[{"title":"Neural collapse versus low-rank bias: Is deep neural collapse really optimal?","volume":37,"acknowledged_ssus":[{"_id":"ScienComp"}],"status":"public","corr_author":"1","arxiv":1,"conference":{"location":"Vancouver, Canada","name":"NeurIPS: Neural Information Processing Systems","start_date":"2024-12-16","end_date":"2024-12-16"},"year":"2024","ddc":["000"],"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","month":"12","alternative_title":["Advances in Neural Information Processing Systems"],"date_published":"2024-12-01T00:00:00Z","_id":"18891","date_updated":"2025-06-04T07:19:21Z","language":[{"iso":"eng"}],"quality_controlled":"1","department":[{"_id":"GradSch"},{"_id":"MaMo"},{"_id":"ChLa"}],"acknowledgement":"Marco Mondelli is partially supported by the 2019 Lopez-Loreta prize. This research was supported by the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"external_id":{"arxiv":["2405.14468"]},"author":[{"full_name":"Súkeník, Peter","last_name":"Súkeník","id":"d64d6a8d-eb8e-11eb-b029-96fd216dec3c","first_name":"Peter"},{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert"},{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","orcid":"0000-0002-3242-7020","last_name":"Mondelli","full_name":"Mondelli, Marco"}],"OA_type":"gold","OA_place":"publisher","file_date_updated":"2025-02-04T08:11:25Z","day":"01","intvolume":" 37","oa":1,"article_processing_charge":"No","type":"conference","citation":{"ieee":"P. Súkeník, C. Lampert, and M. Mondelli, “Neural collapse versus low-rank bias: Is deep neural collapse really optimal?,” in 38th Annual Conference on Neural Information Processing Systems, Vancouver, Canada, 2024, vol. 37.","mla":"Súkeník, Peter, et al. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” 38th Annual Conference on Neural Information Processing Systems, vol. 37, Neural Information Processing Systems Foundation, 2024.","ista":"Súkeník P, Lampert C, Mondelli M. 2024. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? 38th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 37.","apa":"Súkeník, P., Lampert, C., & Mondelli, M. (2024). Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In 38th Annual Conference on Neural Information Processing Systems (Vol. 37). Vancouver, Canada: Neural Information Processing Systems Foundation.","chicago":"Súkeník, Peter, Christoph Lampert, and Marco Mondelli. “Neural Collapse versus Low-Rank Bias: Is Deep Neural Collapse Really Optimal?” In 38th Annual Conference on Neural Information Processing Systems, Vol. 37. Neural Information Processing Systems Foundation, 2024.","ama":"Súkeník P, Lampert C, Mondelli M. Neural collapse versus low-rank bias: Is deep neural collapse really optimal? In: 38th Annual Conference on Neural Information Processing Systems. Vol 37. Neural Information Processing Systems Foundation; 2024.","short":"P. Súkeník, C. Lampert, M. Mondelli, in:, 38th Annual Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2024."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems Foundation","date_created":"2025-01-27T11:15:18Z","publication_status":"published","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) exhibit a surprising structure in their final layer\r\nknown as neural collapse (NC), and a growing body of works has currently investigated the propagation of neural collapse to earlier layers of DNNs – a phenomenon\r\ncalled deep neural collapse (DNC). However, existing theoretical results are restricted to special cases: linear models, only two layers or binary classification.\r\nIn contrast, we focus on non-linear models of arbitrary depth in multi-class classification and reveal a surprising qualitative shift. As soon as we go beyond two\r\nlayers or two classes, DNC stops being optimal for the deep unconstrained features\r\nmodel (DUFM) – the standard theoretical framework for the analysis of collapse.\r\nThe main culprit is a low-rank bias of multi-layer regularization schemes: this bias\r\nleads to optimal solutions of even lower rank than the neural collapse. We support\r\nour theoretical findings with experiments on both DUFM and real data, which show\r\nthe emergence of the low-rank structure in the solution found by gradient descent."}],"publication":"38th Annual Conference on Neural Information Processing Systems","file":[{"date_updated":"2025-02-04T08:11:25Z","file_id":"18989","creator":"dernst","success":1,"file_name":"2024_NeurIPS_Sukenik.pdf","checksum":"b7b79f1ea3ac1e9e11b3d91faaeb0780","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2025-02-04T08:11:25Z","file_size":1784118}],"oa_version":"Published Version"},{"author":[{"first_name":"Riccardo","id":"0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b","last_name":"Cadei","full_name":"Cadei, Riccardo"},{"orcid":"0000-0002-4850-0683","first_name":"Francesco","id":"26cfd52f-2483-11ee-8040-88983bcc06d4","last_name":"Locatello","full_name":"Locatello, Francesco"},{"full_name":"Cremer, Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia M","orcid":"0000-0002-2193-3868"},{"first_name":"Lukas","id":"85f0e6d3-06b3-11ec-8982-8c5049fa4455","last_name":"Lindorfer","full_name":"Lindorfer, Lukas"},{"full_name":"Schmid, Cordelia","last_name":"Schmid","first_name":"Cordelia"}],"OA_type":"gold","title":"ISTAnt","department":[{"_id":"SyCr"},{"_id":"FrLo"},{"_id":"GradSch"}],"citation":{"ieee":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, and C. Schmid, “ISTAnt.” Institute of Science and Technology Austria, 2024.","mla":"Cadei, Riccardo, et al. ISTAnt. Institute of Science and Technology Austria, 2024, doi:10.6084/M9.FIGSHARE.26484934.V2.","apa":"Cadei, R., Locatello, F., Cremer, S., Lindorfer, L., & Schmid, C. (2024). ISTAnt. Institute of Science and Technology Austria. https://doi.org/10.6084/M9.FIGSHARE.26484934.V2","ista":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. 2024. ISTAnt, Institute of Science and Technology Austria, 10.6084/M9.FIGSHARE.26484934.V2.","chicago":"Cadei, Riccardo, Francesco Locatello, Sylvia Cremer, Lukas Lindorfer, and Cordelia Schmid. “ISTAnt.” Institute of Science and Technology Austria, 2024. https://doi.org/10.6084/M9.FIGSHARE.26484934.V2.","short":"R. Cadei, F. Locatello, S. Cremer, L. Lindorfer, C. Schmid, (2024).","ama":"Cadei R, Locatello F, Cremer S, Lindorfer L, Schmid C. ISTAnt. 2024. doi:10.6084/M9.FIGSHARE.26484934.V2"},"corr_author":"1","oa":1,"article_processing_charge":"No","type":"research_data_reference","status":"public","OA_place":"repository","day":"23","date_created":"2025-01-27T11:45:43Z","month":"10","publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"relation":"used_in_publication","id":"18847","status":"public"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"year":"2024","oa_version":"Published Version","date_updated":"2025-01-27T11:58:38Z","date_published":"2024-10-23T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://10.6084/M9.FIGSHARE.26484934.V2"}],"_id":"18895","abstract":[{"text":"ISTAnt is a new ecological dataset for social immunity and represents the first real-world benchmark for causal inference downstream tasks on high-dimensional observations. It analyzes grooming behavior in the ant Lasius neglectus in groups of three worker ants. The workers for the experiment were obtained from their laboratory stock colony, which had been collected from the field in 2022 in the Botanical Garden Jena, Germany. Ant collection and all experimental work were performed in compliance with international, national and institutional regulations and ethical guidelines. For the experiment, the body surface of one of the three ants was treated with a suspension of either of two microparticle types (diameter ~5 µm) to induce grooming by the two nestmates, which were individually color-coded by application of a dot of blue or orange paint, respectively. The three ants were housed in small plastic containers (diameter 28mm, height 30mm) with moistened, plastered ground and the interior walls covered with PTFE (polytetrafluoroethane) to hamper climbing by the ants. Filming occurred in a temperature- and humidity-controlled room at 23°C within a custom-made filming box with controlled lighting and ventilation conditions. We set up nine ant groups at a time (always containing both treatments) and placed them randomly on positions 1-9 marked on the floor in a 3x3 grid, about 3mm from each other. The experiment was performed on two consecutive days. Videos were acquired using a USB camera (FLIR blackfly S BFS-U3-120S4C, Teledyne FLIR) with a high-performance lens (HP Series 25mm Focal Length, Edmund optics 86-572) in OBS studio 29.0.0 \\citep{bailey2017obs} at a framerate of 30 FPS and a resolution of 2500x2500 pixels. From each original video (105x105 mm), we generated nine individual videos .mkv (each ~32x32 mm, 770x770 pixels) by determining exact coordinates per container from one frame in GIMP 2.10.36 and cropping of the videos with FFmpeg 6.1.1. Annotation was performed over two consecutive days by three observers who had not been involved in the experimental setup or recording and were unaware of the treatment assignments to ensure bias-free behavioral annotation. They annotated the behavior of the ants during video observations, using custom-made software that saves the start and end frames of behaviors marked in a .csv file (see 'annotations' folder). In one of the videos, one of the nestmates' legs got inadvertently stuck to its body surface during the color-coding, interfering with its behavior, so the video was discarded. This left 44 videos from 5 independent setups (n=24 of treatment 1 and n=20 of treatment 2) of 10 minutes each for a total of 792 000 annotated frames (see 'video' folder). For each video, we provide the following information: the number of the set to which it belongs (1-5); the number of the position within the set reflecting the position of the ant group under the camera (1-9), for which we also provide ‘coordinates’ in the 3x3 grid (taking values -1/0/1 for both X and Y axis); treatment (1 or 2); the hour of the day when the recording was started (in 24h CEST); experimental day (A or B); the top left coordinate of the cropping square from the original video (CropX/CropY); the person annotating the video (given as A, B, C); the date of annotation (1: first day, 2: second day) and in which order the videos were annotated by each person, both reflecting a possible training effect of the person (see 'experiments_settings.csv' file).","lang":"eng"}],"doi":"10.6084/M9.FIGSHARE.26484934.V2"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-27T14:19:17Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","publication_status":"published","publication":"40th International Symposium on Computational Geometry","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":880725,"date_created":"2025-01-27T14:17:37Z","date_updated":"2025-01-27T14:17:37Z","creator":"dernst","file_id":"18918","checksum":"443aa29ea5d948e917cfccd681dcf176","success":1,"file_name":"2024_LIPICs_Aronov.pdf"}],"abstract":[{"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}).","lang":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2024.8","publication_identifier":{"isbn":["9783959773164"]},"oa_version":"Published Version","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"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.","author":[{"full_name":"Aronov, Boris","last_name":"Aronov","first_name":"Boris"},{"first_name":"Abdul","full_name":"Basit, Abdul","last_name":"Basit"},{"full_name":"Ramesh, Indu","last_name":"Ramesh","first_name":"Indu"},{"id":"0433290C-AF8F-11E9-A4C7-F729E6697425","first_name":"Gianluca","full_name":"Tasinato, Gianluca","last_name":"Tasinato"},{"last_name":"Wagner","full_name":"Wagner, Uli","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568"}],"OA_type":"gold","external_id":{"arxiv":["2403.02627"]},"scopus_import":"1","intvolume":" 293","file_date_updated":"2025-01-27T14:17:37Z","OA_place":"publisher","day":"06","citation":{"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.","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. In: 40th International Symposium on Computational Geometry. