[{"publication_status":"published","file":[{"access_level":"open_access","file_size":7752253,"file_name":"Teresa_Heiss_PhD_Thesis_final.pdf","checksum":"247bb057aed2fba1cd4711917aaa2d77","creator":"theiss","file_id":"18686","content_type":"application/pdf","success":1,"date_created":"2024-12-19T10:24:46Z","relation":"main_file","date_updated":"2024-12-19T10:24:46Z"},{"creator":"theiss","checksum":"9648b45c07a008ee11a07f99856a139d","file_id":"18687","content_type":"application/zip","file_name":"PhD_Thesis.zip","access_level":"closed","file_size":17197731,"date_updated":"2024-12-19T10:24:50Z","relation":"source_file","date_created":"2024-12-19T10:24:50Z"}],"alternative_title":["ISTA Thesis"],"date_published":"2024-12-17T00:00:00Z","file_date_updated":"2024-12-19T10:24:50Z","day":"17","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"page":"111","type":"dissertation","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"10828"},{"status":"public","id":"11440","relation":"part_of_dissertation"},{"status":"public","id":"18673","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9345","status":"public"}]},"corr_author":"1","acknowledgement":"I was supported by the European Research Council (ERC) Horizon 2020 project\r\n“Alpha Shape Theory Extended” No. 788183 and by the Pöttinger Scholarship. In addition,\r\nI am very thankful for having been able to attend the second Workshop for Women in\r\nComputational Topology in July 2019, funded by the Mathematical Sciences Institute at\r\nANU, the US National Science Foundation through the award CCF-1841455, the Australian\r\nMathematical Sciences Institute and the Association for Women in Mathematics. Two of the\r\nprojects presented in this thesis started there. One of them reached completion thanks to\r\nfunding from the MSRI Summer Research in Mathematics program awarded to me and my\r\ncollaborators in 2020.","date_updated":"2026-07-07T13:43:27Z","author":[{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","last_name":"Heiss","orcid":"0000-0002-1780-2689","first_name":"Teresa","full_name":"Heiss, Teresa"}],"publication_identifier":{"isbn":["978-3-99078-052-7"],"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","status":"public","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended"}],"date_created":"2024-12-17T16:17:55Z","month":"12","citation":{"apa":"Heiss, T. (2024). <i>New methods for applying topological data analysis to materials science</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>","ama":"Heiss T. New methods for applying topological data analysis to materials science. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>","ieee":"T. Heiss, “New methods for applying topological data analysis to materials science,” Institute of Science and Technology Austria, 2024.","mla":"Heiss, Teresa. <i>New Methods for Applying Topological Data Analysis to Materials Science</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18667\">10.15479/at:ista:18667</a>.","chicago":"Heiss, Teresa. “New Methods for Applying Topological Data Analysis to Materials Science.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18667\">https://doi.org/10.15479/at:ista:18667</a>.","ista":"Heiss T. 2024. New methods for applying topological data analysis to materials science. Institute of Science and Technology Austria.","short":"T. Heiss, New Methods for Applying Topological Data Analysis to Materials Science, Institute of Science and Technology Austria, 2024."},"degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.15479/at:ista:18667","supervisor":[{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["514","516","004"],"article_processing_charge":"No","_id":"18667","oa":1,"year":"2024","has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"New methods for applying topological data analysis to materials science","abstract":[{"text":"Many chemical and physical properties of materials are determined by the material’s shape,\r\nfor example the size of its pores and the width of its tunnels. This makes materials science\r\na prime application area for geometrical and topological methods. Nevertheless many\r\nmethods in topological data analysis have not been satisfyingly extended to the needs of\r\nmaterials science. This thesis provides new methods and new mathematical theorems\r\ntargeted at those specific needs by answering four different research questions. While the\r\nmotivation for each of the research questions arises from materials science, the methods\r\nare versatile and can be applied in different areas as well. \r\n\r\nThe first research question is concerned with image data, for example a three-dimensional\r\ncomputed tomography (CT) scan of a material, like sand or stone. There are two commonly\r\nused topologies for digital images and depending on the application either of them might be\r\nrequired. However, software for computing the topological data analysis method persistence\r\nhomology, usually supports only one of the two topologies. We answer the question how to\r\ncompute persistent homology of an image with respect to one of the two topologies using\r\nsoftware that is intended for the other topology. \r\n\r\nThe second research question is concerned with image data as well, and asks how much\r\nof the topological information of an image is lost when the resolution is coarsened. As\r\ncomputer tomography scanners are more expensive the higher the resolution, it is an\r\nimportant question in materials science to know which resolution is enough to get satisfying\r\npersistent homology. We give theoretical bounds on the information loss based on different\r\ngeometrical properties of the object to be scanned. In addition, we conduct experiments on\r\nsand and stone CT image data. \r\n\r\nThe third research question is motivated by comparing crystalline materials efficiently. As\r\nthe atoms within a crystal repeat periodically, crystalline materials are either modeled by\r\nunmanageable infinite periodic point sets, or by one of their fundamental domains, which is\r\nunstable under perturbation. Therefore a fingerprint of crystalline materials is needed, with\r\nappropriate properties such that comparing the crystals can be eased by comparing the\r\nfingerprints instead. We define the density fingerprint and prove the necessary properties. \r\n\r\nThe fourth research question is motivated by studying the hole-structure or connectedness,\r\ni.e. persistent homology or merge trees, of crystalline materials. A common way to deal\r\nwith periodicity is to take a fundamental domain and identify opposite boundaries to form a\r\ntorus. However, computing persistent homology or merge trees on that torus loses some\r\nof the information materials scientists are interested in and is additionally not stable under\r\ncertain noise. We therefore decorate the merge tree stemming from the torus with additional\r\ninformation describing the density and growth rate of the periodic copies of a component\r\nwithin a growing spherical window. We prove all desired properties, like stability and efficient\r\ncomputability.","lang":"eng"}],"keyword":["persistent homology","topological data analysis","periodic","crystalline materials","images","fingerprint"]},{"date_published":"2024-07-11T00:00:00Z","type":"dissertation","page":"79","department":[{"_id":"GradSch"},{"_id":"OnHo"}],"file_date_updated":"2024-07-11T10:26:22Z","day":"11","alternative_title":["ISTA Thesis"],"file":[{"date_updated":"2024-07-11T10:26:22Z","relation":"main_file","date_created":"2024-07-11T10:26:22Z","success":1,"file_id":"17228","content_type":"application/pdf","creator":"vli","checksum":"15b2dbe8d2c9ed7ca5dd413827928077","file_name":"PhD_Thesis_Vyacheslav_Li_no_signatures_PDFA.pdf","file_size":6729761,"access_level":"open_access"},{"file_id":"17229","content_type":"application/x-zip-compressed","creator":"vli","checksum":"16e904a11d8d0ebb167cb654ddfc7fe5","access_level":"closed","file_size":9542859,"file_name":"PhD Thesis Vyacheslav Li.zip","relation":"source_file","date_updated":"2024-07-11T10:26:22Z","date_created":"2024-07-11T10:26:22Z"}],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Li, Vyacheslav","first_name":"Vyacheslav","last_name":"Li","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"11438","status":"public"}]},"date_updated":"2026-07-08T08:50:57Z","corr_author":"1","article_processing_charge":"No","_id":"17225","ddc":["530"],"supervisor":[{"full_name":"Hosten, Onur","first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"citation":{"apa":"Li, V. (2024). <i>Towards a quantum entanglement enhanced atom interferomter</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>","ama":"Li V. Towards a quantum entanglement enhanced atom interferomter. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>","ieee":"V. Li, “Towards a quantum entanglement enhanced atom interferomter,” Institute of Science and Technology Austria, 2024.","mla":"Li, Vyacheslav. <i>Towards a Quantum Entanglement Enhanced Atom Interferomter</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17225\">10.15479/at:ista:17225</a>.","chicago":"Li, Vyacheslav. “Towards a Quantum Entanglement Enhanced Atom Interferomter.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17225\">https://doi.org/10.15479/at:ista:17225</a>.","ista":"Li V. 2024. Towards a quantum entanglement enhanced atom interferomter. Institute of Science and Technology Austria.","short":"V. Li, Towards a Quantum Entanglement Enhanced Atom Interferomter, Institute of Science and Technology Austria, 2024."},"month":"07","project":[{"_id":"bdb2a702-d553-11ed-ba76-f12e3e5a3bc6","grant_number":"101087907","name":"A quantum hybrid of atoms and milligram-scale pendulums: towards gravitational quantum mechanics"}],"date_created":"2024-07-11T09:46:48Z","status":"public","doi":"10.15479/at:ista:17225","OA_place":"publisher","language":[{"iso":"eng"}],"degree_awarded":"PhD","title":"Towards a quantum entanglement enhanced atom interferomter","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"publisher":"Institute of Science and Technology Austria","abstract":[{"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.","lang":"eng"}],"has_accepted_license":"1","year":"2024"},{"date_published":"2024-06-06T00:00:00Z","day":"06","file_date_updated":"2025-01-27T14:17:37Z","department":[{"_id":"UlWa"},{"_id":"GradSch"}],"type":"conference","page":"8:1-8:15","publication_status":"published","file":[{"file_name":"2024_LIPICs_Aronov.pdf","file_size":880725,"access_level":"open_access","file_id":"18918","content_type":"application/pdf","checksum":"443aa29ea5d948e917cfccd681dcf176","creator":"dernst","success":1,"date_created":"2025-01-27T14:17:37Z","date_updated":"2025-01-27T14:17:37Z","relation":"main_file"}],"intvolume":"       293","publication_identifier":{"isbn":["9783959773164"]},"author":[{"full_name":"Aronov, Boris","first_name":"Boris","last_name":"Aronov"},{"last_name":"Basit","full_name":"Basit, Abdul","first_name":"Abdul"},{"last_name":"Ramesh","full_name":"Ramesh, Indu","first_name":"Indu"},{"first_name":"Gianluca","full_name":"Tasinato, Gianluca","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","last_name":"Tasinato"},{"orcid":"0000-0002-1494-0568","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","arxiv":1,"related_material":{"record":[{"relation":"later_version","status":"public","id":"19860"}]},"publication":"40th International Symposium on Computational Geometry","corr_author":"1","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.","date_updated":"2026-07-23T11:14:45Z","ddc":["510"],"_id":"18917","quality_controlled":"1","article_processing_charge":"Yes","oa":1,"conference":{"location":"Athens, Greece","end_date":"2024-06-14","start_date":"2024-06-11","name":"SoCG: Symposium on Computational Geometry"},"external_id":{"arxiv":["2403.02627"]},"OA_type":"gold","status":"public","date_created":"2025-01-27T14:19:17Z","month":"06","citation":{"apa":"Aronov, B., Basit, A., Ramesh, I., Tasinato, G., &#38; Wagner, U. (2024). Eight-partitioning points in 3D, and efficiently too. In <i>40th International Symposium on Computational Geometry</i> (Vol. 293, p. 8:1-8:15). Athens, Greece: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">https://doi.org/10.4230/LIPIcs.SoCG.2024.8</a>","ama":"Aronov B, Basit A, Ramesh I, Tasinato G, Wagner U. Eight-partitioning points in 3D, and efficiently too. In: <i>40th International Symposium on Computational Geometry</i>. Vol 293. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024:8:1-8:15. