":"original","day":"26","month":"01","department":[{"_id":"TiBr"}],"volume":30,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","external_id":{"isi":["001148959100001"],"arxiv":["2206.15240"]},"citation":{"apa":"Lombardo, D., &#38; Verzobio, M. (2024). On the local-global principle for isogenies of abelian surfaces. <i>Selecta Mathematica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-023-00908-0\">https://doi.org/10.1007/s00029-023-00908-0</a>","chicago":"Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies of Abelian Surfaces.” <i>Selecta Mathematica</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/s00029-023-00908-0\">https://doi.org/10.1007/s00029-023-00908-0</a>.","ama":"Lombardo D, Verzobio M. On the local-global principle for isogenies of abelian surfaces. <i>Selecta Mathematica</i>. 2024;30(2). doi:<a href=\"https://doi.org/10.1007/s00029-023-00908-0\">10.1007/s00029-023-00908-0</a>","ieee":"D. Lombardo and M. Verzobio, “On the local-global principle for isogenies of abelian surfaces,” <i>Selecta Mathematica</i>, vol. 30, no. 2. Springer Nature, 2024.","ista":"Lombardo D, Verzobio M. 2024. On the local-global principle for isogenies of abelian surfaces. Selecta Mathematica. 30(2), 18.","mla":"Lombardo, Davide, and Matteo Verzobio. “On the Local-Global Principle for Isogenies of Abelian Surfaces.” <i>Selecta Mathematica</i>, vol. 30, no. 2, 18, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1007/s00029-023-00908-0\">10.1007/s00029-023-00908-0</a>.","short":"D. Lombardo, M. Verzobio, Selecta Mathematica 30 (2024)."},"isi":1,"author":[{"first_name":"Davide","last_name":"Lombardo","full_name":"Lombardo, Davide"},{"orcid":"0000-0002-0854-0306","first_name":"Matteo","last_name":"Verzobio","id":"7aa8f170-131e-11ed-88e1-a9efd01027cb","full_name":"Verzobio, Matteo"}],"quality_controlled":"1","year":"2024","article_number":"18","oa_version":"Published Version","file_date_updated":"2024-07-22T09:33:58Z"},{"doi":"10.48550/arXiv.2408.16848","date_updated":"2026-07-29T08:59:31Z","title":"Anomalous multi-gap topological phases in periodically driven quantum  rotors","date_published":"2024-08-29T00:00:00Z","abstract":[{"text":"We demonstrate that periodically driven quantum rotors provide a promising and broadly applicable platform to implement multi-gap topological phases, where groups of bands can acquire topological invariants due to non-Abelian braiding of band degeneracies. By adiabatically varying the periodic kicks to the rotor we find nodal-line braiding, which causes sign flips of topological charges of band nodes and can prevent them from annihilating, indicated by non-zero values of the %non-Abelian patch Euler class. In particular, we report\r\non the emergence of an anomalous Dirac string phase arising in the strongly driven regime, a truly out-of-equilibrium phase of the quantum rotor. This phase emanates from braiding processes involving all (quasienergy) gaps and manifests itself with edge states at zero angular momentum. Our results reveal direct applications in state-of-the-art experiments of quantum rotors, such as linear molecules driven by periodic far-off-resonant laser pulses or artificial\r\nquantum rotors in optical lattices, whose extensive versatility offers precise modification and observation of novel non-Abelian topological properties. ","lang":"eng"}],"acknowledgement":"We thank G. M. Koutentakis, S. Wimberger, J. G. E. Harris, T. Enss and A. Ghazaryan for fruitful discussions. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). R.-J. S. acknowledges funding from a EPSRC ERC underwrite grant EP/X025829/1, a EPSRC New Investigator Award grant EP/W00187X/1, as well as Trinity College, Cambridge. F.N.U. acknowledges support from the Marie ¨Sk lodowska-Curie programme of the European Commission [Grant No. 893915], Simons Investigator Award\r\n[Grant No. 511029] and Trinity College Cambridge.","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.16848","open_access":"1"}],"oa":1,"publication":"arXiv","publication_status":"draft","OA_place":"repository","language":[{"iso":"eng"}],"date_created":"2025-03-20T07:48:23Z","type":"preprint","article_processing_charge":"No","arxiv":1,"_id":"19425","status":"public","ec_funded":1,"related_material":{"record":[{"id":"19393","relation":"dissertation_contains","status":"public"},{"id":"21009","relation":"later_version","status":"public"}]},"day":"29","month":"08","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2408.16848"]},"citation":{"short":"V. Karle, M. Lemeshko, A. Bouhon, R.-J. Slager, F.N. Ünal, ArXiv (n.d.).","mla":"Karle, Volker, et al. “Anomalous Multi-Gap Topological Phases in Periodically Driven Quantum  Rotors.” <i>ArXiv</i>, 2408.16848, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.16848\">10.48550/arXiv.2408.16848</a>.","ista":"Karle V, Lemeshko M, Bouhon A, Slager R-J, Ünal FN. Anomalous multi-gap topological phases in periodically driven quantum  rotors. arXiv, 2408.16848.","chicago":"Karle, Volker, Mikhail Lemeshko, Adrien Bouhon, Robert-Jan Slager, and F. Nur Ünal. “Anomalous Multi-Gap Topological Phases in Periodically Driven Quantum  Rotors.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.16848\">https://doi.org/10.48550/arXiv.2408.16848</a>.","ieee":"V. Karle, M. Lemeshko, A. Bouhon, R.-J. Slager, and F. N. Ünal, “Anomalous multi-gap topological phases in periodically driven quantum  rotors,” <i>arXiv</i>. .","ama":"Karle V, Lemeshko M, Bouhon A, Slager R-J, Ünal FN. Anomalous multi-gap topological phases in periodically driven quantum  rotors. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.16848\">10.48550/arXiv.2408.16848</a>","apa":"Karle, V., Lemeshko, M., Bouhon, A., Slager, R.-J., &#38; Ünal, F. N. (n.d.). Anomalous multi-gap topological phases in periodically driven quantum  rotors. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.16848\">https://doi.org/10.48550/arXiv.2408.16848</a>"},"project":[{"call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle"}],"author":[{"id":"D7C012AE-D7ED-11E9-95E8-1EC5E5697425","full_name":"Karle, Volker","orcid":"0000-0002-6963-0129","first_name":"Volker","last_name":"Karle"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802"},{"first_name":"Adrien","last_name":"Bouhon","full_name":"Bouhon, Adrien"},{"full_name":"Slager, Robert-Jan","last_name":"Slager","first_name":"Robert-Jan"},{"full_name":"Ünal, F. Nur","first_name":"F. Nur","last_name":"Ünal"}],"OA_type":"green","year":"2024","article_number":"2408.16848","oa_version":"Preprint"}]