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:8:1-8:15. doi:10.4230/LIPIcs.SoCG.2024.8","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” In 40th International Symposium on Computational Geometry, 293:8:1-8:15. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.SoCG.2024.8.","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” 40th International Symposium on Computational Geometry, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15, doi:10.4230/LIPIcs.SoCG.2024.8.","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., & Wagner, U. (2024). Eight-partitioning points in 3D, and efficiently too. In 40th International Symposium on Computational Geometry (Vol. 293, p. 8:1-8:15). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2024.8","ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” in 40th International Symposium on Computational Geometry, Athens, Greece, 2024, vol. 293, p. 8:1-8:15."},"oa":1,"type":"conference","article_processing_charge":"Yes","conference":{"location":"Athens, Greece","name":"SoCG: Symposium on Computational Geometry","start_date":"2024-06-11","end_date":"2024-06-14"},"year":"2024","ddc":["510"],"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","month":"06","related_material":{"record":[{"id":"19860","relation":"later_version","status":"public"}]},"date_published":"2024-06-06T00:00:00Z","_id":"18917","quality_controlled":"1","date_updated":"2026-06-18T18:18:27Z","language":[{"iso":"eng"}],"volume":293,"title":"Eight-partitioning points in 3D, and efficiently too","status":"public","page":"8:1-8:15","corr_author":"1","arxiv":1},{"author":[{"id":"ec98511c-eb8e-11eb-b029-edd25d7271a1","first_name":"Christoph Ullrich","full_name":"Günther, Christoph Ullrich","last_name":"Günther"},{"full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"gold","acknowledgement":"We thank Raluca-Georgia Diugan for her initial contributions and support afterward.\r\nThis research was funded in whole or in part by the Austrian Science Fund (FWF) 10.55776/F85.","issue":"4","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"project":[{"grant_number":"F8509","name":"Security and Privacy by Design for Complex Systems","_id":"34a34d57-11ca-11ed-8bc3-a2688a8724e1"}],"citation":{"ama":"Günther CU, Pietrzak KZ. Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. 2024;2024(4):636-648. doi:10.56553/popets-2024-0134","short":"C.U. Günther, K.Z. Pietrzak, Proceedings on Privacy Enhancing Technologies 2024 (2024) 636–648.","chicago":"Günther, Christoph Ullrich, and Krzysztof Z Pietrzak. “Deniability in Automated Contact Tracing: Impossibilities and Possibilities.” Proceedings on Privacy Enhancing Technologies. Privacy Enhancing Technologies Symposium Advisory Board, 2024. https://doi.org/10.56553/popets-2024-0134.","mla":"Günther, Christoph Ullrich, and Krzysztof Z. Pietrzak. “Deniability in Automated Contact Tracing: Impossibilities and Possibilities.” Proceedings on Privacy Enhancing Technologies, vol. 2024, no. 4, Privacy Enhancing Technologies Symposium Advisory Board, 2024, pp. 636–48, doi:10.56553/popets-2024-0134.","apa":"Günther, C. U., & Pietrzak, K. Z. (2024). Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. Bristol, UK/Virtual: Privacy Enhancing Technologies Symposium Advisory Board. https://doi.org/10.56553/popets-2024-0134","ista":"Günther CU, Pietrzak KZ. 2024. Deniability in automated contact tracing: Impossibilities and possibilities. Proceedings on Privacy Enhancing Technologies. 2024(4), 636–648.","ieee":"C. U. Günther and K. Z. Pietrzak, “Deniability in automated contact tracing: Impossibilities and possibilities,” Proceedings on Privacy Enhancing Technologies, vol. 2024, no. 4. Privacy Enhancing Technologies Symposium Advisory Board, pp. 636–648, 2024."},"oa":1,"article_processing_charge":"No","type":"journal_article","intvolume":" 2024","OA_place":"publisher","file_date_updated":"2025-01-29T13:44:47Z","day":"01","date_created":"2025-01-29T13:39:34Z","article_type":"original","publisher":"Privacy Enhancing Technologies Symposium Advisory Board","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","publication_identifier":{"issn":["2299-0984"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":611567,"date_created":"2025-01-29T13:44:47Z","date_updated":"2025-01-29T13:44:47Z","creator":"dernst","file_id":"18962","checksum":"348ed6adcf6ad2f925227bde1758cae6","file_name":"2024_ProcPrivacyEnhTech_Guenther.pdf","success":1}],"publication":"Proceedings on Privacy Enhancing Technologies","abstract":[{"text":"Automated contact tracing (ACT) emerged as a promising measure to curb the spread of Covid-19. Users enable ACT on their smartphones to automatically record contacts with other users. If a user tests positive for the disease, they report their diagnosis to alert their contacts.\r\nDesigning effective ACT protocols is challenging since they need to be efficient and secure while also ensuring users' privacy. As ACT protocols necessarily leak some information by design, defining privacy is difficult. For example, a user cannot deny having met another user. Ideally, however, the user can plausibly deny everything else, in particular, when they met. We call this privacy property contact-time deniability.\r\nWhile some early works discussed contact-time deniability informally, it has received little attention since then. We investigate deniability from a rigorous, theoretical point of view and arrive at the following impossibility result:\r\nA decentralized protocol with unidirectional communication cannot be contact-time deniable and replay-secure. This holds even if malicious users treat smartphones as black-boxes.\r\n Unidirectional protocols are usually very efficient and many proposals are unidirectional, e.g., the widely-deployed Google-Apple Exposure Notifications. So the impossibility result considerably constrains the design space of efficient, secure, and private ACT protocols. However, it can also be used as a guide; we discuss several possibilities to achieve contact-time deniability in practice.","lang":"eng"}],"doi":"10.56553/popets-2024-0134","volume":2024,"title":"Deniability in automated contact tracing: Impossibilities and possibilities","page":"636-648","corr_author":"1","status":"public","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"},"month":"07","conference":{"location":"Bristol, UK/Virtual","name":"PETs: Privacy Enhancing Technologies Symposium ","start_date":"2024-07-15","end_date":"2024-07-20"},"year":"2024","ddc":["000"],"quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2025-04-15T08:16:04Z","date_published":"2024-07-01T00:00:00Z","_id":"18961"},{"day":"01","OA_place":"publisher","file_date_updated":"2025-02-10T08:20:34Z","citation":{"chicago":"Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” In Findings of the Association for Computational Linguistics: EMNLP 2024, 12080–99. Association for Computational Linguistics, 2024. https://doi.org/10.18653/v1/2024.findings-emnlp.705.","ama":"Draganov O, Skiena S. The shape of word embeddings: Quantifying non-isometry with topological data analysis. In: Findings of the Association for Computational Linguistics: EMNLP 2024. Association for Computational Linguistics; 2024:12080-12099. doi:10.18653/v1/2024.findings-emnlp.705","short":"O. Draganov, S. Skiena, in:, Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–12099.","ieee":"O. Draganov and S. Skiena, “The shape of word embeddings: Quantifying non-isometry with topological data analysis,” in Findings of the Association for Computational Linguistics: EMNLP 2024, Miami, FL, United States, 2024, pp. 12080–12099.","mla":"Draganov, Ondrej, and Steven Skiena. “The Shape of Word Embeddings: Quantifying Non-Isometry with Topological Data Analysis.” Findings of the Association for Computational Linguistics: EMNLP 2024, Association for Computational Linguistics, 2024, pp. 12080–99, doi:10.18653/v1/2024.findings-emnlp.705.","ista":"Draganov O, Skiena S. 2024. The shape of word embeddings: Quantifying non-isometry with topological data analysis. Findings of the Association for Computational Linguistics: EMNLP 2024. EMNLP: Conference on Empirical Methods in Natural Language Processing, 12080–12099.","apa":"Draganov, O., & Skiena, S. (2024). The shape of word embeddings: Quantifying non-isometry with topological data analysis. In Findings of the Association for Computational Linguistics: EMNLP 2024 (pp. 12080–12099). Miami, FL, United States: Association for Computational Linguistics. https://doi.org/10.18653/v1/2024.findings-emnlp.705"},"article_processing_charge":"No","type":"conference","oa":1,"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"OA_type":"gold","author":[{"id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0464-3823","first_name":"Ondrej","full_name":"Draganov, Ondrej","last_name":"Draganov"},{"last_name":"Skiena","full_name":"Skiena, Steven","first_name":"Steven"}],"scopus_import":"1","external_id":{"arxiv":["2404.00500"]},"abstract":[{"text":"Word embeddings represent language vocabularies as clouds of d-dimensional points. We investigate how information is conveyed by the general shape of these clouds, instead of representing the semantic meaning of each token. Specifically, we use the notion of persistent homology from topological data analysis (TDA) to measure the distances between language pairs from the shape of their unlabeled embeddings. These distances quantify the degree of non-isometry of the embeddings. To distinguish whether these differences are random training errors or capture real information about the languages, we use the computed distance matrices to construct language phylogenetic trees over 81 Indo-European languages. Careful evaluation shows that our reconstructed trees exhibit strong and statistically-significant similarities to the reference.","lang":"eng"}],"file":[{"file_size":1312638,"date_created":"2025-02-10T08:20:34Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"f4416a5962194f0181ab0dc7f9ef93c0","file_name":"2024_EMNLP_Draganov.pdf","success":1,"creator":"dernst","file_id":"19016","date_updated":"2025-02-10T08:20:34Z"}],"publication":"Findings