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">10.4230/LIPIcs.SoCG.2024.8</a>","ieee":"B. Aronov, A. Basit, I. Ramesh, G. Tasinato, and U. Wagner, “Eight-partitioning points in 3D, and efficiently too,” in <i>40th International Symposium on Computational Geometry</i>, Athens, Greece, 2024, vol. 293, p. 8:1-8:15.","mla":"Aronov, Boris, et al. “Eight-Partitioning Points in 3D, and Efficiently Too.” <i>40th International Symposium on Computational Geometry</i>, vol. 293, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, p. 8:1-8:15, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">10.4230/LIPIcs.SoCG.2024.8</a>.","chicago":"Aronov, Boris, Abdul Basit, Indu Ramesh, Gianluca Tasinato, and Uli Wagner. “Eight-Partitioning Points in 3D, and Efficiently Too.” In <i>40th International Symposium on Computational Geometry</i>, 293:8:1-8:15. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2024.8\">https://doi.org/10.4230/LIPIcs.SoCG.2024.8</a>.","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.","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."},"volume":293,"language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.4230/LIPIcs.SoCG.2024.8","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","title":"Eight-partitioning points in 3D, and efficiently too","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"An eight-partition of a finite set of points (respectively, of a continuous mass distribution) in ℝ³ consists of three planes that divide the space into 8 octants, such that each open octant contains at most 1/8 of the points (respectively, of the mass). In 1966, Hadwiger showed that any mass distribution in ℝ³ admits an eight-partition; moreover, one can prescribe the normal direction of one of the three planes. The analogous result for finite point sets follows by a standard limit argument.\r\nWe prove the following variant of this result: Any mass distribution (or point set) in ℝ³ admits an eight-partition for which the intersection of two of the planes is a line with a prescribed direction.\r\nMoreover, we present an efficient algorithm for calculating an eight-partition of a set of n points in ℝ³ (with prescribed normal direction of one of the planes) in time O^*(n^{5/2})."}],"year":"2024","has_accepted_license":"1","scopus_import":"1"},{"date_updated":"2026-07-27T12:47:43Z","acknowledgement":"This work was partially supported by project SERICS (PE00000014) under the MUR National Recovery and Resilience Plan funded by the European Union - NextGenerationEU.\r\n","corr_author":"1","publication":"Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition","related_material":{"record":[{"id":"19759","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://github.com/berndprach/1LipschitzLayersCompared","relation":"software"}]},"oa_version":"Preprint","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2311.16833"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","author":[{"full_name":"Prach, Bernd","first_name":"Bernd","id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach"},{"last_name":"Brau","first_name":"Fabio","full_name":"Brau, Fabio"},{"last_name":"Buttazzo","full_name":"Buttazzo, Giorgio","first_name":"Giorgio"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph"}],"publication_status":"published","page":"24574-24583","type":"conference","isi":1,"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"day":"01","date_published":"2024-06-01T00:00:00Z","has_accepted_license":"1","year":"2024","abstract":[{"lang":"eng","text":"The robustness of neural networks against input perturbations with bounded\r\nmagnitude represents a serious concern in the deployment of deep learning\r\nmodels in safety-critical systems. Recently, the scientific community has\r\nfocused on enhancing certifiable robustness guarantees by crafting 1-Lipschitz\r\nneural networks that leverage Lipschitz bounded dense and convolutional layers.\r\nAlthough different methods have been proposed in the literature to achieve this\r\ngoal, understanding the performance of such methods is not straightforward,\r\nsince different metrics can be relevant (e.g., training time, memory usage,\r\naccuracy, certifiable robustness) for different applications. For this reason,\r\nthis work provides a thorough theoretical and empirical comparison between\r\nmethods by evaluating them in terms of memory usage, speed, and certifiable\r\nrobust accuracy. The paper also provides some guidelines and recommendations to\r\nsupport the user in selecting the methods that work best depending on the\r\navailable resources. We provide code at\r\nhttps://github.com/berndprach/1LipschitzLayersCompared."}],"title":"1-Lipschitz layers compared: Memory, speed, and certifiable robustness","publisher":"Computer Vision Foundation","doi":"10.1109/CVPR52733.2024.02320","OA_place":"repository","language":[{"iso":"eng"}],"citation":{"apa":"Prach, B., Brau, F., Buttazzo, G., &#38; Lampert, C. (2024). 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24574–24583). Seattle, WA, United States: Computer Vision Foundation. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>","ama":"Prach B, Brau F, Buttazzo G, Lampert C. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In: <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. Computer Vision Foundation; 2024:24574-24583. doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>","ieee":"B. Prach, F. Brau, G. Buttazzo, and C. Lampert, “1-Lipschitz layers compared: Memory, speed, and certifiable robustness,” in <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Seattle, WA, United States, 2024, pp. 24574–24583.","mla":"Prach, Bernd, et al. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Computer Vision Foundation, 2024, pp. 24574–83, doi:<a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">10.1109/CVPR52733.2024.02320</a>.","chicago":"Prach, Bernd, Fabio Brau, Giorgio Buttazzo, and Christoph Lampert. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” In <i>Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24574–83. Computer Vision Foundation, 2024. <a href=\"https://doi.org/10.1109/CVPR52733.2024.02320\">https://doi.org/10.1109/CVPR52733.2024.02320</a>.","ista":"Prach B, Brau F, Buttazzo G, Lampert C. 2024. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24574–24583.","short":"B. Prach, F. Brau, G. Buttazzo, C. Lampert, in:, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Computer Vision Foundation, 2024, pp. 24574–24583."},"month":"06","date_created":"2024-08-14T08:42:32Z","status":"public","external_id":{"isi":["001344387500055"],"arxiv":["2311.16833"]},"OA_type":"green","conference":{"location":"Seattle, WA, United States","end_date":"2024-06-22","start_date":"2024-06-16","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"oa":1,"_id":"17426","article_processing_charge":"No","quality_controlled":"1"},{"date_published":"2024-12-05T00:00:00Z","_id":"18874","article_processing_charge":"No","day":"05","oa":1,"department":[{"_id":"GradSch"},{"_id":"ChLa"}],"type":"preprint","external_id":{"arxiv":["2412.04245"]},"status":"public","publication_status":"draft","date_created":"2025-01-24T16:57:29Z","month":"12","citation":{"chicago":"Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2412.04245\">https://doi.org/10.48550/arXiv.2412.04245</a>.","ista":"Prach B, Lampert C. Intriguing properties of robust classification. arXiv, 2412.04245.","short":"B. Prach, C. Lampert, ArXiv (n.d.).","apa":"Prach, B., &#38; Lampert, C. (n.d.). Intriguing properties of robust classification. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2412.04245\">https://doi.org/10.48550/arXiv.2412.04245</a>","ama":"Prach B, Lampert C. Intriguing properties of robust classification. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2412.04245\">10.48550/arXiv.2412.04245</a>","ieee":"B. Prach and C. Lampert, “Intriguing properties of robust classification,” <i>arXiv</i>. .","mla":"Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” <i>ArXiv</i>, 2412.04245, doi:<a href=\"https://doi.org/10.48550/arXiv.2412.04245\">10.48550/arXiv.2412.04245</a>."},"language":[{"iso":"eng"}],"OA_place":"repository","doi":"10.48550/arXiv.2412.04245","author":[{"id":"2D561D42-C427-11E9-89B4-9C1AE6697425","last_name":"Prach","first_name":"Bernd","full_name":"Prach, Bernd"},{"full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Intriguing properties of robust classification","article_number":"2412.04245","abstract":[{"lang":"eng","text":"Despite extensive research since the community learned about adversarial\r\nexamples 10 years ago, we still do not know how to train high-accuracy\r\nclassifiers that are guaranteed to be robust to small perturbations of their\r\ninputs. Previous works often argued that this might be because no classifier\r\nexists that is robust and accurate at the same time. However, in computer\r\nvision this assumption does not match reality where humans are usually accurate\r\nand robust on most tasks of interest. We offer an alternative explanation and\r\nshow that in certain settings robust generalization is only possible with\r\nunrealistically large amounts of data. More precisely we find a setting where a\r\nrobust classifier exists, it is easy to learn an accurate classifier, yet it\r\nrequires an exponential amount of data to learn a robust classifier. Based on\r\nthis theoretical result, we explore how well robust classifiers generalize on\r\ndatasets such as CIFAR-10. We come to the conclusion that on this datasets, the\r\nlimitation of current robust models also lies in the generalization, and that\r\nthey require a lot of data to do well on the test set. We also show that the\r\nproblem is not in the expressiveness or generalization capabilities of current\r\narchitectures, and that there are low magnitude features in the data which are\r\nuseful for non-robust generalization but are not available for robust\r\nclassifiers."}],"oa_version":"Preprint","arxiv":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2412.04245"}],"related_material":{"record":[{"relation":"later_version","id":"20455","status":"public"},{"id":"19759","status":"public","relation":"dissertation_contains"}]},"publication":"arXiv","corr_author":"1","year":"2024","date_updated":"2026-07-27T12:47:43Z"},{"publication_status":"published","file":[{"date_updated":"2024-09-05T14:26:02Z","relation":"main_file","success":1,"date_created":"2024-09-05T14:26:02Z","creator":"esarac","checksum":"43e432f82be376434b358f3dd7a94b71","content_type":"application/pdf","file_id":"17635","file_name":"isola24.pdf","file_size":847422,"access_level":"open_access"},{"relation":"main_file","date_updated":"2025-01-21T14:39:49Z","success":1,"date_created":"2025-01-21T14:39:49Z","file_id":"18865","content_type":"application/pdf","creator":"dernst","checksum":"6bc04f07bb5612c0e7ea00ac121a69b6","file_size":1358706,"access_level":"open_access","file_name":"2024_LNCS_Chalupa.pdf"}],"intvolume":"     15222","alternative_title":["LNCS"],"date_published":"2024-10-26T00:00:00Z","file_date_updated":"2025-01-21T14:39:49Z","day":"26","department":[{"_id":"GradSch"},{"_id":"ToHe"}],"type":"conference","isi":1,"page":"3-20","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20147"}]},"publication":"12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation","corr_author":"1","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when his collaboration started.","date_updated":"2026-07-27T12:48:18Z","publication_identifier":{"isbn":["9783031753862"],"eissn":["1611-3349"],"issn":["0302-9743"]},"author":[{"full_name":"Chalupa, Marek","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463","last_name":"Chalupa"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Mazzocchi","id":"b26baa86-3308-11ec-87b0-8990f34baa85","first_name":"Nicolas Adrien","full_name":"Mazzocchi, Nicolas Adrien"},{"first_name":"Naci E","full_name":"Sarac, Naci E","last_name":"Sarac","id":"8C6B42F8-C8E6-11E9-A03A-F2DCE5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Published Version","arxiv":1,"status":"public","date_created":"2024-09-05T14:27:08Z","project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093"}],"month":"10","citation":{"short":"M. Chalupa, T.A. Henzinger, N.A. Mazzocchi, N.E. Sarac, in:, 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Springer Nature, 2024, pp. 3–20.","ista":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. 2024. QuAK: Quantitative Automata Kit. 