of the Association for Computational Linguistics: EMNLP 2024","publication_status":"published","doi":"10.18653/v1/2024.findings-emnlp.705","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-02-04T16:19:28Z","publisher":"Association for Computational Linguistics","status":"public","arxiv":1,"corr_author":"1","page":"12080-12099","title":"The shape of word embeddings: Quantifying non-isometry with topological data analysis","_id":"18998","date_published":"2024-11-01T00:00:00Z","quality_controlled":"1","date_updated":"2025-02-10T08:21:37Z","language":[{"iso":"eng"}],"ddc":["500"],"year":"2024","conference":{"end_date":"2024-11-16","start_date":"2024-11-12","name":"EMNLP: Conference on Empirical Methods in Natural Language Processing","location":"Miami, FL, United States"},"month":"11","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"},{"publication":"arXiv","abstract":[{"text":"Exploring the shape of point configurations has been a key driver in the evolution of TDA (short for topological data analysis) since its infancy. This survey illustrates the recent efforts to broaden these ideas to model spatial interactions among multiple configurations, each distinguished by a color. It describes advances in this area and prepares the ground for further exploration by mentioning unresolved questions and promising research avenues while focusing on the overlap with discrete geometry.","lang":"eng"}],"publication_status":"submitted","doi":"10.48550/ARXIV.2406.04102","oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-02-04T16:21:21Z","day":"06","OA_place":"repository","citation":{"short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic topological data analysis. arXiv. doi:10.48550/ARXIV.2406.04102","chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Topological Data Analysis.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2406.04102.","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Topological Data Analysis.” ArXiv, 2406.04102, doi:10.48550/ARXIV.2406.04102.","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic topological data analysis. arXiv, 2406.04102.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic topological data analysis. arXiv. https://doi.org/10.48550/ARXIV.2406.04102","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic topological data analysis,” arXiv. ."},"article_processing_charge":"No","type":"preprint","oa":1,"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"OA_type":"green","author":[{"orcid":"0000-0001-6249-0832","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano"},{"first_name":"Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0464-3823","full_name":"Draganov, Ondrej","last_name":"Draganov"},{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"last_name":"Saghafian","full_name":"Saghafian, Morteza","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824"}],"article_number":"2406.04102","external_id":{"arxiv":["2406.04102"]},"_id":"18999","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2406.04102"}],"date_published":"2024-06-06T00:00:00Z","date_updated":"2025-02-10T08:14:27Z","language":[{"iso":"eng"}],"year":"2024","ddc":["510"],"month":"06","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","status":"public","arxiv":1,"corr_author":"1","title":"Chromatic topological data analysis"},{"acknowledgement":"The authors would like to sincerely thank Juan Rocamonde for valuable feedback to our manuscript. We acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp). We thank Dan Alistarh for providing us with computational resources. This work was partially funded by the German Federal Ministry of Education and Research (BMBF) under the grant AIgenCY (16KIS2012) and ELSA – European Lighthouse on Secure and Safe AI funded by the European Union under grant agreement No. 101070617. Views and opinions expressed are however those of the authors only and do not necessarily reflect those of the European Union or European Commission. Neither the European Union nor the European Commission can be held responsible for them.","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"author":[{"first_name":"Egor","id":"05162b19-1340-11ed-8f02-fa94e0e8c3bc","last_name":"Zverev","full_name":"Zverev, Egor"},{"first_name":"Sahar","full_name":"Abdelnabi, Sahar","last_name":"Abdelnabi"},{"last_name":"Tabesh","full_name":"Tabesh, Soroush","orcid":"0009-0003-4119-6281","id":"06000900-6068-11ef-8d61-c2472ef2e752","first_name":"Soroush"},{"first_name":"Mario","full_name":"Fritz, Mario","last_name":"Fritz"},{"last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"green","external_id":{"arxiv":["2403.06833"]},"article_number":"2403.06833","OA_place":"repository","file_date_updated":"2025-02-20T10:11:45Z","day":"01","citation":{"short":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, C. Lampert, ArXiv (2024).","ama":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. Can LLMs separate instructions from data? And what do we even mean by that? arXiv. 2024. doi:10.48550/arXiv.2403.06833","chicago":"Zverev, Egor, Sahar Abdelnabi, Soroush Tabesh, Mario Fritz, and Christoph Lampert. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” ArXiv, 2024. https://doi.org/10.48550/arXiv.2403.06833.","apa":"Zverev, E., Abdelnabi, S., Tabesh, S., Fritz, M., & Lampert, C. (2024). Can LLMs separate instructions from data? And what do we even mean by that? arXiv. https://doi.org/10.48550/arXiv.2403.06833","ista":"Zverev E, Abdelnabi S, Tabesh S, Fritz M, Lampert C. 2024. Can LLMs separate instructions from data? And what do we even mean by that? arXiv, 2403.06833.","mla":"Zverev, Egor, et al. “Can LLMs Separate Instructions from Data? And What Do We Even Mean by That?” ArXiv, 2403.06833, 2024, doi:10.48550/arXiv.2403.06833.","ieee":"E. Zverev, S. Abdelnabi, S. Tabesh, M. Fritz, and C. Lampert, “Can LLMs separate instructions from data? And what do we even mean by that?,” arXiv. 2024."},"oa":1,"type":"preprint","article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-02-20T10:13:42Z","publication_status":"published","file":[{"creator":"ezverev","file_id":"19064","date_updated":"2025-02-20T10:11:45Z","checksum":"35eb43968684b87be59144603ef10af0","file_name":"2403.06833v3.pdf","success":1,"file_size":530972,"date_created":"2025-02-20T10:11:45Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"abstract":[{"text":"Instruction-tuned Large Language Models (LLMs) show impressive results in numerous practical applications, but they lack essential safety features that are common in other areas of computer science, particularly an explicit separation of instructions and data. This makes them vulnerable to manipulations such as indirect prompt injections and generally unsuitable for safety-critical tasks. Surprisingly, there is currently no established definition or benchmark to quantify this phenomenon. In this work, we close this gap by introducing a formal measure for instruction-data separation and an empirical variant that is calculable from a model's outputs. We also present a new dataset, SEP, that allows estimating the measure for real-world models. Our results on various LLMs show that the problem of instruction-data separation is real: all models fail to achieve high separation, and canonical mitigation techniques, such as prompt engineering and fine-tuning, either fail to substantially improve separation or reduce model utility. The source code and SEP dataset are openly accessible at https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed.\r\n","lang":"eng"}],"publication":"arXiv","doi":"10.48550/arXiv.2403.06833","oa_version":"Preprint","license":"https://creativecommons.org/licenses/by-sa/4.0/","title":"Can LLMs separate instructions from data? And what do we even mean by that?","acknowledged_ssus":[{"_id":"ScienComp"}],"status":"public","corr_author":"1","arxiv":1,"year":"2024","ddc":["000"],"has_accepted_license":"1","tmp":{"image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)"},"month":"03","related_material":{"link":[{"url":" https://github.com/egozverev/Shold-It-Be-Executed-Or-Processed","relation":"software"}]},"date_published":"2024-03-01T00:00:00Z","_id":"19063","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2403.06833"}],"language":[{"iso":"eng"}],"date_updated":"2025-02-24T12:52:23Z"},{"external_id":{"arxiv":["2409.08119"]},"article_number":"2409.08119","author":[{"full_name":"Dvorak, Martin","last_name":"Dvorak","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","first_name":"Martin","orcid":"0000-0001-5293-214X"},{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"green","acknowledgement":"We would like to thank David Bartl and Jasmin Blanchette for frequent consultations. We would also like to express gratitude to Andrew Yang for the proof of Finset.univ sum of zero when not and to Henrik B¨oving for a help with generalization from extended rationals to extended linearly ordered fields. We would also like to acknowledge Antoine Chambert-Loir, Apurva Nakade, Ya¨el Dillies, Richard Copley, Edward van de Meent, Markus Himmel, Mario Carneiro, and Kevin Buzzard.","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"oa":1,"article_processing_charge":"No","type":"preprint","citation":{"mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” ArXiv, 2409.08119, doi:10.48550/arXiv.2409.08119.","apa":"Dvorak, M., & Kolmogorov, V. (n.d.). Duality theory in linear optimization and its extensions -- formally verified. arXiv. https://doi.org/10.48550/arXiv.2409.08119","ista":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. arXiv, 2409.08119.","ieee":"M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally verified,” arXiv. .","short":"M. Dvorak, V. Kolmogorov, ArXiv (n.d.).","ama":"Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally verified. arXiv. doi:10.48550/arXiv.2409.08119","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally Verified.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.08119."},"OA_place":"repository","keyword":["Farkas lemma","linear programming","extended reals","calculus of inductive constructions"],"day":"12","date_created":"2025-07-23T11:21:52Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Preprint","doi":"10.48550/arXiv.2409.08119","publication_status":"draft","publication":"arXiv","abstract":[{"lang":"eng","text":"Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take \"infinite values\"."}],"title":"Duality theory in linear optimization and its extensions -- formally verified","corr_author":"1","arxiv":1,"status":"public","related_material":{"record":[{"relation":"dissertation_contains","id":"21393","status":"public"}],"link":[{"description":"full version of all definitions, statement, and proofs","url":"https://github.com/madvorak/duality/tree/v3.2","relation":"software"}]},"month":"09","year":"2024","language":[{"iso":"eng"}],"date_updated":"2026-03-27T12:36:59Z","date_published":"2024-09-12T00:00:00Z","_id":"20071","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2409.08119","open_access":"1"}]},{"_id":"17202","date_published":"2024-07-30T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"date_updated":"2026-04-07T13:01:55Z","ddc":["530"],"year":"2024","month":"07","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","related_material":{"record":[{"id":"17196","relation":"research_data","status":"public"},{"relation":"dissertation_contains","id":"18076","status":"public"}],"link":[{"url":"https://doi.org/10.1038/s41467-024-53910-1","relation":"erratum"}]},"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"NanoFab"}],"status":"public","corr_author":"1","arxiv":1,"volume":15,"title":"A gate tunable transmon qubit in planar Ge","publication":"Nature Communications","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-08-05T08:38:01Z","file_size":1928001,"date_updated":"2024-08-05T08:38:01Z","file_id":"17388","creator":"dernst","success":1,"file_name":"2024_NatureComm_Sagi.pdf","checksum":"ddf5361dcb6c543e2cea818501c09910"}],"abstract":[{"lang":"eng","text":"Gate-tunable transmons (gatemons) employing semiconductor Josephson junctions have recently emerged as building blocks for hybrid quantum circuits. In this study, we present a gatemon fabricated in planar Germanium. We induce superconductivity in a two-dimensional hole gas by evaporating aluminum atop a thin spacer, which separates the superconductor from the Ge quantum well. The Josephson junction is then integrated into an Xmon circuit and capacitively coupled to a transmission line resonator. We showcase the qubit tunability in a broad frequency range with resonator and two-tone spectroscopy. Time-domain characterizations reveal energy relaxation and coherence times up to 75 ns. Our results, combined with the recent advances in the spin qubit field, pave the way towards novel hybrid and protected qubits in a group IV, CMOS-compatible material."}],"publication_status":"published","DOAJ_listed":"1","doi":"10.1038/s41467-024-50763-6","oa_version":"Published Version","pmid":1,"publication_identifier":{"eissn":["2041-1723"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2024-07-04T11:40:45Z","publisher":"Springer Nature","article_type":"original","APC_amount":"6828 EUR","intvolume":" 15","day":"30","OA_place":"publisher","file_date_updated":"2024-08-05T08:38:01Z","citation":{"ieee":"O. Sagi et al., “A gate tunable transmon qubit in planar Ge,” Nature Communications, vol. 15. Springer Nature, 2024.","ista":"Sagi O, Crippa A, Valentini M, Janik M, Baghumyan L, Fabris G, Kapoor L, Hassani F, Fink JM, Calcaterra S, Chrastina D, Isella G, Katsaros G. 2024. A gate tunable transmon qubit in planar Ge. Nature Communications. 15, 6400.","apa":"Sagi, O., Crippa, A., Valentini, M., Janik, M., Baghumyan, L., Fabris, G., … Katsaros, G. (2024). A gate tunable transmon qubit in planar Ge. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-50763-6","mla":"Sagi, Oliver, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications, vol. 15, 6400, Springer Nature, 2024, doi:10.1038/s41467-024-50763-6.","chicago":"Sagi, Oliver, Alessandro Crippa, Marco Valentini, Marian Janik, Levon Baghumyan, Giorgio Fabris, Lucky Kapoor, et al. “A Gate Tunable Transmon Qubit in Planar Ge.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-50763-6.","ama":"Sagi O, Crippa A, Valentini M, et al. A gate tunable transmon qubit in planar Ge. Nature Communications. 2024;15. doi:10.1038/s41467-024-50763-6","short":"O. Sagi, A. Crippa, M. Valentini, M. Janik, L. Baghumyan, G. Fabris, L. Kapoor, F. Hassani, J.M. Fink, S. Calcaterra, D. Chrastina, G. Isella, G. Katsaros, Nature Communications 15 (2024)."},"article_processing_charge":"Yes","type":"journal_article","oa":1,"project":[{"_id":"bd8bd29e-d553-11ed-ba76-f0070d4b237a","grant_number":"P36507","name":"Merging spin and superconducting qubits in planar Ge"},{"name":"High impedance circuit quantum electrodynamics with hole spins","_id":"c0977eea-5a5b-11eb-8a69-a862db0cf4d1","grant_number":"I05060"},{"name":"Hybrid Semiconductor - Superconductor Quantum Devices","_id":"262116AA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund"}],"department":[{"_id":"GeKa"},{"_id":"JoFi"},{"_id":"GradSch"}],"acknowledgement":"We acknowledge Lucas Casparis, Jeroen Danon, Valla Fatemi, Morten Kjaergard and Javad Shabani for their valuable insights and comments. This research was supported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop\r\nand the Nanofabrication facility. This research and related results were made possible with the support of the NOMIS Foundation and the FWF Projects with DOI:10.55776/I5060 and DOI:10.55776/P36507. We also acknowledge the NextGenerationEU PRIN project\r\n2022A8CJP3 (GAMESQUAD) for partial financial support.","OA_type":"gold","author":[{"last_name":"Sagi","full_name":"Sagi, Oliver","id":"71616374-A8E9-11E9-A7CA-09ECE5697425","first_name":"Oliver"},{"id":"1F2B21A2-F6E7-11E9-9B82-F7DBE5697425","first_name":"Alessandro","orcid":"0000-0002-2968-611X","full_name":"Crippa, Alessandro","last_name":"Crippa"},{"last_name":"Valentini","full_name":"Valentini, Marco","first_name":"Marco","id":"C0BB2FAC-D767-11E9-B658-BC13E6697425"},{"id":"396A1950-F248-11E8-B48F-1D18A9856A87","first_name":"Marian","orcid":"0009-0003-9037-8831","last_name":"Janik","full_name":"Janik, Marian"},{"first_name":"Levon","id":"7aa1f788-b527-11ee-aa9e-e6111a79e0c7","full_name":"Baghumyan, Levon","last_name":"Baghumyan"},{"id":"298cf6f3-1ff6-11ee-9fa6-d94cfa0b3352","first_name":"Giorgio","last_name":"Fabris","full_name":"Fabris, Giorgio"},{"last_name":"Kapoor","full_name":"Kapoor, Lucky","orcid":"0000-0001-8319-2148","id":"84b9700b-15b2-11ec-abd3-831089e67615","first_name":"Lucky"},{"id":"2AED110C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6937-5773","first_name":"Farid","last_name":"Hassani","full_name":"Hassani, Farid"},{"last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Calcaterra, Stefano","last_name":"Calcaterra","first_name":"Stefano"},{"first_name":"Daniel","last_name":"Chrastina","full_name":"Chrastina, Daniel"},{"last_name":"Isella","full_name":"Isella, Giovanni","first_name":"Giovanni"},{"last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"article_number":"6400","scopus_import":"1","isi":1,"external_id":{"pmid":["39080279"],"arxiv":["2403.16774"],"isi":["001281271000022"]}},{"supervisor":[{"orcid":"0000-0002-2399-5827","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn"}],"page":"133","corr_author":"1","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"title":"Exploring the optimization landscape of variational quantum algorithms","date_updated":"2026-04-07T12:43:22Z","language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"date_published":"2024-07-09T00:00:00Z","_id":"17208","related_material":{"record":[{"status":"public","id":"10545","relation":"part_of_dissertation"},{"id":"10067","relation":"part_of_dissertation","status":"public"},{"id":"17222","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"13125"},{"status":"public","relation":"part_of_dissertation","id":"11471"}]},"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","month":"07","ddc":["539"],"year":"2024","oa":1,"type":"dissertation","article_processing_charge":"No","citation":{"ista":"Medina Ramos RA. 2024. Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria.","apa":"Medina Ramos, R. A. (2024). Exploring the optimization landscape of variational quantum algorithms. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17208","mla":"Medina Ramos, Raimel A. Exploring the Optimization Landscape of Variational Quantum Algorithms. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17208.","ieee":"R. A. Medina Ramos, “Exploring the optimization landscape of variational quantum algorithms,” Institute of Science and Technology Austria, 2024.","short":"R.A. Medina Ramos, Exploring the Optimization Landscape of Variational Quantum Algorithms, Institute of Science and Technology Austria, 2024.","ama":"Medina Ramos RA. Exploring the optimization landscape of variational quantum algorithms. 2024. doi:10.15479/at:ista:17208","chicago":"Medina Ramos, Raimel A. “Exploring the Optimization Landscape of Variational Quantum Algorithms.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17208."},"file_date_updated":"2024-07-17T09:23:24Z","keyword":["Quantum computing","Variational Quantum Algorithms","Optimization"],"OA_place":"publisher","day":"09","author":[{"orcid":"0000-0002-5383-2869","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A","full_name":"Medina Ramos, Raimel A","last_name":"Medina Ramos"}],"department":[{"_id":"GradSch"},{"_id":"MaSe"}],"project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020"}],"ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","doi":"10.15479/at:ista:17208","degree_awarded":"PhD","publication_status":"published","file":[{"creator":"rmedinar","file_id":"17212","date_updated":"2024-07-10T11:34:09Z","checksum":"6f45273d04f4418bc2adc018baed0525","file_name":"Raimel_Thesis-Final.zip","file_size":"14218691","date_created":"2024-07-09T09:21:44Z","relation":"source_file","content_type":"application/zip","access_level":"closed"},{"date_updated":"2024-07-17T09:23:24Z","creator":"rmedinar","file_id":"17275","checksum":"6724a95bec772dbabc0111b9f08a805e","success":1,"file_name":"Raimel_Thesis-20_pdfa.pdf","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_size":11253627,"date_created":"2024-07-17T09:23:24Z"}],"abstract":[{"lang":"eng","text":"Can current quantum computers provide a speedup over their classical counterparts for some kinds of problems? In this thesis, with a focus on ground state search/preparation, we address some of the challenges that both quantum annealing and variational quantum algorithms suffer from, hindering any possible practical speedup in comparison to the best classical counterparts. \r\n\r\nIn the first part of the thesis, we study the performance of quantum annealing for solving a particular combinatorial optimization problem called 3-XOR satisfability (3-XORSAT). The classical problem is mapped into a ground state search of a 3-local classical Hamiltonian $H_C$. We consider how modifying the initial problem, by adding more interaction terms to the corresponding Hamiltonian, leads to the emergence of a first-order phase transition during the annealing process. This phenomenon causes the total annealing duration, $T$, required to prepare the ground state of $H_C$ with a high probability to increase exponentially with the size of the problem. Our findings indicate that with the growing complexity of problem instances, the likelihood of encountering first-order phase transitions also increases, making quantum annealing an impractical solution for these types of combinatorial optimization problems.