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. ISoLA: International Symposium on Leveraging Applications, LNCS, vol. 15222, 3–20.","chicago":"Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “QuAK: Quantitative Automata Kit.” In <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, 15222:3–20. Springer Nature, 2024. <a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">https://doi.org/10.1007/978-3-031-75387-9_1</a>.","ieee":"M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative Automata Kit,” in <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, Crete, Greece, 2024, vol. 15222, pp. 3–20.","mla":"Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>, vol. 15222, Springer Nature, 2024, pp. 3–20, doi:<a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">10.1007/978-3-031-75387-9_1</a>.","ama":"Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata Kit. In: <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i>. Vol 15222. Springer Nature; 2024:3-20. doi:<a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">10.1007/978-3-031-75387-9_1</a>","apa":"Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., &#38; Sarac, N. E. (2024). QuAK: Quantitative Automata Kit. In <i>12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation</i> (Vol. 15222, pp. 3–20). Crete, Greece: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-75387-9_1\">https://doi.org/10.1007/978-3-031-75387-9_1</a>"},"volume":15222,"language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.1007/978-3-031-75387-9_1","APC_amount":"2748 EUR","ddc":["000"],"_id":"17634","article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","oa":1,"conference":{"name":"ISoLA: International Symposium on Leveraging Applications","start_date":"2024-10-27","end_date":"2024-10-31","location":"Crete, Greece"},"OA_type":"hybrid","external_id":{"isi":["001419008700001"],"arxiv":["2409.03569"]},"year":"2024","has_accepted_license":"1","ec_funded":1,"scopus_import":"1","publisher":"Springer Nature","title":"QuAK: Quantitative Automata Kit","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"System behaviors are traditionally evaluated through binary classifications of correctness, which do not suffice for properties involving quantitative aspects of systems and executions. Quantitative automata offer a more nuanced approach, mapping each execution to a real number by incorporating weighted transitions and value functions generalizing acceptance conditions. In this paper, we introduce QuAK, the first tool designed to automate the analysis of quantitative automata. QuAK currently supports a variety of quantitative automaton types, including Inf, Sup, LimInf, LimSup, LimInfAvg, and LimSupAvg automata, and implements decision procedures for problems such as emptiness, universality, inclusion, equivalence, as well as for checking whether an automaton is safe, live, or constant. Additionally, QuAK is able to compute extremal values when possible, construct safety-liveness decompositions, and monitor system behaviors. We demonstrate the effectiveness of QuAK through experiments focusing on the inclusion, constant-function check, and monitoring problems."}]},{"keyword":["General Chemistry","Catalysis"],"abstract":[{"text":"The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity.","lang":"eng"}],"publisher":"Wiley","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries","scopus_import":"1","year":"2024","ec_funded":1,"has_accepted_license":"1","pmid":1,"oa":1,"external_id":{"isi":["001241932700001"],"pmid":["38095355"]},"ddc":["540"],"article_processing_charge":"Yes (via OA deal)","_id":"14687","quality_controlled":"1","language":[{"iso":"eng"}],"volume":63,"doi":"10.1002/anie.202316476","project":[{"name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413"}],"date_created":"2023-12-15T16:10:13Z","status":"public","citation":{"ista":"Jethwa RB, Mondal S, Pant B, Freunberger SA. 2024. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 63(28), e202316476.","chicago":"Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>. Wiley, 2024. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>.","short":"R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition 63 (2024).","apa":"Jethwa, R. B., Mondal, S., Pant, B., &#38; Freunberger, S. A. (2024). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.202316476\">https://doi.org/10.1002/anie.202316476</a>","ieee":"R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28. Wiley, 2024.","mla":"Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” <i>Angewandte Chemie International Edition</i>, vol. 63, no. 28, e202316476, Wiley, 2024, doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>.","ama":"Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. <i>Angewandte Chemie International Edition</i>. 2024;63(28). doi:<a href=\"https://doi.org/10.1002/anie.202316476\">10.1002/anie.202316476</a>"},"issue":"28","month":"07","article_type":"review","article_number":"e202316476","oa_version":"Published Version","author":[{"id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","last_name":"Jethwa","orcid":"0000-0002-0404-4356","first_name":"Rajesh B","full_name":"Jethwa, Rajesh B"},{"last_name":"Mondal","id":"d25d21ef-dc8d-11ea-abe3-ec4576307f48","full_name":"Mondal, Soumyadip","first_name":"Soumyadip"},{"full_name":"Pant, Bhargavi","first_name":"Bhargavi","last_name":"Pant","id":"50c64d4d-eb97-11eb-a6c2-d33e5e14f112"},{"full_name":"Freunberger, Stefan Alexander","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","last_name":"Freunberger","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"}],"publication_identifier":{"issn":["1433-7851"],"eissn":["1521-3773"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","date_updated":"2026-07-27T14:29:01Z","acknowledgement":"S.A.F. is indebted to ISTA for support. R.B.J. thanks the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413 for funding. B.P. thanks Alistore ERI for providing a PhD scholarship.","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"20607"}]},"publication":"Angewandte Chemie International Edition","file_date_updated":"2024-07-16T11:54:46Z","day":"08","type":"journal_article","isi":1,"department":[{"_id":"StFr"},{"_id":"GradSch"}],"date_published":"2024-07-08T00:00:00Z","publication_status":"published","intvolume":"        63","file":[{"file_size":4766445,"access_level":"open_access","file_name":"2024_AngChemieInt_Jethwa.pdf","checksum":"fe2c23454279eb9d76ed6ca9970c21c7","creator":"dernst","file_id":"17261","content_type":"application/pdf","success":1,"date_created":"2024-07-16T11:54:46Z","relation":"main_file","date_updated":"2024-07-16T11:54:46Z"}]},{"related_material":{"record":[{"status":"public","id":"11160","relation":"part_of_dissertation"},{"status":"public","id":"18688","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"18677"},{"relation":"part_of_dissertation","id":"18689","status":"public"}]},"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"corr_author":"1","date_updated":"2026-07-28T08:33:52Z","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-048-0"]},"doi_confirm":"1","author":[{"first_name":"Mojtaba","full_name":"Tavakoli, Mojtaba","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa_version":"Published Version","publication_status":"published","file":[{"date_created":"2024-12-20T10:23:17Z","relation":"source_file","date_updated":"2024-12-20T10:31:37Z","file_size":118593521,"access_level":"closed","file_name":"Thesis_Mojtaba Tavakoli_.docx","file_id":"18699","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"mtavakol","checksum":"b61651d417cafddd740a8528f46068c5"},{"file_id":"18700","embargo":"2027-08-01","content_type":"application/pdf","creator":"mtavakol","checksum":"c80bcfd1a34c23afc3538052325283e5","access_level":"closed","file_size":63885521,"file_name":"Thesis_Mojtaba Tavakoli_.pdf","embargo_to":"open_access","relation":"main_file","date_updated":"2026-07-28T08:33:51Z","date_created":"2024-12-20T10:25:12Z"}],"alternative_title":["ISTA Thesis"],"date_published":"2024-12-20T00:00:00Z","file_date_updated":"2026-07-28T08:33:51Z","day":"20","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"type":"dissertation","page":"230","OA_embargo":"20","year":"2024","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","title":"Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"status":"public","das_tickbox":"1","date_created":"2024-12-19T02:30:39Z","project":[{"_id":"6285a163-2b32-11ec-9570-8e204ca2dba5","grant_number":"26137","name":"Studying Organelle Structure and Function at Nanoscale Resolution with Expansion Microscopy"},{"_id":"26AA4EF2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets"}],"month":"12","citation":{"chicago":"Tavakoli, Mojtaba. “Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>.","ista":"Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.","short":"M. Tavakoli, Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy, Institute of Science and Technology Austria, 2024.","apa":"Tavakoli, M. (2024). <i>Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18681\">https://doi.org/10.15479/at:ista:18681</a>","ieee":"M. Tavakoli, “Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy,” Institute of Science and Technology Austria, 2024.","mla":"Tavakoli, Mojtaba. <i>Developing Molecular and Structural Tools for Studying Brain Architecture with Super Resolution Expansion Microscopy. LICONN: Molecularly-Informed Connectomics Reconstruction with Light Microscopy</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>.","ama":"Tavakoli M. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18681\">10.15479/at:ista:18681</a>"},"degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.15479/at:ista:18681","supervisor":[{"full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"ddc":["600","570"],"article_processing_charge":"No","_id":"18681"},{"acknowledged_ssus":[{"_id":"ScienComp"}],"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"11420"},{"id":"14459","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"9198","status":"public"},{"relation":"part_of_dissertation","id":"17469","status":"public"}]},"date_updated":"2026-06-18T17:55:53Z","corr_author":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"]},"author":[{"last_name":"Shevchenko","id":"F2B06EC2-C99E-11E9-89F0-752EE6697425","first_name":"Aleksandr","full_name":"Shevchenko, Aleksandr"}],"oa_version":"Published Version","file":[{"content_type":"application/pdf","embargo":"2024-10-04","file_id":"17482","creator":"ashevche","checksum":"da6dd3166078934577f6af93d27000e2","file_size":4468610,"access_level":"open_access","file_name":"thesis_a2b.pdf","relation":"main_file","date_updated":"2024-10-05T22:30:05Z","date_created":"2024-09-02T09:23:32Z"},{"file_name":"Thesis Alex - ISTA.zip","access_level":"closed","file_size":15930999,"creator":"ashevche","checksum":"76a39ef252239560923cdda4ce0a31a4","content_type":"application/zip","file_id":"17483","date_created":"2024-09-02T09:23:46Z","date_updated":"2024-10-05T22:30:05Z","relation":"source_file","embargo_to":"open_access"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_published":"2024-08-29T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"MaMo"}],"type":"dissertation","page":"232","file_date_updated":"2024-10-05T22:30:05Z","day":"29","has_accepted_license":"1","year":"2024","title":"High-dimensional limits in artificial neural networks","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"In the modern age of machine learning, artificial neural networks have become an integral part\r\nof many practical systems. One of the key ingredients of the success of the deep learning\r\napproach is recent computational advances which allowed the training of models with billions\r\nof parameters on large-scale data. Such over-parameterized and data-hungry regimes pose a\r\nchallenge for the theoretical analysis of modern models since “classical” statistical wisdom\r\nis no longer applicable. In this view, it is paramount to extend or develop new machinery\r\nthat will allow tackling the neural network analysis under new challenging asymptotic regimes,\r\nwhich is the focus of this thesis.\r\nLarge neural network systems are usually optimized via “local” search algorithms, such\r\nas stochastic gradient descent (SGD). However, given the high-dimensional nature of the\r\nparameter space, it is a priori not clear why such a crude “local” approach works so remarkably\r\nwell in practice. We take a step towards demystifying this phenomenon by showing that\r\nthe landscape of the SGD training dynamics exhibits a few beneficial properties for the\r\noptimization. First, we show that along the SGD trajectory an over-parameterized network\r\nis dropout stable. The emergence of dropout stability allows to conclude that the minima\r\nfound by SGD are connected via a continuous path of small loss. This in turn means that\r\nthe high-dimensional landscape of the neural network optimization problem is provably not so\r\nunfavourable to gradient-based training, due to mode connectivity. Next, we show that SGD\r\nfor an over-parameterized network tends to find solutions that are functionally more “simple”.\r\nThis in turn means that the SGD minima are more robust, since a less complicated solution\r\nwill less likely overfit the data. More formally, for a prototypical example of a wide two-layer\r\nReLU network on a 1d regression task we show that the SGD algorithm is implicitly selective in\r\nits choice of an interpolating solution. Namely, at convergence the neural network implements\r\na piece-wise linear function with the number of linear regions depending only on the amount\r\nof training data. This is in contrast to a “smooth”-like behaviour which one would expect\r\ngiven such a severe over-parameterization of the model.\r\nDiverging from the generic supervised setting of classification and regression problems, we\r\nanalyze an auto-encoder model that is commonly used for representation learning and data\r\ncompression. Despite the wide applicability of the auto-encoding paradigm, the theoretical\r\nunderstanding of their behaviour is limited even in the simplistic shallow case. The related\r\nwork is restricted to extreme asymptotic regimes in which the auto-encoder is either severely\r\nover-parameterized or under-parameterized. In contrast, we provide a tight characterization\r\nfor the 1-bit compression of Gaussian signals in the challenging proportional regime, i.e., the\r\ninput dimension and the size of the compressed representation obey the same asymptotics.\r\nWe also show that gradient-based methods are able to find a globally optimal solution and\r\nthat the predictions made for Gaussian data extrapolate beyond - to the case of compression\r\nof natural images. Next, we relax the Gaussian assumption and study more structured input\r\nsources. We show that the shallow model is sometimes agnostic to the structure of the data\r\nvii\r\nwhich results in a Gaussian-like behaviour. We prove that making the decoding component\r\nslightly less shallow is already enough to escape the “curse” of Gaussian performance.\r\n","lang":"eng"}],"month":"08","citation":{"chicago":"Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>.","ista":"Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria.","short":"A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024.","apa":"Shevchenko, A. (2024). <i>High-dimensional limits in artificial neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17465\">https://doi.org/10.15479/at:ista:17465</a>","ama":"Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>","mla":"Shevchenko, Alexander. <i>High-Dimensional Limits in Artificial Neural Networks</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17465\">10.15479/at:ista:17465</a>.","ieee":"A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024."},"status":"public","project":[{"_id":"059876FA-7A3F-11EA-A408-12923DDC885E","name":"Prix Lopez-Loretta 2019 - Marco Mondelli"},{"name":"Vienna Graduate School on Computational Optimization","grant_number":"W1260-N35","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"}],"date_created":"2024-08-28T15:14:25Z","OA_place":"repository","doi":"10.15479/at:ista:17465","degree_awarded":"PhD","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"17465","supervisor":[{"first_name":"Marco","full_name":"Mondelli, Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian"}],"ddc":["519"],"oa":1},{"publication_identifier":{"isbn":["978-3-99078-043-5"],"issn":["2663-337X"]},"author":[{"id":"FDE60288-A89D-11E9-947F-1AF6E5697425","orcid":"0000-0001-5263-5559","last_name":"Mukhopadhyay","first_name":"Soham","full_name":"Mukhopadhyay, Soham"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"14032"},{"relation":"part_of_dissertation","status":"public","id":"18057"}]},"acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"corr_author":"1","date_updated":"2026-06-03T07:16:04Z","date_published":"2024-09-10T00:00:00Z","day":"10","file_date_updated":"2025-03-13T23:30:04Z","page":"82","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"AnHi"}],"publication_status":"published","alternative_title":["ISTA Thesis"],"file":[{"file_size":10297052,"access_level":"open_access","file_name":"PhD_Thesis_Soham_Mukhopadhyay.pdf","checksum":"ed7763c3bbd59e1d7e1b664de3a26f3c","creator":"smukhopa","file_id":"18059","embargo":"2025-03-13","content_type":"application/pdf","date_created":"2024-09-12T10:46:04Z","relation":"main_file","date_updated":"2025-03-13T23:30:04Z"},{"file_size":29178634,"access_level":"closed","file_name":"PhD_Thesis_Soham_Mukhopadhyay_source.zip","checksum":"e352667482701dd18a9a0e7418aef465","creator":"smukhopa","file_id":"18060","content_type":"application/zip","date_created":"2024-09-12T10:50:58Z","relation":"source_file","date_updated":"2025-03-13T23:30:04Z","embargo_to":"open_access"}],"publisher":"Institute of Science and Technology Austria","title":"Thermal effects in one dimensional Josephson chains","abstract":[{"lang":"eng","text":"This work can be broadly classified into the study of critical phenomena in a one dimensional\r\narray of Josephson junctions. While we study quantum criticality when the array is in thermal\r\nequilibrium at zero bias, the non-equilibrium study involves understanding the bistability of the\r\narray at a critical non-zero bias. This work furthers our knowledge in understanding quantum\r\ncritical behaviour at finite temperatures in a one dimensional Josephson array, while also\r\nestablishing relaxation behaviour dual to that observed in a single Josephson junction.\r\nChapter 1 briefly introduces the model to understand superconductor-insulator phase transition\r\nin a one dimensional Josephson array and points out the state of the field from where we\r\nstarted our zero-bias experiments. In this context it discusses the phase-charge duality observed\r\nin a Josephson array and its dual hysteretic behaviour to that of a single junction, setting the\r\nground for our non-equilibrium study of the array.\r\nChapter 2 shows the experimental setup and the chip layout of the device we measured.\r\nIn chapter 3 we show that, unlike the typical quantum-critical broadening scenario, in one dimensional Josephson arrays temperature dramatically shifts the critical region. This shift leads\r\nto a regime of superconductivity at high temperature, arising from the melted zero-temperature\r\ninsulator. Our results quantitatively explain the low-temperature onset of superconductivity in\r\nnominally insulating regimes, and the transition to the strongly insulating phase. We further\r\npresent, to our knowledge, the first understanding of the onset of anomalous-metallic resistance\r\nsaturation [30]. This work demonstrates a non-trivial interplay between thermal effects and\r\nquantum criticality. A practical consequence is that, counterintuitively, the coherence of\r\nhigh-impedance quantum circuits is expected to be stabilized by thermal fluctuations.\r\nIn chapter 4, we show relaxation oscillations in a current-biased one dimensional array of\r\nJosephson junctions. These oscillations are well described by a circuit model, dual to the\r\nordinary Josephson relaxation oscillations [72]. Injection locking these oscillations results in\r\ncurrent plateaux. The relaxation step is found to obey a characteristic self-consistent relation,\r\nsuggesting that it is governed by overheating effects.\r\nChapter 5 describes the various checks and analysis we performed to support our conclusions\r\nmade in chapters 3 and 4.\r\nFinally, chapter 6 describes the nanofabrication steps and the finite element electromagnetic\r\nsimulations we performed to fabricate our devices."}],"has_accepted_license":"1","year":"2024","ddc":["539"],"supervisor":[{"orcid":"0000-0003-2607-2363","last_name":"Higginbotham","id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrew P","full_name":"Higginbotham, Andrew P"}],"_id":"17881","article_processing_charge":"No","oa":1,"project":[{"grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931","name":"Cavity electromechanics across a quantum phase transition"}],"date_created":"2024-09-08T10:23:25Z","status":"public","citation":{"chicago":"Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>.","ista":"Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria.","short":"S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024.","apa":"Mukhopadhyay, S. (2024). <i>Thermal effects in one dimensional Josephson chains</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17881\">https://doi.org/10.15479/at:ista:17881</a>","mla":"Mukhopadhyay, Soham. <i>Thermal Effects in One Dimensional Josephson Chains</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>.","ieee":"S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024.","ama":"Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17881\">10.15479/at:ista:17881</a>"},"month":"09","language":[{"iso":"eng"}],"degree_awarded":"PhD","doi":"10.15479/at:ista:17881","OA_place":"publisher"},{"citation":{"apa":"Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., &#38; Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>","ieee":"S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” <i>arXiv</i>. .","mla":"Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, 2408.07829, doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>.","ama":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2408.07829\">10.48550/arXiv.2408.07829</a>","ista":"Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829.","chicago":"Mukhopadhyay, Soham, Diego A Lancheros Naranjo, Jorden L Senior, and Andrew P Higginbotham. “Dual Relaxation Oscillations in a Josephson Junction Array.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2408.07829\">https://doi.org/10.48550/arXiv.2408.07829</a>.","short":"S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.)."},"month":"08","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020"},{"name":"Cavity electromechanics across a quantum phase transition","grant_number":"P33692","_id":"0aa3608a-070f-11eb-9043-e9cd8a2bd931"},{"name":"Protected states of quantum matter","_id":"eb9b30ac-77a9-11ec-83b8-871f581d53d2"}],"date_created":"2024-09-11T09:25:22Z","status":"public","OA_place":"repository","doi":"10.48550/arXiv.2408.07829","language":[{"iso":"eng"}],"_id":"18057","article_processing_charge":"No","external_id":{"arxiv":["2408.07829"]},"oa":1,"year":"2024","ec_funded":1,"title":"Dual relaxation oscillations in a Josephson junction array","abstract":[{"text":"We report relaxation oscillations in a one-dimensional array of Josephson\r\njunctions. The oscillations are circuit-dual to those ordinarily observed in\r\nsingle junctions. The dual circuit quantitatively accounts for temporal\r\ndynamics of the array, including the dependence on biasing conditions.\r\nInjection locking the oscillations results in well-developed current plateaux.\r\nA thermal model explains the relaxation step of the oscillations.","lang":"eng"}],"publication_status":"draft","date_published":"2024-08-14T00:00:00Z","type":"preprint","department":[{"_id":"AnHi"},{"_id":"GradSch"}],"day":"14","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication":"arXiv","related_material":{"record":[{"id":"20324","status":"public","relation":"later_version"},{"status":"public","id":"17881","relation":"dissertation_contains"}]},"date_updated":"2026-07-28T22:30:19Z","acknowledgement":"We gratefully acknowledge support from the MIBA machine shop and Nanofabrication Facility at IST Austria. Work was supported by Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation program under the Marie Sk lodowska-Curie Grant Agreement No. 754411 (J.S.), and a NOMIS foundation research grant (A.P.H.).