\r\n\r\nIn the second part, we focus on the problem of barren plateaus in generic variational quantum algorithms. Barren plateaus correspond to flat regions in the parameter space where the gradient of the cost function is zero in expectation, and with the variance decaying exponentially with the system size, thus obstructing an efficient parameter optimization. We propose an algorithm to circumvent Barren Plateaus by monitoring the entanglement entropy of k-local reduced density matrices, alongside a method for estimating entanglement entropy via classical shadow tomography. We illustrate the approach with the paradigmatic example of the variational quantum eigensolver, and show that our algorithm effectively avoids barren plateaus in the initialization as well as during the optimization stage. \r\n\r\nLastly, in the last two Chapters of this thesis, we focus on the quantum approximate optimization algorithm (QAOA), originally introduced as an algorithm for solving generic combinatorial optimization problems in near-term quantum devices. Specifically, we focus on how to develop rigorous initialization strategies with guarantee improvement. Our motivation for this study lies in that for random initialization, the optimization typically leads to local minima with poor performance. Our main result corresponds to the analytical construction of index-1 saddle points or transition states, stationary points with a single direction of descent, as a tool for systematically exploring the QAOA optimization landscape. This leads us to propose a novel greedy parameter initialization strategy that guarantees for the energy to decrease with an increasing number of circuit layers. Furthermore, with precise estimates for the negative Hessian eigenvalue and its eigenvector, we establish a lower bound for energy improvement following a QAOA iteration."}],"publisher":"Institute of Science and Technology Austria","date_created":"2024-07-09T09:14:24Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"status":"public","corr_author":"1","title":"Primal-dual non-smooth friction for rigid body animation","date_published":"2024-07-01T00:00:00Z","_id":"17214","date_updated":"2025-09-08T08:54:38Z","language":[{"iso":"eng"}],"quality_controlled":"1","conference":{"location":"Denver, United States","end_date":"2024-08-01","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","start_date":"2024-07-28"},"year":"2024","ddc":["621","531","006"],"has_accepted_license":"1","month":"07","keyword":["physical simulation","frictional contact","rigid body mechanics","non-smooth dynamics"],"file_date_updated":"2024-07-10T11:03:58Z","day":"01","oa":1,"article_processing_charge":"Yes (via OA deal)","type":"conference","citation":{"ista":"Chen Y-L, Ly M, Wojtan C. 2024. Primal-dual non-smooth friction for rigid body animation. Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. SIGGRAPH: Computer Graphics and Interactive Techniques Conference.","apa":"Chen, Y.-L., Ly, M., & Wojtan, C. (2024). Primal-dual non-smooth friction for rigid body animation. In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Denver, United States: Association for Computing Machinery. https://doi.org/10.1145/3641519.3657485","mla":"Chen, Yi-Lu, et al. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024, doi:10.1145/3641519.3657485.","ieee":"Y.-L. Chen, M. Ly, and C. Wojtan, “Primal-dual non-smooth friction for rigid body animation,” in Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Denver, United States, 2024.","short":"Y.-L. Chen, M. Ly, C. Wojtan, in:, Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24, Association for Computing Machinery, 2024.","ama":"Chen Y-L, Ly M, Wojtan C. Primal-dual non-smooth friction for rigid body animation. In: Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery; 2024. doi:10.1145/3641519.3657485","chicago":"Chen, Yi-Lu, Mickaël Ly, and Chris Wojtan. “Primal-Dual Non-Smooth Friction for Rigid Body Animation.” In Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers ’24. Association for Computing Machinery, 2024. https://doi.org/10.1145/3641519.3657485."},"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"acknowledgement":"We thank Vincent Acary for his help with Siconos, as well as the anonymous reviewers and the members of the Visual Computing Group at ISTA for their helpful comments. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"isi":1,"external_id":{"isi":["001282218200091"]},"scopus_import":"1","author":[{"id":"0b467602-dbcd-11ea-9d1d-ed480aa46b70","first_name":"Yi-Lu","last_name":"Chen","full_name":"Chen, Yi-Lu"},{"full_name":"Ly, Mickaël","last_name":"Ly","id":"6340d7f0-b48d-11eb-b10d-b7487e71d9f1","first_name":"Mickaël"},{"orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","last_name":"Wojtan"}],"doi":"10.1145/3641519.3657485","publication_status":"published","abstract":[{"text":"Current numerical algorithms for simulating friction fall in one of two camps: smooth solvers sacrifice the stable treatment of static friction in exchange for fast convergence, and non-smooth solvers accurately compute friction at convergence rates that are often prohibitive for large graphics applications. We introduce a novel bridge between these two ideas that computes static and dynamic friction stably and efficiently. Our key idea is to convert the highly constrained non-smooth problem into an unconstrained smooth problem using logarithmic barriers that converges to the exact solution as accuracy increases. We phrase the problem as an interior point primal-dual problem that can be solved efficiently with Newton iteration. We observe quadratic convergence despite the non-smooth nature of the original problem, and our method is well-suited for large systems of tightly packed objects with many contact points. We demonstrate the efficacy of our method with stable piles of grains and stacks of objects, complex granular flows, and robust interlocking assemblies of rigid bodies.","lang":"eng"}],"publication":"Special Interest Group on Computer Graphics and Interactive Techniques Conference Conference Papers '24","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":47309472,"date_created":"2024-07-10T11:03:14Z","date_updated":"2024-07-10T11:03:14Z","creator":"yichen","file_id":"17215","checksum":"b8b203ed09e3995ba0d7e6a76288663a","file_name":"sig24_friction_authors.pdf","success":1},{"checksum":"89d81b397b4b6469d828808a68b70820","file_name":"sig24_friction_supplementary.pdf","success":1,"creator":"yichen","file_id":"17216","date_updated":"2024-07-10T11:03:12Z","file_size":10518286,"date_created":"2024-07-10T11:03:12Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access"},{"file_name":"friction_paper_extra_video_finished.mp4","success":1,"checksum":"7123deed34a5456810e7b5336a31c657","file_id":"17217","creator":"yichen","date_updated":"2024-07-10T11:03:51Z","date_created":"2024-07-10T11:03:51Z","file_size":71789192,"access_level":"open_access","content_type":"video/mp4","relation":"main_file"},{"access_level":"open_access","relation":"main_file","content_type":"video/mp4","date_created":"2024-07-10T11:03:58Z","file_size":280610763,"date_updated":"2024-07-10T11:03:58Z","file_id":"17218","creator":"yichen","success":1,"file_name":"friction_paper_video_finished.mp4","checksum":"e606fc1ae8f2610ce3b4421566800b45"}],"oa_version":"Published Version","publication_identifier":{"isbn":["9798400705250"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Association for Computing Machinery","date_created":"2024-07-10T11:06:20Z"},{"status":"public","corr_author":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","title":"Multi-material mesh-based surface tracking with implicit topology changes","volume":43,"date_published":"2024-07-01T00:00:00Z","_id":"17219","date_updated":"2026-04-07T13:02:36Z","language":[{"iso":"eng"}],"quality_controlled":"1","ddc":["004"],"year":"2024","related_material":{"record":[{"status":"public","id":"19630","relation":"dissertation_contains"},{"status":"public","id":"18301","relation":"dissertation_contains"}]},"has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"month":"07","keyword":["surface tracking","topology change","non- manifold meshes","multi-material flows","solid modeling"],"file_date_updated":"2025-11-11T09:50:52Z","OA_place":"publisher","day":"01","intvolume":" 43","oa":1,"article_processing_charge":"Yes (via OA deal)","type":"journal_article","citation":{"apa":"Synak, P., Kalinov, A., Strugaru, I.-M., Etemadi, A., Yang, H., & Wojtan, C. (2024). Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. Association for Computing Machinery. https://doi.org/10.1145/3658223","ista":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. 2024. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 43(4), 54.","mla":"Synak, Peter, et al. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics, vol. 43, no. 4, 54, Association for Computing Machinery, 2024, doi:10.1145/3658223.","ieee":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, and C. Wojtan, “Multi-material mesh-based surface tracking with implicit topology changes,” ACM Transactions on Graphics, vol. 43, no. 4. Association for Computing Machinery, 2024.","ama":"Synak P, Kalinov A, Strugaru I-M, Etemadi A, Yang H, Wojtan C. Multi-material mesh-based surface tracking with implicit topology changes. ACM Transactions on Graphics. 2024;43(4). doi:10.1145/3658223","short":"P. Synak, A. Kalinov, I.-M. Strugaru, A. Etemadi, H. Yang, C. Wojtan, ACM Transactions on Graphics 43 (2024).","chicago":"Synak, Peter, Aleksei Kalinov, Irina-Malina Strugaru, Arian Etemadi, Huidong Yang, and Chris Wojtan. “Multi-Material Mesh-Based Surface Tracking with Implicit Topology Changes.” ACM Transactions on Graphics. Association for Computing Machinery, 2024. https://doi.org/10.1145/3658223."},"issue":"4","department":[{"_id":"GradSch"},{"_id":"ChWo"}],"acknowledgement":"Peter Heiss-Synak helped conceive the project, helped formulate the algorithm structure, contributed ideas and code to Sections 6 & 8, the mesh data structure, algorithm robustness and benchmarks, helped write the paper, and provided supervision and conceptual solutions throughout the project. Aleksei Kalinov contributed ideas and code to Sections 7, 8.5, and 5, the sparse grid data structure, algorithm robustness and benchmarks, optimized the performance, produced all results, most figures, and the supplementary video, helped write the text, and provided conceptual solutions throughout the project. Malina Strugaru helped implement the mesh data structure and designed re-meshing operations for non-manifold triangle meshes. Arian Etemadi developed early prototypes for ideas in Sections 8.1 and 8.3 and helped write the paper. Huidong Yang developed early prototypes for isosurface extraction and visualization. Chris Wojtan helped conceive the project, helped write the paper, and provided supervision, prototype grid data structure code, and conceptual solutions throughout the project. We thank the anonymous reviewers for their helpful comments, the members of the Visual Computing Group at ISTA for their feedback, Christopher Batty for discussions about LosTopos, and SideFX for the Houdini Education software licenses. This research was funded in part by the European Union (ERC-2021-COG 101045083 CoDiNA).","project":[{"name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena","grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088"}],"isi":1,"external_id":{"isi":["001289270900021"]},"scopus_import":"1","article_number":"54","author":[{"first_name":"Peter","id":"331776E2-F248-11E8-B48F-1D18A9856A87","last_name":"Synak","full_name":"Synak, Peter"},{"first_name":"Aleksei","orcid":"0000-0003-2189-3904","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","full_name":"Kalinov, Aleksei","last_name":"Kalinov"},{"id":"2afc607f-f128-11eb-9611-8f2a0dfcf074","first_name":"Irina-Malina","full_name":"Strugaru, Irina-Malina","last_name":"Strugaru"},{"id":"36cea3aa-f38e-11ec-8ae0-c65ae6f6098f","first_name":"Arian","last_name":"Etemadihaghighi","full_name":"Etemadihaghighi, Arian"},{"last_name":"Yang","full_name":"Yang, Huidong","first_name":"Huidong"},{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"}],"OA_type":"hybrid","doi":"10.1145/3658223","publication_status":"published","abstract":[{"text":"We introduce a multi-material non-manifold mesh-based surface tracking algorithm that converts self-intersections into topological changes. Our algorithm generalizes prior work on manifold surface tracking with topological changes: it preserves surface features like mesh-based methods, and it robustly handles topological changes like level set methods. Our method also offers improved efficiency and robustness over the state of the art. We demonstrate the effectiveness of the approach on a range of examples, including complex soap film simulations with thousands of interacting bubbles, and boolean unions of non-manifold meshes consisting of millions of triangles.","lang":"eng"}],"file":[{"file_id":"17317","creator":"dernst","date_updated":"2024-07-23T06:35:15Z","success":1,"file_name":"2024_ACMToG_HeissSynak.pdf","checksum":"1917067d4b52d7729019b03560004e43","date_created":"2024-07-23T06:35:15Z","file_size":48763368,"access_level":"open_access","content_type":"application/pdf","relation":"main_file"},{"date_created":"2024-07-10T12:23:44Z","file_size":48021463,"access_level":"open_access","relation":"main_file","content_type":"video/mp4","file_id":"17221","creator":"akalinov","date_updated":"2024-07-10T12:23:44Z","success":1,"file_name":"sdtopofixer_final.mp4","checksum":"a4f0e293184bfa034c0c585848806b17"},{"file_name":"SuperDuperTopoFixer.pdf","checksum":"18fc310a78ec91651148c45a8b89fa44","date_updated":"2025-11-11T09:50:52Z","file_id":"20633","creator":"akalinov","access_level":"open_access","title":"Authors' version of the text","relation":"preprint","content_type":"application/pdf","date_created":"2025-11-11T09:50:52Z","file_size":48639581}],"publication":"ACM Transactions on Graphics","oa_version":"Published Version","publication_identifier":{"eissn":["1557-7368"],"issn":["0730-0301"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","article_type":"original","date_created":"2024-07-10T12:24:00Z"},{"title":"Towards a quantum entanglement enhanced atom interferomter","page":"79","corr_author":"1","supervisor":[{"first_name":"Onur","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","full_name":"Hosten, Onur","last_name":"Hosten"}],"status":"public","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"month":"07","related_material":{"record":[{"status":"public","id":"11438","relation":"part_of_dissertation"}]},"ddc":["530"],"year":"2024","language":[{"iso":"eng"}],"date_updated":"2026-04-07T12:42:28Z","date_published":"2024-07-11T00:00:00Z","_id":"17225","alternative_title":["ISTA Thesis"],"author":[{"first_name":"Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Vyacheslav"}],"department":[{"_id":"GradSch"},{"_id":"OnHo"}],"project":[{"_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"citation":{"chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17225.","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:10.15479/at:ista:17225","short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024.","ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","mla":"Li, Vyacheslav. Towards a Quantum Entanglement Enhanced Atom Interferomter. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17225.","ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","apa":"Li, V. (2024). Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17225"},"oa":1,"type":"dissertation","article_processing_charge":"No","OA_place":"publisher","file_date_updated":"2024-07-11T10:26:22Z","day":"11","date_created":"2024-07-11T09:46:48Z","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","publication_status":"published","abstract":[{"lang":"eng","text":"This thesis describes the development of an atom interferometer designed to exploit the\r\nadvantages of utilizing quantum entanglement for enhanced precision measurements beyond\r\nthe standard quantum limit. While the project remains ongoing, significant progress has been\r\nmade.\r\nA key contribution of this work is the development of Quantrol, an experimental control\r\nsystem leveraging the ARTIQ framework. This software enables precise timing and control\r\nwithout requiring prior knowledge of ARTIQ’s implementation details or coding experience.\r\nThe interface offers user friendly visual comprehension of the experimental sequence and\r\nextended capabilities, allowing researchers to scan variables with a simple click of a mouse.\r\nThe main proposed project is to implement atom interferometric sequence with squeezed input\r\nstates inside of a dipole trap generated by a high finesse cavity. The presence of the dipole\r\ntrap allows one dimensional atomic cloud split while maintaining relatively strong confinement\r\nin other directions.\r\nWe are currently able to trap and cool 87Rb atoms to few micro kelvin temperatures, load\r\nthem into the dipole trap and state prepare them to be used for squeezing and interferometric\r\nsequence."}],"file":[{"date_updated":"2024-07-11T10:26:22Z","file_id":"17228","creator":"vli","file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","success":1,"checksum":"15b2dbe8d2c9ed7ca5dd413827928077","access_level":"open_access","content_type":"application/pdf","relation":"main_file","date_created":"2024-07-11T10:26:22Z","file_size":6729761},{"date_created":"2024-07-11T10:26:22Z","file_size":9542859,"access_level":"closed","relation":"source_file","content_type":"application/x-zip-compressed","file_id":"17229","creator":"vli","date_updated":"2024-07-11T10:26:22Z","file_name":"PhD Thesis Vyacheslav Li.zip","checksum":"16e904a11d8d0ebb167cb654ddfc7fe5"}],"doi":"10.15479/at:ista:17225","degree_awarded":"PhD"},{"article_processing_charge":"No","type":"journal_article","oa":1,"citation":{"ieee":"X. Wang and B. Cheng, “Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures,” Journal of Chemical Physics, vol. 161, no. 3. AIP Publishing, 2024.","ista":"Wang X, Cheng B. 2024. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 161(3), 034111.","apa":"Wang, X., & Cheng, B. (2024). Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0217232","mla":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal of Chemical Physics, vol. 161, no. 3, 034111, AIP Publishing, 2024, doi:10.1063/5.0217232.","chicago":"Wang, Xiaoyu, and Bingqing Cheng. “Integrating Molecular Dynamics Simulations and Experimental Data for Azeotrope Predictions in Binary Mixtures.” Journal of Chemical Physics. AIP Publishing, 2024. https://doi.org/10.1063/5.0217232.","short":"X. Wang, B. Cheng, Journal of Chemical Physics 161 (2024).","ama":"Wang X, Cheng B. Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures. Journal of Chemical Physics. 2024;161(3). doi:10.1063/5.0217232"},"day":"14","intvolume":" 161","article_number":"034111","scopus_import":"1","external_id":{"isi":["001281819100016"],"pmid":["39007379"],"arxiv":["2405.02216"]},"isi":1,"author":[{"full_name":"Wang, Xiaoyu","last_name":"Wang","id":"8dff9c62-32b0-11ee-9fa8-fc73025e10f3","first_name":"Xiaoyu"},{"full_name":"Cheng, Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing"}],"acknowledgement":"B.C. thanks Alessandro Laio, who introduced the phenomenon of azeotrope and suggested using the S0 method to compute it. B.C. and X.W. thank Felix Wodaczek for the insightful comments and suggestions on the manuscript. B.C. and X.W. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service, funded by EPSRC Tier-2 capital (Grant No. EP/P020259/1).","issue":"3","department":[{"_id":"BiCh"},{"_id":"GradSch"}],"oa_version":"Preprint","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"pmid":1,"doi":"10.1063/5.0217232","publication":"Journal of Chemical Physics","abstract":[{"lang":"eng","text":"An azeotrope is a constant boiling point mixture, and its behavior is important for fluid separation processes. Predicting azeotropes from atomistic simulations is difficult due to the complexities and convergence problems of Monte Carlo and free-energy perturbation techniques. Here, we present a methodology for predicting the azeotropes of binary mixtures, which computes the compositional dependence of chemical potentials from molecular dynamics simulations using the S0 method and employs experimental boiling point and vaporization enthalpy data. Using this methodology, we reproduce the azeotropes, or lack thereof, in five case studies, including ethanol/water, ethanol/isooctane, methanol/water, hydrazine/water, and acetone/chloroform mixtures. We find that it is crucial to use the experimental boiling point and vaporization enthalpy for reliable azeotrope predictions, as empirical force fields are not accurate enough for these quantities. Finally, we use regular solution models to rationalize the azeotropes and reveal that they tend to form when the mixture components have similar boiling points and strong interactions."}],"publication_status":"published","article_type":"original","publisher":"AIP Publishing","date_created":"2024-07-21T22:01:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","arxiv":1,"status":"public","title":"Integrating molecular dynamics simulations and experimental data for azeotrope predictions in binary mixtures","volume":161,"language":[{"iso":"eng"}],"date_updated":"2025-09-08T08:26:09Z","quality_controlled":"1","_id":"17278","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2405.02216"}],"date_published":"2024-07-14T00:00:00Z","related_material":{"link":[{"url":"https://github.com/Xiaoyu-Wang-Stone/Azeotrope_S0","relation":"software"}]},"month":"07","year":"2024"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","article_type":"original","date_created":"2024-07-21T22:01:01Z","doi":"10.1145/3656462","file":[{"file_size":355421,"date_created":"2024-07-22T07:17:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"8cbf220f284a4a87d093db5320c5afdd","success":1,"file_name":"2024_ACMProgLang_Chatterjee.pdf","creator":"dernst","file_id":"17290","date_updated":"2024-07-22T07:17:14Z"}],"publication":"Proceedings of the ACM on Programming Languages","abstract":[{"text":"We consider the problems of statically refuting equivalence and similarity of output distributions defined by a pair of probabilistic programs. Equivalence and similarity are two fundamental relational properties of probabilistic programs that are essential for their correctness both in implementation and in compilation. In this work, we present a new method for static equivalence and similarity refutation. Our method refutes equivalence and similarity by computing a function over program outputs whose expected value with respect to the output distributions of two programs is different. The function is computed simultaneously with an upper expectation supermartingale and a lower expectation submartingale for the two programs, which we show to together provide a formal certificate for refuting equivalence and similarity. To the best of our knowledge, our method is the first approach to relational program analysis to offer the combination of the following desirable features: (1) it is fully automated, (2) it is applicable to infinite-state probabilistic programs, and (3) it provides formal guarantees on the correctness of its results. We implement a prototype of our method and our experiments demonstrate the effectiveness of our method to refute equivalence and similarity for a number of examples collected from the literature.","lang":"eng"}],"publication_status":"published","oa_version":"Published Version","publication_identifier":{"eissn":["2475-1421"]},"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant. Petr Novotný\r\nis supported by the Czech Science Foundation grant no. GA23-06963S.