\r\n","corr_author":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Soham","full_name":"Mukhopadhyay, Soham","last_name":"Mukhopadhyay","orcid":"0000-0001-5263-5559","id":"FDE60288-A89D-11E9-947F-1AF6E5697425"},{"first_name":"Diego A","full_name":"Lancheros Naranjo, Diego A","last_name":"Lancheros Naranjo","id":"6c55e976-15b2-11ec-abd3-d790e8937fde"},{"orcid":"0000-0002-0672-9295","last_name":"Senior","id":"5479D234-2D30-11EA-89CC-40953DDC885E","full_name":"Senior, Jorden L","first_name":"Jorden L"},{"id":"4AD6785A-F248-11E8-B48F-1D18A9856A87","last_name":"Higginbotham","orcid":"0000-0003-2607-2363","full_name":"Higginbotham, Andrew P","first_name":"Andrew P"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2408.07829","open_access":"1"}],"arxiv":1,"oa_version":"Preprint","article_number":"2408.07829"},{"related_material":{"record":[{"relation":"part_of_dissertation","id":"542","status":"public"},{"relation":"part_of_dissertation","id":"10767","status":"public"}]},"corr_author":"1","date_updated":"2026-04-07T13:21:37Z","author":[{"full_name":"Kelemen, Réka K","first_name":"Réka K","orcid":"0000-0002-8489-9281","last_name":"Kelemen","id":"48D3F8DE-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-039-8"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","publication_status":"published","file":[{"content_type":"application/zip","file_id":"17121","creator":"rkelemen","checksum":"fab59146e3b3dc2e5d214576984a2a63","file_name":"thesis.zip","access_level":"closed","file_size":180557931,"embargo_to":"open_access","date_updated":"2025-01-10T23:30:10Z","relation":"source_file","date_created":"2024-06-07T16:09:17Z"},{"file_size":19405484,"access_level":"open_access","file_name":"thesis_to_archive.pdf","embargo":"2025-01-10","file_id":"17213","content_type":"application/pdf","creator":"rkelemen","checksum":"91cc4c25a792239e8a7688e8aec7c62a","date_created":"2024-07-10T08:00:20Z","relation":"main_file","date_updated":"2025-01-10T23:30:10Z"}],"alternative_title":["ISTA Thesis"],"date_published":"2024-06-20T00:00:00Z","day":"20","file_date_updated":"2025-01-10T23:30:10Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"type":"dissertation","page":"105","year":"2024","has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"title":"Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver","abstract":[{"lang":"eng","text":"Genomes are shaped by natural selection at the level of the organism, as genomic variants that\r\nhave a beneficial effect on the viability or fecundity of their carriers are on average expected\r\nto be passed on to more offspring than less beneficial alleles. However, selection also favors\r\ngenomic variants that drive their own transmission to the next generation above the mendelian\r\nexpectation of 50 percent in heterozygotes, even if these self-promoting variants are less\r\nbeneficial to the organism than other variants at the same locus. Such variants, called meiotic\r\ndrivers, are found in diverse taxa, and often impose fitness costs on their host organisms. As\r\nmeiotic drivers often require multiple genes and sequences for transmission ratio distortion,\r\nthey are often found in regions of low recombination, such as inversions, which prevent their\r\nrecombination with the non-driving homologous regions. Reduced recombination rates are\r\nexpected to lead to the accumulation of deleterious mutations, which may affect hundreds\r\nof genes trapped in the inversions of meiotic drivers. Although the observed fitness costs of\r\nself-promoting haplotypes are thought to possibly reflect sequence degeneration, no study has\r\nsystematically investigated the level of degeneration on a meiotic driver. Further, the low\r\nrates of recombination between driving and non-driving haplotypes have limited the power of\r\ntraditional genetic studies in uncovering the gene content of meiotic drivers, and made the\r\nthe identification of the genes causing transmission ratio distortion difficult.\r\nAfter an introduction to meiotic drivers in Chapter 1, this thesis presents three studies that\r\nmake use of next generation sequencing data to characterize the sequence and expression\r\nevolution of genes on the t-haplotype, a large and ancient meiotic driver in house mice that is\r\ntransmitted to up to 100% of the offspring in males heterozygous for it. Chapter 2 presents\r\na comprehensive assessment of the t-haplotype’s sequence evolution, which shows signs of\r\nsequence degeneration counteracted by occasional recombination with the non-driving homolog\r\nover large parts of the meiotic driver, proposing an explanation for its long-term survival.\r\nChapter 3 investigates the sequence and expression evolution of genes on the t-haplotype,\r\nand finds widespread expression and copy number changes and signs of less efficient purifying\r\nselection compared to the genes on the non-driving homolog. Further, this chapter finds\r\ncandidates for involvment in drive: two positively selected genes on the t-haplotype, and\r\nthe discovery of a t-specific gene duplicate, which was gained from another chromosome,\r\nand which acquired novel sequence and testis-specific expression on the t-haplotype. Finally,\r\nChapter 4 provides unprecedented insights into the gene expression landscape in testes of\r\nt-carrier mice, using single nucleus sequencing. Cell-resolved RNA-sequencing allows the\r\ncomparison of expression in spermatids carrying or not carrying the t-haplotype as well as the\r\ntiming of t-haplotype-induced expression changes along spermatogenesis. This study shows\r\nthe timing of previously found drive-associated genes, and uncovers novel candidate genes and\r\nbiological processes that may underlie the complex biology of transmission ratio distortion of\r\nthe t-haplotype. Chapter 5 synthesizes the findings of the three studies, and discusses them in\r\nthe context of the current state of meiotic drive research."}],"keyword":["meiotic driver","neofunctionalization","single nucleus sequencing"],"status":"public","date_created":"2024-06-07T16:14:13Z","project":[{"grant_number":"715257","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution"},{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"month":"06","citation":{"mla":"Kelemen, Réka K. <i>Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>.","ieee":"R. K. Kelemen, “Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver,” Institute of Science and Technology Austria, 2024.","ama":"Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:17119\">10.15479/at:ista:17119</a>","apa":"Kelemen, R. K. (2024). <i>Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>","short":"R.K. Kelemen, Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver, Institute of Science and Technology Austria, 2024.","ista":"Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria.","chicago":"Kelemen, Réka K. “Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:17119\">https://doi.org/10.15479/at:ista:17119</a>."},"degree_awarded":"PhD","language":[{"iso":"eng"}],"OA_place":"publisher","doi":"10.15479/at:ista:17119","supervisor":[{"full_name":"Vicoso, Beatriz","first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"ddc":["576"],"_id":"17119","article_processing_charge":"No","oa":1},{"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"}],"date_updated":"2026-04-07T13:23:59Z","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"isbn":["978-3-99078-045-9"],"issn":["2663-337X"]},"author":[{"full_name":"Kaczmarek, Beata M","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","last_name":"Kaczmarek"}],"oa_version":"Published Version","file":[{"access_level":"closed","file_size":23136626,"file_name":"20241029_PhD_thesis_BKaczmarek.docx","creator":"bkaczmar","checksum":"2053294ea4d770c495e4cc501e2a218b","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18485","date_created":"2024-10-29T11:56:36Z","relation":"source_file","date_updated":"2025-10-29T23:30:02Z","embargo_to":"open_access"},{"relation":"main_file","date_updated":"2025-10-29T23:30:02Z","date_created":"2024-10-29T11:56:44Z","creator":"bkaczmar","checksum":"8ce857a4cd44b776791eaf180ac9dbb3","embargo":"2025-10-29","file_id":"18486","content_type":"application/pdf","access_level":"open_access","file_size":11707360,"file_name":"20241029_PhD_thesis_BKaczmarek.pdf"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_published":"2024-10-29T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"CaBe"}],"page":"124","type":"dissertation","day":"29","file_date_updated":"2025-10-29T23:30:02Z","year":"2024","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"title":"Biochemical and structural insights into ADAR1 RNA editing","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"ADAR1 is broadly expressed across various tissues and is vital in regulating pathways\r\nassociated with innate immune responses. ADAR1 marks double-stranded RNA as \"self\"\r\nthrough its A-to-I editing activity, effectively repressing autoimmunity and maintaining\r\nimmune tolerance. This editing process has been detected at millions of sites across the\r\nhuman genome. However, the mechanism underlying ADAR1's substrate selectivity\r\nproperties remains largely unclear, with much of the current knowledge derived from\r\ncomparisons to its more extensively studied homolog, ADAR2. By studying ADAR1 in complex\r\nwith its RNA substrates and applying a combination of biochemical techniques and structural\r\nstudies using CryoEM, we aim to gain a more comprehensive understanding of the substrate\r\nselectivity characteristics of ADAR1.\r\nIn this thesis, the purification protocol for ADAR1 was successfully optimized, resulting in the\r\nfirst report in the literature to achieve high protein purity and activity. This advancement\r\nenabled the investigation of complex formation between ADAR1 and various RNA substrates,\r\nleading to the identification of optimal conditions for preparing the cryoEM sample. However,\r\ndespite comprehensive optimization of the cryo-EM conditions, the resulting data lacked the\r\ndesired quality, highlighting the need for similar rigorous optimization of the RNA substrates\r\nto facilitate structural studies of the ADAR1-RNA complex. The study was complemented by\r\nAlphaFold predictions, which provided some insights into this mechanism.\r\nMoreover, during this project I established a collaboration with a research group focused on\r\nstudying ADAR homologs. Notably ADAR homologs were identified in bivalve species, and it\r\nwas further demonstrated that ADAR and its A-to-I editing activity are upregulated in Pacific\r\noysters during infections with Ostreid herpesvirus-1—a highly infectious virus that leads to\r\nsignificant losses in oyster populations globally. I successfully purified oyster ADAR and\r\nprepared in vitro edited RNA for nanopore sequencing—a direct sequencing technology\r\ncapable of detecting modified nucleotides without the need for reverse transcription. The\r\ncollaborators initiated optimization of this nanopore-based approach. However, current\r\ntechnological limitations still constrain the reliable detection of modified nucleotides.\r\nThe project also examined the impact of RNA editing on RNA binding and filament formation\r\nby MDA5, a key cytosolic dsRNA sensor that triggers an interferon response. A primary target\r\nof ADAR1's editing activity is RNA derived from repetitive elements present in the genome,\r\nparticularly Alu elements forming double-stranded RNA. When unedited, these RNA\r\nsequences are recognized by MDA5. However, the mechanisms by which MDA5 interacts with\r\nAlu RNAs, as well as the role of A-to-I editing in influencing this binding, are still not well\r\nunderstood.\r\nThe interaction between MDA5 and Alu elements, was successfully established. This was\r\nachieved through the testing of different RNA variants and the evaluation of filament\r\nformation using binding techniques and electron microscopy imaging. This groundwork has\r\nset the conditions for further evaluation using CryoEM. Furthermore, the effects of A-to-I\r\nediting on the binding properties of MDA5 with Alu RNA were investigated. Given the recent\r\nresearch that has provided new insights into MDA5's interaction with dsRNA, it is essential to\r\nrevise the experimental setup to integrate these findings before moving forward with the\r\nCryoEM sample analysis."}],"month":"10","citation":{"short":"B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024.","ista":"Kaczmarek BM. 2024. Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria.","chicago":"Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>.","ama":"Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>","ieee":"B. M. Kaczmarek, “Biochemical and structural insights into ADAR1 RNA editing,” Institute of Science and Technology Austria, 2024.","mla":"Kaczmarek, Beata M. <i>Biochemical and Structural Insights into ADAR1 RNA Editing</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18477\">10.15479/at:ista:18477</a>.","apa":"Kaczmarek, B. M. (2024). <i>Biochemical and structural insights into ADAR1 RNA editing</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18477\">https://doi.org/10.15479/at:ista:18477</a>"},"status":"public","date_created":"2024-10-27T07:35:13Z","doi":"10.15479/at:ista:18477","OA_place":"publisher","degree_awarded":"PhD","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"18477","supervisor":[{"first_name":"Carrie A","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","last_name":"Bernecky","orcid":"0000-0003-0893-7036"}],"ddc":["572"],"oa":1},{"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"last_name":"Murmann","id":"1d390868-f128-11eb-9611-a0ca5f7833b5","full_name":"Murmann, Julie Stefanie","first_name":"Julie Stefanie"}],"publication_identifier":{"issn":["2791-4585"]},"date_updated":"2026-04-07T13:05:00Z","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"}],"department":[{"_id":"SaSi"},{"_id":"GradSch"}],"page":"54","type":"dissertation","day":"02","file_date_updated":"2025-05-02T22:30:04Z","date_published":"2024-05-02T00:00:00Z","file":[{"access_level":"open_access","file_size":5936142,"file_name":"Murmann_Thesis_final_2024_2.pdf","checksum":"095817a6c944954ac3f277e547031a33","creator":"cchlebak","content_type":"application/pdf","file_id":"15354","embargo":"2025-05-02","date_created":"2024-05-02T12:26:13Z","relation":"main_file","date_updated":"2025-05-02T22:30:04Z"},{"date_created":"2024-05-02T12:37:56Z","embargo_to":"open_access","date_updated":"2025-05-02T22:30:04Z","relation":"source_file","file_name":"Murmann_Thesis_final_2024.zip","file_size":20645510,"access_level":"closed","file_id":"15355","content_type":"application/x-zip-compressed","creator":"cchlebak","checksum":"43b632255372973a437ac87739cfd4db"}],"alternative_title":["ISTA Master's Thesis"],"publication_status":"published","abstract":[{"lang":"eng","text":"Epilepsy affects about 50 to 65 million people globally. It summarizes a spectrum of neurological\r\ndisorders that have in common a hyperactivity of the neuronal network resulting in seizures. A common\r\nassumption is that an imbalance between neuronal excitation and inhibition is a key mechanism in\r\nseizure generation and epileptogeneisis. In at least one-third of the patients, current therapies have\r\nproven unsuccessful in treating seizure progression. One potential reason could be that the therapies\r\nonly focus on neurons. Recent studies suggest that neuronal hyperactivity causes a microglial\r\nresponse, which reinstates brain homeostasis. Additionally, interactions between microglia and neurons\r\nhave been shown to inhibit neuronal firing and dampen seizure activity. However, the exact relationship\r\nbetween microglia and seizure progression in epilepsy is yet to be elucidated. A main bottleneck is that\r\nseveral studies investigate microglia dynamics in ex vivo slice models, which can severely affect the\r\nmicroglia dynamics due to their rapid response to environmental changes. On the other hand, in vivo\r\nstudies focus mostly on behavior characterization of the epileptic seizure phenotype and their long-term\r\nconsequences on microglia activity leaving out the direct consequences of acute seizure activity on\r\nmicroglia dynamics.\r\nHere, we perform a pilot study to combine electroencephalography (EEG) and in vivo live imaging to\r\ndirectly monitor and correlate the onset of seizure activity with microglia response. To induce seizures,\r\nwe take advantage of the kainic acid (KA) model, which represents similar neuropathological and\r\nelectroencephalographic features seen in human patients with temporal lobe epilepsy (TLE). After\r\nconfirmation of induction of the seizure and microglia activity in the hippocampus as a focal point, we\r\ninvestigated whether these changes also reached the primary visual cortex (V1) as a secondary\r\ngeneralized seizure activity. Indeed, we found that microglia changed their morphology at high doses\r\nof KA in the V1. Next, we optimized each of the two methodological components: for the EEG recording,\r\nour initial attempts under the microscope suffered from extensive electrical noise, which overlaid the\r\nactual signal. Thus, we built a customized Faraday-cage and confirmed that the signal-to-noise ratio\r\nwas sufficiently reduced to be able to record brain oscillatory activity. For the in vivo live imaging of\r\nmicroglia, we had to optimize the imaging parameters, so that we would be able to detect microglial\r\nprocesses in a sufficient resolution to track their process changes. Finally, we combined both\r\nmethodologies with the KA model. We confirmed that KA induced seizure activity and found first\r\nindication that those correlate with microglia volume changes.\r\nOverall, we have developed a first methodological approach, which allows the analysis of the acute\r\neffects of seizure onset on microglia. Future studies will have to continue to optimize the drift during\r\nimaging recording and the post-image analysis. "}],"title":"Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","year":"2024","oa":1,"_id":"15352","article_processing_charge":"No","supervisor":[{"id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","first_name":"Sandra","full_name":"Siegert, Sandra"}],"ddc":["570"],"doi":"10.15479/at:ista:15352","OA_place":"publisher","degree_awarded":"MS","language":[{"iso":"eng"}],"month":"05","citation":{"apa":"Murmann, J. S. (2024). <i>Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>","mla":"Murmann, Julie Stefanie. <i>Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>.","ieee":"J. S. Murmann, “Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording,” Institute of Science and Technology Austria, 2024.","ama":"Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15352\">10.15479/at:ista:15352</a>","chicago":"Murmann, Julie Stefanie. “Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15352\">https://doi.org/10.15479/at:ista:15352</a>.","ista":"Murmann JS. 2024. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria.","short":"J.S. Murmann, Investigating Acute Microglia Response to Seizure Activity in Vivo: Combining 2-Photon Imaging and EEG Recording, Institute of Science and Technology Austria, 2024."},"status":"public","date_created":"2024-05-02T08:31:38Z"},{"year":"2024","has_accepted_license":"1","ec_funded":1,"title":"Adaptive hierarchical representations in the hippocampus","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"The hippocampus is central to memory formation, storage and retrieval over many\r\ntimescales. Neurons in this brain area are highly selective to spatial position as well as to many\r\nother variables of the environment. It is believed that the selectivity patterns of hippocampal\r\nneurons reflect the structure of tasks an animal performs. However, especially at timescales\r\nlonger than a few minutes or hours it is not fully known how these representations evolve, nor\r\nhow they map to behaviour in the process. In this thesis, I monitored the evolution of\r\nhippocampal representations in a novel spatial-associative memory task for rats. Reward\r\nlocations were associated with global sensory cues (i.e. context); animals had to remember the\r\nassociations and dig for food in those locations only. I used in vivo electrophysiology to record\r\nthe activity of the hippocampus dorsal CA1 neurons during the learning period of a few days.\r\nI report here a novel and simple method to classify behaviour performance to account\r\nfor individual variability in learning speed and spurious performance unrelated to true task rule\r\nlearning. Using this classification I was then able to investigate neural responses on different\r\nstages of learning matched across animals. On the first day of learning, I observed a fast\r\nformation of single-cell selectivity to task variables which remained stable over days. I also\r\nobserved that reward tuning was not a single process but dependent on task-related cognitive\r\nload. At the population level, a linear decoding approach revealed a hierarchy in the\r\nrepresentation of task variables that changed with learning. In the high-dimensional space of\r\npopulation activity, the representation of contexts was specific to each position in the maze, and\r\ncould thus be better decoded if the position was known. The decoding of position did not improve\r\nwith knowledge of other variables. As learning progressed, the hippocampal code underwent a\r\nreorganisation of high-variance directions in population activity, identified by principal\r\ncomponent analysis. I found that dominant dimensions started carrying increasing amounts of\r\ninformation about task context specifically at those positions where it mattered for task\r\nperformance. When I contrasted this with variables less relevant to task performance (e.g.\r\nmovement direction), I did not observe differences in decoding quality over positions nor a\r\nreduction of dimensionality with learning.\r\nOverall, the largest changes in CA1 neural response with task learning happened in a\r\nmatter of a few trials; over days, changes undetectable in single-cell statistics were responsible\r\nfor re-structuring the hierarchy of neural representations at the population level; these changes\r\nwere task-specific and reflected different stages of learning. This indicates that complex task\r\nlearning may involve different magnitudes of response modulation in CA1, which happen at\r\nspecific time scales linked to behaviour.","lang":"eng"}],"citation":{"apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024.","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024."},"month":"01","date_created":"2024-01-16T14:25:21Z","project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"status":"public","doi":"10.15479/at:ista:14821","OA_place":"publisher","language":[{"iso":"eng"}],"degree_awarded":"PhD","article_processing_charge":"No","_id":"14821","ddc":["570"],"supervisor":[{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","orcid":"0000-0002-5193-4036"}],"oa":1,"date_updated":"2026-04-07T13:21:56Z","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"author":[{"first_name":"Heloisa","full_name":"Chiossi, Heloisa","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","orcid":"0009-0004-2973-278X","last_name":"Chiossi"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"file":[{"file_size":8656268,"access_level":"closed","file_name":"PhD_Thesis_190124.docx","file_id":"14838","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"hchiossi","checksum":"d3fa3de1abd5af5204c13e9d55375615","date_created":"2024-01-19T11:04:05Z","embargo_to":"open_access","relation":"source_file","date_updated":"2025-01-19T23:30:04Z"},{"date_created":"2024-01-19T11:03:59Z","relation":"main_file","date_updated":"2025-01-19T23:30:04Z","access_level":"open_access","file_size":6567275,"file_name":"PhD_Thesis_190124.pdf","file_id":"14839","content_type":"application/pdf","embargo":"2025-01-19","creator":"hchiossi","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd"}],"publication_status":"published","date_published":"2024-01-19T00:00:00Z","page":"89","type":"dissertation","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"file_date_updated":"2025-01-19T23:30:04Z","day":"19"},{"status":"public","project":[{"_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","grant_number":"692692","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glutamatergic synapse"},{"name":"Synaptic communication in neuronal microcircuits","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Z00312"},{"name":"Mechanisms of GABA release in hippocampal circuits","grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5"},{"name":"Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse","grant_number":"25383","_id":"26B66A3E-B435-11E9-9278-68D0E5697425"}],"date_created":"2024-03-11T10:09:54Z","month":"03","citation":{"chicago":"Chen, JingJing. “Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>.","ista":"Chen J. 2024. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. Institute of Science and Technology Austria.","short":"J. Chen, Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse, Institute of Science and Technology Austria, 2024.","apa":"Chen, J. (2024). <i>Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15101\">https://doi.org/10.15479/at:ista:15101</a>","mla":"Chen, JingJing. <i>Developmental Transformation of Nanodomain Coupling between Ca2+ Channels and Release Sensors at a Central GABAergic Synapse</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>.","ieee":"J. Chen, “Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse,” Institute of Science and Technology Austria, 2024.","ama":"Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15101\">10.15479/at:ista:15101</a>"},"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:15101","OA_place":"publisher","supervisor":[{"last_name":"Jonas","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M"}],"ddc":["570"],"_id":"15101","article_processing_charge":"No","oa":1,"year":"2024","has_accepted_license":"1","ec_funded":1,"publisher":"Institute of Science and Technology Austria","title":"Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"The coupling between presynaptic Ca2+ channels and release sensors is a key factor that\r\ndetermines speed and efficacy of synapse transmission. At some excitatory synapses,\r\nchannel–sensor coupling becomes tighter during development, and tightening is often\r\nassociated with a switch in the reliance on different Ca2+ channel subtypes. However, the\r\ncoupling topography at many synapses remains unknown, and it is unclear how it changes\r\nduring development. To address this question, we analyzed the coupling configuration at the\r\ncerebellar basket cell (BC) to Purkinje cell (PC) synapse at different developmental stages,\r\ncombining biophysical analysis, structural analysis, and modeling.\r\nQuantal analysis of BC–PC indicated that release probability decreased, while the\r\nnumber of functional sites increased during development. Although transmitter release\r\npersistently relied on P/Q-type Ca2+ channels in the time period postnatal day 7–23, effects\r\nof the Ca2+ chelator EGTA and BAPTA applied by intracellular pipette perfusion decreased\r\nduring development, indicative of tightening of source-sensor coupling. Furthermore,\r\npresynaptic action potentials became shorter during development, suggesting reduced\r\nefficacy of Ca2+ channel activation.\r\nStructural analysis by freeze-fracture replica labeling (FRL) and transmission electron\r\nmicroscopy (EM) indicated that presynaptic P/Q-type Ca2+ channels formed nanoclusters\r\nthroughout development, whereas docked vesicles were only clustered at later\r\ndevelopmental stages. The number of functional release sites correlated better with the AZ\r\nnumber early in development, but match better with the Ca2+ channel cluster number at later\r\nstages.\r\nModeling suggested a developmental transformation from a more random to a more\r\nclustered coupling nanotopography. Thus, presynaptic signaling developmentally approaches\r\na point-to-point configuration, optimizing speed, reliability, and energy efficiency of synaptic\r\ntransmission."}],"publication_status":"published","file":[{"access_level":"closed","file_size":11271363,"file_name":"Thesis_Jingjing CHEN.docx","file_id":"15104","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"db4947474ffa271e66c254b6fe876a55","creator":"jchen","date_created":"2024-03-11T14:10:58Z","embargo_to":"open_access","relation":"source_file","date_updated":"2024-04-02T22:30:03Z"},{"relation":"main_file","date_updated":"2024-04-02T22:30:03Z","date_created":"2024-03-11T14:11:06Z","file_id":"15105","embargo":"2024-04-01","content_type":"application/pdf","creator":"jchen","checksum":"a5eeae8b5702cd540f5d03469bc33dde","access_level":"open_access","file_size":16627311,"file_name":"Thesis_Jingjing CHEN_merged.pdf"}],"alternative_title":["ISTA Thesis"],"date_published":"2024-03-11T00:00:00Z","file_date_updated":"2024-04-02T22:30:03Z","day":"11","department":[{"_id":"GradSch"},{"_id":"PeJo"}],"type":"dissertation","page":"84","related_material":{"record":[{"id":"14843","status":"public","relation":"part_of_dissertation"}]},"acknowledged_ssus":[{"_id":"EM-Fac"}],"corr_author":"1","date_updated":"2026-04-07T13:24:22Z","author":[{"first_name":"JingJing","full_name":"Chen, JingJing","id":"2C4E65C8-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"}],"publication_identifier":{"issn":["2663-337X"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version"},{"OA_place":"publisher","doi":"10.15479/at:ista:18471","degree_awarded":"PhD","language":[{"iso":"eng"}],"month":"10","citation":{"ista":"Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria.","chicago":"Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>.","short":"N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024.","apa":"Agudelo Duenas, N. (2024). <i>Visualizing the neuronal transcriptional landscape with tissue context</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18471\">https://doi.org/10.15479/at:ista:18471</a>","ieee":"N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024.","mla":"Agudelo Duenas, Nathalie. <i>Visualizing the Neuronal Transcriptional Landscape with Tissue Context</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>.","ama":"Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18471\">10.15479/at:ista:18471</a>"},"status":"public","date_created":"2024-10-26T20:02:42Z","project":[{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2548AE96-B435-11E9-9278-68D0E5697425","grant_number":"W1232","call_identifier":"FWF","name":"Molecular Drug Targets"}],"oa":1,"_id":"18471","article_processing_charge":"No","supervisor":[{"first_name":"Johann G","full_name":"Danzl, Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"ec_funded":1,"has_accepted_license":"1","year":"2024","abstract":[{"text":"Spatial omics technologies are enriching our understanding of complex biological samples, by\r\nallowing us to study their molecular composition while preserving the spatial relationships\r\nbetween molecules in their native context. As the field continues to advance, there are\r\ntechnical challenges that need to be addressed in order to take full advantage of the spatial\r\ncapabilities of these methods. In this work, I present two technical developments that I\r\nestablished for multiplexed error robust FISH (MERFISH) throughout my PhD: (1) pushing the\r\nspatial resolution limits to the nanoscale, and (2) adding rich tissue context to the mouse brain\r\ntranscriptome. To achieve nanoscale resolution with MERFISH in cultured cells, I combined it\r\nwith stimulated emission depletion (STED) and expansion microscopy (ExM) to achieve a\r\nspatial resolution as low as ~20 nm, and explored the compatibility of MERFISH with singlemolecule localization microscopy (SMLM) techniques. To visualize targeted mRNAs in mouse\r\nbrain tissue, I applied the comprehensive analysis of tissues across scales (CATS) toolbox, which\r\nprovides an unbiased morphological readout by labeling the extracellular domain. I\r\nsuccessfully established this method, which we call CATS-MERFISH-ExM, to work with thick\r\nmouse brain slices, being able to extract transcriptomics information with 3D tissue context.\r\nCATS-MERFISH-ExM enabled us to identify cell types and further visualize the subcellular\r\ndistribution of transcripts in mouse brain tissue, shedding light on the neuropil-specific\r\ntranscriptome. This method provides integrated information on cellular structure and\r\ntranscriptomes in situ, and could potentially be applied with other modalities, opening new\r\navenues for scientific discovery. ","lang":"eng"}],"title":"Visualizing the neuronal transcriptional landscape with tissue context","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)"},"publisher":"Institute of Science and Technology Austria","file":[{"file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx","file_size":183077763,"access_level":"closed","file_id":"18475","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"nagudelo","checksum":"6d7c7725d040d8debc070dcb35ac965d","date_created":"2024-10-26T22:29:06Z","embargo_to":"open_access","date_updated":"2025-05-05T22:30:04Z","relation":"source_file"},{"creator":"nagudelo","checksum":"52f9c0bf2bdafa3baf827b73814a53ff","embargo":"2025-05-05","file_id":"18476","content_type":"application/pdf","file_size":47027710,"access_level":"open_access","file_name":"PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf","relation":"main_file","date_updated":"2025-05-05T22:30:04Z","date_created":"2024-10-26T23:13:33Z"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"JoDa"}],"type":"dissertation","page":"97","file_date_updated":"2025-05-05T22:30:04Z","day":"28","date_published":"2024-10-28T00:00:00Z","date_updated":"2026-04-14T08:34:37Z","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"ScienComp"}],"oa_version":"Published Version","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"isbn":["978-3-99078-044-2"],"issn":["2663-337X"]},"author":[{"first_name":"Nathalie","full_name":"Agudelo Duenas, Nathalie","last_name":"Agudelo Duenas","id":"40E7F008-F248-11E8-B48F-1D18A9856A87"}]},{"month":"11","citation":{"short":"D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024.","ista":"Gupta D. 2024. Visual adaptations to natural statistics. Institute of Science and Technology Austria.","chicago":"Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>.","mla":"Gupta, Divyansh. <i>Visual Adaptations to Natural Statistics</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>.","ieee":"D. Gupta, “Visual adaptations to natural statistics,” Institute of Science and Technology Austria, 2024.","ama":"Gupta D. Visual adaptations to natural statistics. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18574\">10.15479/at:ista:18574</a>","apa":"Gupta, D. (2024). <i>Visual adaptations to natural statistics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18574\">https://doi.org/10.15479/at:ista:18574</a>"},"status":"public","date_created":"2024-11-20T21:30:44Z","project":[{"name":"Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses","_id":"bdaf81a8-d553-11ed-ba76-c95961984540","grant_number":"101086580"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"756502","name":"Circuits of Visual Attention"}],"doi":"10.15479/at:ista:18574","OA_place":"publisher","degree_awarded":"PhD","language":[{"iso":"eng"}],"_id":"18574","article_processing_charge":"No","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"ddc":["573"],"oa":1,"OA_embargo":"12","year":"2024","has_accepted_license":"1","ec_funded":1,"tmp":{"short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)"},"title":"Visual adaptations to natural statistics","publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Biological vision is unlike a camera; rather than transmitting light information faithfully, early\r\nvisual circuits process the visual scene to convey only the relevant information in an efficient\r\nmanner. Consequentially, the nature of this visual processing then depends on what is the\r\nrelevant information in a scene and on the notion of efficiency. In this work, I study how visual\r\nprocessing is modulated by two different variations in the visual scene. First, I discovered that\r\nin the mouse (Mus musculus) retina, Retinal Ganglion Cells in the upper and lower visual\r\nfield have differences in the center surround structure of their receptive fields. Comparison\r\nwith models of efficient coding show that this adaptation likely evolved to cope with the\r\nbrightness gradient from the sky to the ground that is pervasive in natural scenes. In the\r\nsecond project, I study how the downstream neurons in the Superior Colliculus dynamically\r\nchange their temporal selectivity depending on the ambient luminance and behavioral state.\r\nAs the scene gets darker or when the animal is is less aroused, the neuronal responses get\r\nlaggier, while still maintaining their relative timing with respect to the population. Overall, this\r\nwork emphasises the need to understand visual processing in the context of specific demands\r\nof the animal in its the environment. The adaptive changes in the visual system, from the\r\nretinal ganglion cells to the superior colliculus, highlight the intricate ways in which biological\r\nvision optimizes the processing of visual information.