\r\n","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"ec_funded":1,"scopus_import":"1","article_number":"232","external_id":{"arxiv":["2404.03430"]},"OA_type":"hybrid","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"103b4fa0-896a-11ed-bdf8-87b697bef40d","orcid":"0000-0002-8595-0587","first_name":"Ehsan","last_name":"Kafshdar Goharshadi","full_name":"Kafshdar Goharshadi, Ehsan"},{"full_name":"Novotný, Petr","last_name":"Novotný","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr"},{"first_name":"Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","last_name":"Zikelic"}],"day":"20","OA_place":"publisher","file_date_updated":"2024-07-22T07:17:14Z","intvolume":" 8","article_processing_charge":"Yes (via OA deal)","type":"journal_article","oa":1,"citation":{"ieee":"K. Chatterjee, E. Goharshady, P. Novotný, and D. Zikelic, “Equivalence and similarity refutation for probabilistic programs,” Proceedings of the ACM on Programming Languages, vol. 8. Association for Computing Machinery, 2024.","apa":"Chatterjee, K., Goharshady, E., Novotný, P., & Zikelic, D. (2024). Equivalence and similarity refutation for probabilistic programs. Proceedings of the ACM on Programming Languages. Association for Computing Machinery. https://doi.org/10.1145/3656462","ista":"Chatterjee K, Goharshady E, Novotný P, Zikelic D. 2024. Equivalence and similarity refutation for probabilistic programs. Proceedings of the ACM on Programming Languages. 8, 232.","mla":"Chatterjee, Krishnendu, et al. “Equivalence and Similarity Refutation for Probabilistic Programs.” Proceedings of the ACM on Programming Languages, vol. 8, 232, Association for Computing Machinery, 2024, doi:10.1145/3656462.","chicago":"Chatterjee, Krishnendu, Ehsan Goharshady, Petr Novotný, and Dorde Zikelic. “Equivalence and Similarity Refutation for Probabilistic Programs.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2024. https://doi.org/10.1145/3656462.","ama":"Chatterjee K, Goharshady E, Novotný P, Zikelic D. Equivalence and similarity refutation for probabilistic programs. Proceedings of the ACM on Programming Languages. 2024;8. doi:10.1145/3656462","short":"K. Chatterjee, E. Goharshady, P. Novotný, D. Zikelic, Proceedings of the ACM on Programming Languages 8 (2024)."},"year":"2024","ddc":["000"],"month":"06","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","_id":"17283","date_published":"2024-06-20T00:00:00Z","date_updated":"2025-04-14T07:52:47Z","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Equivalence and similarity refutation for probabilistic programs","volume":8,"status":"public","arxiv":1,"corr_author":"1"},{"oa":1,"type":"dissertation","article_processing_charge":"No","citation":{"mla":"Pedrotti, Francesco. Functional Inequalities and Convergence of Stochastic Processes. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17336.","apa":"Pedrotti, F. (2024). Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17336","ista":"Pedrotti F. 2024. Functional inequalities and convergence of stochastic processes. Institute of Science and Technology Austria.","ieee":"F. Pedrotti, “Functional inequalities and convergence of stochastic processes,” Institute of Science and Technology Austria, 2024.","ama":"Pedrotti F. Functional inequalities and convergence of stochastic processes. 2024. doi:10.15479/at:ista:17336","short":"F. Pedrotti, Functional Inequalities and Convergence of Stochastic Processes, Institute of Science and Technology Austria, 2024.","chicago":"Pedrotti, Francesco. “Functional Inequalities and Convergence of Stochastic Processes.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17336."},"OA_place":"publisher","file_date_updated":"2024-08-02T09:27:15Z","day":"31","author":[{"last_name":"Pedrotti","full_name":"Pedrotti, Francesco","id":"d3ac8ac6-dc8d-11ea-abe3-e2a9628c4c3c","first_name":"Francesco"}],"department":[{"_id":"GradSch"},{"_id":"JaMa"}],"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"ec_funded":1,"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/at:ista:17336","degree_awarded":"PhD","publication_status":"published","abstract":[{"lang":"eng","text":"This thesis deals with the study of stochastic processes and their ergodicity properties. The\r\nvariety of problems encountered calls for a set of different approaches, ranging from classical to\r\nmodern ones: a special place is held by probabilistic methods based on couplings, by functional\r\ninequalities, and by the theory of gradient flows in the space of measures.\r\n\r\nThe material is organized as follows. Chapter 1 contains the introduction to this thesis, starting\r\nwith a general presentation of some of the relevant topics. Section 1.1 is dedicated to the\r\ntheory of gradient flows in metric spaces, and introduces the first contribution of this thesis\r\n[DSMP24], which is presented in detail in Chapter 2. Section 1.2 moves to the topic of\r\ncurvature of Markov chains, concluding with a brief description of our second contribution\r\n[Ped23], which is included in Chapter 3. Section 1.3 discusses applications of stochastic\r\nprocesses to the theory of sampling, in particular the recent framework of score-based diffusion\r\nmodels, and our contribution [PMM24], which is contained in Chapter 4. Section 1.4 discusses\r\nsome related problems, concerning the regularization properties of the heat flow. It serves\r\nas a motivation for the work [BP24], which we report in Chapter 5. Finally, Section 1.5\r\ndiscusses the last contribution of this thesis, which can be found in Chapter 6. It deals with\r\nthe convergence to equilibrium of a particular stochastic model from quantitative genetics:\r\nthis is established via some functional inequalities, which we prove with probabilistic arguments\r\nbased on couplings.\r\n"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_size":2941599,"date_created":"2024-08-02T09:23:26Z","date_updated":"2024-08-02T09:23:26Z","creator":"fpedrott","file_id":"17366","checksum":"11650bab714ef85ad43a287060850523","file_name":"thesis_final.pdf","success":1},{"date_created":"2024-08-02T09:27:15Z","file_size":6293375,"access_level":"closed","content_type":"application/x-zip-compressed","relation":"source_file","file_id":"17367","creator":"fpedrott","date_updated":"2024-08-02T09:27:15Z","file_name":"thesis_final_source.zip","checksum":"c30ba5611941226cf1bfc867c25b1e80"}],"publisher":"Institute of Science and Technology Austria","date_created":"2024-07-29T09:14:14Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"first_name":"Jan","orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","last_name":"Maas","full_name":"Maas, Jan"}],"page":"183","corr_author":"1","status":"public","title":"Functional inequalities and convergence of stochastic processes","language":[{"iso":"eng"}],"date_updated":"2026-04-07T13:00:03Z","alternative_title":["ISTA Thesis"],"date_published":"2024-07-31T00:00:00Z","_id":"17336","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"17351"},{"status":"public","relation":"part_of_dissertation","id":"17353"},{"id":"17350","relation":"part_of_dissertation","status":"public"},{"id":"17352","relation":"part_of_dissertation","status":"public"},{"status":"public","id":"17143","relation":"part_of_dissertation"}]},"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"month":"07","ddc":["500","510","515","519"],"year":"2024"},{"citation":{"short":"P. Surendranadh, H. Sachdeva, (2024).","ama":"Surendranadh P, Sachdeva H. Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2024. doi:10.15479/AT:ISTA:17344","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17344.","mla":"Surendranadh, Parvathy, and Himani Sachdeva. Mathematica Notebook for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17344.","apa":"Surendranadh, P., & Sachdeva, H. (2024). Mathematica notebook for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17344","ista":"Surendranadh P, Sachdeva H. 2024. Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17344.","ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2024."},"article_processing_charge":"No","type":"research_data","oa":1,"status":"public","acknowledged_ssus":[{"_id":"ScienComp"}],"file_date_updated":"2024-07-29T13:51:11Z","author":[{"full_name":"Surendranadh, Parvathy","last_name":"Surendranadh","orcid":"0000-0001-6395-386X","first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"title":"Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"oa_version":"Published Version","date_updated":"2025-01-14T13:02:59Z","_id":"17344","abstract":[{"text":"This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. ","lang":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/octet-stream","date_created":"2024-07-29T13:51:11Z","file_size":726132,"date_updated":"2024-07-29T13:51:11Z","file_id":"17345","creator":"psurendr","success":1,"file_name":"Submission.nb","checksum":"75bdbc7ad7cc6afe4459bc4a8824a302"}],"date_published":"2024-07-01T00:00:00Z","doi":"10.15479/AT:ISTA:17344","month":"07","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"},"date_created":"2024-07-29T14:01:43Z","publisher":"Institute of Science and Technology Austria","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["576"],"year":"2024"},{"doi":"10.48550/arXiv.2407.19908","_id":"17361","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2407.19908"}],"abstract":[{"lang":"eng","text":"We present symplectic structures on the shape space of unparameterized space curves that generalize the classical Marsden-Weinstein structure. Our method integrates the Liouville 1-form of the Marsden-Weinstein structure with Riemannian structures that have been introduced in mathematical shape analysis. We also derive Hamiltonian vector fields for several classical Hamiltonian functions with respect to these new symplectic structures."}],"publication":"arXiv","publication_status":"draft","date_published":"2024-07-29T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2026-04-28T09:59:01Z","oa_version":"Preprint","year":"2024","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"id":"20551","relation":"dissertation_contains","status":"public"},{"id":"21743","relation":"later_version","status":"public"}]},"month":"07","date_created":"2024-08-01T06:34:08Z","day":"29","keyword":["space of space curves","symplectic stuctures"],"OA_place":"repository","status":"public","type":"preprint","article_processing_charge":"No","oa":1,"arxiv":1,"citation":{"mla":"Bauer, Martin, et al. “Symplectic Structures on the Space of Space Curves.” ArXiv, doi:10.48550/arXiv.2407.19908.","apa":"Bauer, M., Ishida, S., & Michor, P. W. (n.d.). Symplectic structures on the space of space curves. arXiv. https://doi.org/10.48550/arXiv.2407.19908","ista":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. arXiv, 10.48550/arXiv.2407.19908.","ieee":"M. Bauer, S. Ishida, and P. W. Michor, “Symplectic structures on the space of space curves,” arXiv. .","ama":"Bauer M, Ishida S, Michor PW. Symplectic structures on the space of space curves. arXiv. doi:10.48550/arXiv.2407.19908","short":"M. Bauer, S. Ishida, P.W. Michor, ArXiv (n.d.).","chicago":"Bauer, Martin, Sadashige Ishida, and Peter W. Michor. “Symplectic Structures on the Space of Space Curves.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2407.19908."},"project":[{"_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","grant_number":"101045083","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"acknowledgement":"The authors are grateful to Boris Khesin for valuable comments on the MW symplectic structure and S. Ishida thanks Albert Chern for insightful discussions on space curves and Chris Wojtan for his continuous support. M. Bauer was partially supported by NSF grant DMS-1953244 and by the Binational Science Foundation (BSF). S. Ishida was partially supported by ERC Consolidator Grant 101045083 “CoDiNA” funded by the European Research Council. Some figures were generated by the software Houdini and its education license was provided by SideFX.","external_id":{"arxiv":["2407.19908"]},"title":"Symplectic structures on the space of space curves","author":[{"full_name":"Bauer, Martin","last_name":"Bauer","first_name":"Martin"},{"first_name":"Sadashige","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425","orcid":"0000-0002-3121-3100","full_name":"Ishida, Sadashige","last_name":"Ishida"},{"first_name":"Peter W.","last_name":"Michor","full_name":"Michor, Peter W."}]},{"publisher":"Institute of Science and Technology Austria","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"17890"}]},"month":"08","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"},"date_created":"2024-08-02T07:27:45Z","ddc":["576"],"year":"2024","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-16T12:20:41Z","oa_version":"Published Version","doi":"10.15479/AT:ISTA:17362","abstract":[{"text":"This is the supplementary data for the paper titled \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\", where we described the generation and analysis of single-nucleus expression and chromatin-accessibility data from the female reproductive system of Artemia franciscana. We compared our dataset to the published Drosophila single-nucleus data (over 400 million years of divergence) and highlighted the extreme conservation of several of the molecular pathways of oogenesis and meiosis. We found evidence of global transcriptional quiescence and chromatin condensation in late germ cells, highlighting the conserved role of this repressive stage in arthropod oogenesis. Additionally, we explored the expression patterns of the ZW sex chromosomes during oogenesis. Our data shows that the Z-chromosome is consistently downregulated in germline cells. While this is partly driven by a lack of dosage compensation in the germline, a subset of cells show stronger repression of the Z chromosome.","lang":"eng"}],"_id":"17362","file":[{"file_name":"README.txt","success":1,"checksum":"26b5d41b3103f4284dd97d56e370a5b6","file_id":"17394","creator":"melkrewi","date_updated":"2024-08-05T22:24:18Z","date_created":"2024-08-05T22:24:18Z","file_size":2465,"access_level":"open_access","relation":"main_file","content_type":"text/plain"},{"file_id":"17395","creator":"melkrewi","date_updated":"2024-08-05T23:28:52Z","file_name":"Data_artemia_single_nucleus_atlas.zip","success":1,"checksum":"95adab5e36148015da313505e3910707","date_created":"2024-08-05T23:28:52Z","file_size":2526735400,"access_level":"open_access","content_type":"application/x-zip-compressed","relation":"main_file"}],"date_published":"2024-08-05T00:00:00Z","title":"Data for: \"Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome\"","author":[{"first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","orcid":"0000-0002-4579-8306","last_name":"Vicoso","full_name":"Vicoso, Beatriz"}],"project":[{"grant_number":"F8810","name":"The highjacking of meiosis for asexual reproduction","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"research_data","article_processing_charge":"No","oa":1,"corr_author":"1","citation":{"chicago":"Elkrewi, Marwan N, and Beatriz Vicoso. “Data for: ‘Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17362.","short":"M.N. Elkrewi, B. Vicoso, (2024).","ama":"Elkrewi MN, Vicoso B. Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” 2024. doi:10.15479/AT:ISTA:17362","ieee":"M. N. Elkrewi and B. Vicoso, “Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.’” Institute of Science and Technology Austria, 2024.","mla":"Elkrewi, Marwan N., and Beatriz Vicoso. Data for: “Single-Nucleus Atlas of the Artemia Female Reproductive System Suggests Germline Repression of the Z Chromosome.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17362.","ista":"Elkrewi MN, Vicoso B. 2024. Data for: ‘Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17362.","apa":"Elkrewi, M. N., & Vicoso, B. (2024). Data for: “Single-nucleus atlas of the Artemia female reproductive system suggests germline repression of the Z chromosome.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17362"},"day":"05","file_date_updated":"2024-08-05T23:28:52Z","status":"public","acknowledged_ssus":[{"_id":"ScienComp"}]},{"intvolume":" 2831","day":"13","citation":{"ieee":"O. Miranda, G. T. Cheung, and S. Hippenmeyer, “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers,” in Neuronal Morphogenesis, 1st ed., vol. 2831, K. Toyooka, Ed. New York, NY: Springer Nature, 2024, pp. 283–299.","mla":"Miranda, Osvaldo, et al. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., vol. 2831, Springer Nature, 2024, pp. 283–99, doi:10.1007/978-1-0716-3969-6_19.","ista":"Miranda O, Cheung GT, Hippenmeyer S. 2024.Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Neuronal Morphogenesis. Methods in Molecular Biology, vol. 2831, 283–299.","apa":"Miranda, O., Cheung, G. T., & Hippenmeyer, S. (2024). Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In K. Toyooka (Ed.), Neuronal Morphogenesis (1st ed., Vol. 2831, pp. 283–299). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-3969-6_19","chicago":"Miranda, Osvaldo, Giselle T Cheung, and Simon Hippenmeyer. “Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers.” In Neuronal Morphogenesis, edited by Kazuhito Toyooka, 1st ed., 2831:283–99. MIMB. New York, NY: Springer Nature, 2024. https://doi.org/10.1007/978-1-0716-3969-6_19.","short":"O. Miranda, G.T. Cheung, S. Hippenmeyer, in:, K. Toyooka (Ed.), Neuronal Morphogenesis, 1st ed., Springer Nature, New York, NY, 2024, pp. 283–299.","ama":"Miranda O, Cheung GT, Hippenmeyer S. Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers. In: Toyooka K, ed. Neuronal Morphogenesis. Vol 2831. 1st ed. MIMB. New York, NY: Springer Nature; 2024:283-299. doi:10.1007/978-1-0716-3969-6_19"},"type":"book_chapter","article_processing_charge":"No","acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. This work was supported by the Scientific Service Units (SSU) at ISTA through resources provided by the Imaging & Optics Facility (IOF). O.A.M was a recipient of a DOC Fellowship (26253) of the Austrian Academy of Sciences. This work was supported by ISTA institutional funds, and The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","department":[{"_id":"GradSch"},{"_id":"SiHi"}],"project":[{"_id":"34c9fbcb-11ca-11ed-8bc3-98fa5658610d","name":"Molecular Mechanisms Regulating Cortical Neural Stem Cell Lineage Progression and Astrocyte Development","grant_number":"26253"},{"name":"Stem Cell Modulation in Neural Development and Regeneration/ P05-Molecular Mechanisms of Neural Stem Cell Lineage Progression","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","grant_number":"F7805"}],"author":[{"full_name":"Miranda, Osvaldo","last_name":"Miranda","id":"862A3C56-A8BF-11E9-B4FA-D9E3E5697425","orcid":"0000-0001-6618-6889","first_name":"Osvaldo"},{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8457-2572","first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung"},{"orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon"}],"external_id":{"pmid":["39134857"]},"scopus_import":"1","edition":"1","publication_status":"published","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) is a powerful genetic method typically used for lineage tracing and to disentangle cell autonomous and tissue-wide roles of candidate genes with single cell resolution. Given the relatively sparse labeling, depending on which of the 19 MADM chromosomes one chooses, the MADM approach represents the perfect opportunity for cell morphology analysis. Various MADM studies include reports of morphological anomalies and phenotypes in the central nervous system (CNS). MADM for any candidate gene can easily incorporate morphological analysis within the experimental workflow. Here, we describe the methods of morphological cell analysis which we developed in the course of diverse recent MADM studies. This chapter will specifically focus on methods to quantify aspects of the morphology of neurons and astrocytes within the CNS, but these methods can broadly be applied to any MADM-labeled cells throughout the entire organism. We will cover two analyses—soma volume and dendrite characterization—of physical characteristics of pyramidal neurons in the somatosensory cortex, and two analyses—volume and Sholl analysis—of astrocyte morphology.","lang":"eng"}],"publication":"Neuronal Morphogenesis","doi":"10.1007/978-1-0716-3969-6_19","oa_version":"None","publication_identifier":{"issn":["1064-3745"],"eisbn":["9781071639696"],"eissn":["1940-6029"],"isbn":["9781071639689"]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","series_title":"MIMB","place":"New York, NY","date_created":"2024-08-13T12:16:41Z","publisher":"Springer Nature","status":"public","acknowledged_ssus":[{"_id":"Bio"}],"page":"283-299","corr_author":"1","volume":2831,"title":"Morphological Analysis of Neurons and Glia Using Mosaic Analysis with Double Markers","date_published":"2024-08-13T00:00:00Z","_id":"17425","alternative_title":["Methods in Molecular Biology"],"quality_controlled":"1","editor":[{"first_name":"Kazuhito","full_name":"Toyooka, Kazuhito","last_name":"Toyooka"}],"language":[{"iso":"eng"}],"date_updated":"2026-04-07T12:32:35Z","year":"2024","month":"08","related_material":{"record":[{"relation":"dissertation_contains","id":"20212","status":"public"}]}}]