\r\n","lang":"eng"}],"file":[{"date_created":"2024-11-25T14:44:03Z","embargo_to":"open_access","relation":"source_file","date_updated":"2025-11-11T23:30:02Z","access_level":"closed","file_size":75512262,"file_name":"PhD Thesis - Divyansh Gupta.zip","content_type":"application/zip","file_id":"18589","checksum":"ebb000d361c36b22ed6e639a931c6b7c","creator":"dgupta"},{"date_created":"2024-11-26T11:43:19Z","relation":"main_file","date_updated":"2025-11-11T23:30:02Z","file_size":6412619,"access_level":"open_access","file_name":"PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf","file_id":"18591","content_type":"application/pdf","embargo":"2025-11-11","checksum":"1282401eb71598bc311058b0fcefc6a1","creator":"dgupta"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","date_published":"2024-11-22T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"type":"dissertation","page":"86","file_date_updated":"2025-11-11T23:30:02Z","day":"22","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"12349","status":"public"},{"id":"12370","status":"public","relation":"research_data"}]},"acknowledgement":"This work would have been impossible without the Scientific Service Units of IST Austria. The resources and expertise provided by Scientific Computing (especially Alois Schlögl), the MIBA Machine Shop (especially Todor Asenov), the Preclinical Facility (especially Freyja Langer), the Library, the Lab Support Facility and the Imaging and Optics Facility were the essential bedrock I could build upon. I would also like to thank IT support at ISTA for powering through remote work and a cyberattack.\r\nI am grateful for having been funded initially by the European Union Horizon 2020 Marie Skłodowska-Curie grant 665385 and later by Prof. Maximilian Joesch's the European Research Council Starting (756502) and Consolidator (101086580) Grants.","date_updated":"2026-04-07T13:24:48Z","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"id":"2A485EBE-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","orcid":"0000-0001-7400-6665","first_name":"Divyansh","full_name":"Gupta, Divyansh"}],"publication_identifier":{"isbn":["978-3-99078-050-3"],"issn":["2663-337X"]},"oa_version":"Published Version"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","author":[{"first_name":"Andrea","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","last_name":"Mrnjavac"}],"publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"CampIT"}],"related_material":{"record":[{"status":"public","id":"12521","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"18549","status":"public"}]},"date_updated":"2026-04-07T13:22:45Z","corr_author":"1","date_published":"2024-11-11T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"BeVi"}],"page":"181","type":"dissertation","file_date_updated":"2025-05-11T22:30:04Z","day":"11","file":[{"file_name":"AMrnjavac_thesis_library.docx","file_size":26870629,"access_level":"closed","title":"Early stages of sex chromosome evolution","file_id":"18551","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","checksum":"3e48b163c22114ef5d5371f758668289","creator":"amrnjava","date_created":"2024-11-13T12:15:28Z","embargo_to":"open_access","date_updated":"2025-05-11T22:30:04Z","relation":"source_file"},{"creator":"amrnjava","checksum":"3ead60c1b678e7dcf018043aef3b5db2","file_id":"18552","content_type":"application/pdf","embargo":"2025-05-11","title":"Early stages of sex chromosome evolution","file_name":"AMrnjavac_thesis_library.pdf","access_level":"open_access","file_size":4228766,"date_updated":"2025-05-11T22:30:04Z","relation":"main_file","date_created":"2024-11-13T12:15:54Z"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","title":"Early stages of sex chromosome evolution","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"publisher":"Institute of Science and Technology Austria","abstract":[{"text":"Sex chromosomes and autosomes exhibit very different evolutionary dynamics.\r\nThe Y chromosome usually degenerates, leaving many X-linked loci hemizygous in\r\nmales. Since recessive X-linked mutations are always exposed to selection in males,\r\nselection is more efficient on the X chromosome than on autosomes on recessive\r\nmutations, leading to faster adaptation on the X chromosome than other genomic\r\nregions, if beneficial mutations are on average recessive (known as the Faster-X\r\neffect). In the presence of the functional, but non-recombining gametolog on the Y (as\r\nis often the case in young non-recombining regions), recessive mutations are\r\nsheltered from selection on the X chromosome. We model this scenario and show that\r\nthe efficiency of selection is reduced on diploid X loci due to sheltering by the Y\r\nchromosome. Reduced efficiency of selection leads to slower adaptation and\r\nincreased accumulation of deleterious mutations (Slower-X effect). We extended this\r\nmodel to explore the effect of sex-specific selection on degeneration of sex\r\nchromosomes, showing theoretically that male-limited genes degenerate on the X\r\nchromosome and female-biased genes degenerate on the Y chromosome. This\r\nprediction depends on the effective population size and the mutation rate, explaining\r\nthe variety of sex chromosome degeneration patterns observed in nature.\r\nTo test for direct evidence of a Slower-X (or Slower-Z) effect, we analyzed the\r\nZW sex chromosomes of the flatworm Schistosoma japonicum, which have a very\r\nyoung non-recombining region with non-degenerated W. Diploid Z-linked genes have\r\nhigher ratios of non-synonymous to synonymous polymorphisms than autosomal\r\ngenes, supporting reduced efficiency of selection on the diploid Z region. These results\r\nprovide evidence of sheltering by the W chromosome, a mechanism that could\r\ncontribute to Z (X) chromosome degeneration, and illustrate contrasting evolutionary\r\npatterns in old and young sex chromosome regions. In addition, genes with sexspecific patterns of expression show opposite patterns of selection in the young\r\n(diploid) and old (hemizygous) Z, showing the complex manner in which sex-specific selection shapes the evolutionary patterns of sex chromosomes. ","lang":"eng"}],"keyword":["Sex chromosomes","evolution","selection","sheltering"],"OA_embargo":"6","has_accepted_license":"1","year":"2024","_id":"18531","article_processing_charge":"No","supervisor":[{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4579-8306","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"ddc":["576"],"oa":1,"month":"11","citation":{"ama":"Mrnjavac A. Early stages of sex chromosome evolution. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>","ieee":"A. Mrnjavac, “Early stages of sex chromosome evolution,” Institute of Science and Technology Austria, 2024.","mla":"Mrnjavac, Andrea. <i>Early Stages of Sex Chromosome Evolution</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18531\">10.15479/at:ista:18531</a>.","apa":"Mrnjavac, A. (2024). <i>Early stages of sex chromosome evolution</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>","short":"A. Mrnjavac, Early Stages of Sex Chromosome Evolution, Institute of Science and Technology Austria, 2024.","chicago":"Mrnjavac, Andrea. “Early Stages of Sex Chromosome Evolution.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18531\">https://doi.org/10.15479/at:ista:18531</a>.","ista":"Mrnjavac A. 2024. Early stages of sex chromosome evolution. Institute of Science and Technology Austria."},"status":"public","date_created":"2024-11-11T08:40:45Z","OA_place":"publisher","doi":"10.15479/at:ista:18531","degree_awarded":"PhD","language":[{"iso":"eng"}]},{"_id":"18642","article_processing_charge":"No","supervisor":[{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard"}],"ddc":["576"],"oa":1,"month":"12","citation":{"apa":"Machnik, N. N. (2024). <i>Algorithms for causal learning and comparative analysis for genomic data</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>","ieee":"N. N. Machnik, “Algorithms for causal learning and comparative analysis for genomic data,” Institute of Science and Technology Austria, 2024.","mla":"Machnik, Nick N. <i>Algorithms for Causal Learning and Comparative Analysis for Genomic Data</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>.","ama":"Machnik NN. Algorithms for causal learning and comparative analysis for genomic data. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:18642\">10.15479/at:ista:18642</a>","ista":"Machnik NN. 2024. Algorithms for causal learning and comparative analysis for genomic data. Institute of Science and Technology Austria.","chicago":"Machnik, Nick N. “Algorithms for Causal Learning and Comparative Analysis for Genomic Data.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:18642\">https://doi.org/10.15479/at:ista:18642</a>.","short":"N.N. Machnik, Algorithms for Causal Learning and Comparative Analysis for Genomic Data, Institute of Science and Technology Austria, 2024."},"status":"public","project":[{"name":"Improving estimation and prediction of common complex disease risk","grant_number":"PCEGP3_181181","_id":"9B8D11D6-BA93-11EA-9121-9846C619BF3A"}],"date_created":"2024-12-10T13:49:15Z","OA_place":"publisher","doi":"10.15479/at:ista:18642","degree_awarded":"PhD","language":[{"iso":"eng"}],"title":"Algorithms for causal learning and comparative analysis for genomic data","publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"This thesis consists of two pieces of work in the broader feld of computational biology,\r\nboth of which are methods for the analysis of large scale biological data, implemented in\r\nefcient software.\r\nChapter 2 introduces a statistical software for causal discovery and inference from observed\r\ngenetic marker and phenotypic trait data. We explore in simulation how well the method\r\ncan fne-map genetic efects, fnd the correct causal structure among tens of traits and\r\nmillions of genetic markers, and infer the causal efect size for the discovered causal\r\nrelations. We then apply the method to 8 million markers and 17 traits from the UK\r\nBiobank and show that many relationships found with other methods are likely due to\r\nthe efects of hidden confounders.\r\nChapter 3 describes how this method can be applied to longitudinal data. I show how one\r\ncan incorporate the background knowledge present in the known order of measurements to\r\nimprove the accuracy of the causal discovery process, and explore the method’s ability to\r\nidentify age specifc genetic efects, and how the error rates of this recovery are infuenced\r\nby missing data due to diferent censoring mechanisms.\r\nChapter 4 introduces a statistical software for the comparison of chromatin contact maps\r\nbased on the structural similarity index. We explore the robustness of the method to\r\nnoise and size diferences of the compared maps, show how it can measure evolutionary\r\nconservation of topological features by providing a similarity ranking of syntenic regions,\r\nand fnally how it can detect alterations in 3D genome structure due to genetic mutations\r\nin samples of medical relevance.\r\n"}],"has_accepted_license":"1","year":"2024","date_published":"2024-12-11T00:00:00Z","department":[{"_id":"GradSch"},{"_id":"MaRo"}],"page":"138","type":"dissertation","file_date_updated":"2025-06-12T22:30:02Z","day":"11","file":[{"date_updated":"2025-06-12T22:30:02Z","relation":"main_file","date_created":"2024-12-11T11:59:54Z","content_type":"application/pdf","file_id":"18649","embargo":"2025-06-12","creator":"nmachnik","checksum":"d45e4d170f9a70a1f69b44b99bd058e4","file_name":"NickMachnikThesisFinal_pdfa_conv.pdf","access_level":"open_access","file_size":12845009},{"file_id":"18650","content_type":"application/zip","creator":"nmachnik","checksum":"f88c9acc62002395ec4dcbdb5eea8b82","file_size":14189810,"access_level":"closed","file_name":"thesis.zip","embargo_to":"open_access","relation":"source_file","date_updated":"2025-06-12T22:30:02Z","date_created":"2024-12-11T11:59:34Z"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_identifier":{"issn":["2663-337X"]},"author":[{"full_name":"Machnik, Nick N","first_name":"Nick N","last_name":"Machnik","orcid":"0000-0001-6617-9742","id":"3591A0AA-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"18648","relation":"part_of_dissertation"},{"status":"public","id":"8707","relation":"part_of_dissertation"}]},"acknowledgement":"I would like to thank the Swiss National Science Foundation for funding parts of this work\r\nthrough the Eccellenza Grant \"Improving estimation and prediction of common complex\r\ndisease risk\" with grant number PCEGP3_181181.","date_updated":"2026-04-07T13:23:06Z","corr_author":"1"}]