--- OA_place: repository OA_type: green _id: '17426' 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." 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" article_processing_charge: No arxiv: 1 author: - first_name: Bernd full_name: Prach, Bernd id: 2D561D42-C427-11E9-89B4-9C1AE6697425 last_name: Prach - first_name: Fabio full_name: Brau, Fabio last_name: Brau - first_name: Giorgio full_name: Buttazzo, Giorgio last_name: Buttazzo - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Prach B, Brau F, Buttazzo G, Lampert C. 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition. Computer Vision Foundation; 2024:24574-24583. doi:10.1109/CVPR52733.2024.02320' apa: 'Prach, B., Brau, F., Buttazzo, G., & Lampert, C. (2024). 1-Lipschitz layers compared: Memory, speed, and certifiable robustness. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 24574–24583). Seattle, WA, United States: Computer Vision Foundation. https://doi.org/10.1109/CVPR52733.2024.02320' chicago: 'Prach, Bernd, Fabio Brau, Giorgio Buttazzo, and Christoph Lampert. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 24574–83. Computer Vision Foundation, 2024. https://doi.org/10.1109/CVPR52733.2024.02320.' ieee: 'B. Prach, F. Brau, G. Buttazzo, and C. Lampert, “1-Lipschitz layers compared: Memory, speed, and certifiable robustness,” in Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Seattle, WA, United States, 2024, pp. 24574–24583.' 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.' mla: 'Prach, Bernd, et al. “1-Lipschitz Layers Compared: Memory, Speed, and Certifiable Robustness.” Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, Computer Vision Foundation, 2024, pp. 24574–83, doi:10.1109/CVPR52733.2024.02320.' 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. conference: end_date: 2024-06-22 location: Seattle, WA, United States name: 'CVPR: Conference on Computer Vision and Pattern Recognition' start_date: 2024-06-16 corr_author: '1' date_created: 2024-08-14T08:42:32Z date_published: 2024-06-01T00:00:00Z date_updated: 2026-07-27T12:47:43Z day: '01' department: - _id: GradSch - _id: ChLa doi: 10.1109/CVPR52733.2024.02320 external_id: arxiv: - '2311.16833' isi: - '001344387500055' has_accepted_license: '1' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.16833 month: '06' oa: 1 oa_version: Preprint page: 24574-24583 publication: Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition publication_status: published publisher: Computer Vision Foundation quality_controlled: '1' related_material: link: - relation: software url: https://github.com/berndprach/1LipschitzLayersCompared record: - id: '19759' relation: dissertation_contains status: public status: public title: '1-Lipschitz layers compared: Memory, speed, and certifiable robustness' type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- OA_place: repository _id: '18874' 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." article_number: '2412.04245' article_processing_charge: No arxiv: 1 author: - first_name: Bernd full_name: Prach, Bernd id: 2D561D42-C427-11E9-89B4-9C1AE6697425 last_name: Prach - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Prach B, Lampert C. Intriguing properties of robust classification. arXiv. doi:10.48550/arXiv.2412.04245 apa: Prach, B., & Lampert, C. (n.d.). Intriguing properties of robust classification. arXiv. https://doi.org/10.48550/arXiv.2412.04245 chicago: Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2412.04245. ieee: B. Prach and C. Lampert, “Intriguing properties of robust classification,” arXiv. . ista: Prach B, Lampert C. Intriguing properties of robust classification. arXiv, 2412.04245. mla: Prach, Bernd, and Christoph Lampert. “Intriguing Properties of Robust Classification.” ArXiv, 2412.04245, doi:10.48550/arXiv.2412.04245. short: B. Prach, C. Lampert, ArXiv (n.d.). corr_author: '1' date_created: 2025-01-24T16:57:29Z date_published: 2024-12-05T00:00:00Z date_updated: 2026-07-27T12:47:43Z day: '05' department: - _id: GradSch - _id: ChLa doi: 10.48550/arXiv.2412.04245 external_id: arxiv: - '2412.04245' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2412.04245 month: '12' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: record: - id: '20455' relation: later_version status: public - id: '19759' relation: dissertation_contains status: public status: public title: Intriguing properties of robust classification type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- APC_amount: 2748 EUR OA_place: publisher OA_type: hybrid _id: '17634' 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. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. N. Mazzocchi was affiliated with ISTA when his collaboration started. alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) arxiv: 1 author: - first_name: Marek full_name: Chalupa, Marek id: 87e34708-d6c6-11ec-9f5b-9391e7be2463 last_name: Chalupa - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Nicolas Adrien full_name: Mazzocchi, Nicolas Adrien id: b26baa86-3308-11ec-87b0-8990f34baa85 last_name: Mazzocchi - first_name: Naci E full_name: Sarac, Naci E id: 8C6B42F8-C8E6-11E9-A03A-F2DCE5697425 last_name: Sarac citation: ama: 'Chalupa M, Henzinger TA, Mazzocchi NA, Sarac NE. QuAK: Quantitative Automata Kit. In: 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation. Vol 15222. Springer Nature; 2024:3-20. doi:10.1007/978-3-031-75387-9_1' apa: 'Chalupa, M., Henzinger, T. A., Mazzocchi, N. A., & Sarac, N. E. (2024). QuAK: Quantitative Automata Kit. In 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation (Vol. 15222, pp. 3–20). Crete, Greece: Springer Nature. https://doi.org/10.1007/978-3-031-75387-9_1' chicago: 'Chalupa, Marek, Thomas A Henzinger, Nicolas Adrien Mazzocchi, and Naci E Sarac. “QuAK: Quantitative Automata Kit.” In 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, 15222:3–20. Springer Nature, 2024. https://doi.org/10.1007/978-3-031-75387-9_1.' ieee: 'M. Chalupa, T. A. Henzinger, N. A. Mazzocchi, and N. E. Sarac, “QuAK: Quantitative Automata Kit,” in 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, Crete, Greece, 2024, vol. 15222, 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.' mla: 'Chalupa, Marek, et al. “QuAK: Quantitative Automata Kit.” 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation, vol. 15222, Springer Nature, 2024, pp. 3–20, doi:10.1007/978-3-031-75387-9_1.' 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. conference: end_date: 2024-10-31 location: Crete, Greece name: 'ISoLA: International Symposium on Leveraging Applications' start_date: 2024-10-27 corr_author: '1' date_created: 2024-09-05T14:27:08Z date_published: 2024-10-26T00:00:00Z date_updated: 2026-07-27T12:48:18Z day: '26' ddc: - '000' department: - _id: GradSch - _id: ToHe doi: 10.1007/978-3-031-75387-9_1 ec_funded: 1 external_id: arxiv: - '2409.03569' isi: - '001419008700001' file: - access_level: open_access checksum: 43e432f82be376434b358f3dd7a94b71 content_type: application/pdf creator: esarac date_created: 2024-09-05T14:26:02Z date_updated: 2024-09-05T14:26:02Z file_id: '17635' file_name: isola24.pdf file_size: 847422 relation: main_file success: 1 - access_level: open_access checksum: 6bc04f07bb5612c0e7ea00ac121a69b6 content_type: application/pdf creator: dernst date_created: 2025-01-21T14:39:49Z date_updated: 2025-01-21T14:39:49Z file_id: '18865' file_name: 2024_LNCS_Chalupa.pdf file_size: 1358706 relation: main_file success: 1 file_date_updated: 2025-01-21T14:39:49Z has_accepted_license: '1' intvolume: ' 15222' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 3-20 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 12th International Symposium on Leveraging Applications of Formal Methods, Verification and Validation publication_identifier: eissn: - 1611-3349 isbn: - '9783031753862' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '20147' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'QuAK: Quantitative Automata Kit' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15222 year: '2024' ... --- OA_embargo: '20' OA_place: publisher _id: '18681' acknowledged_ssus: - _id: Bio - _id: PreCl - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Mojtaba full_name: Tavakoli, Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 citation: 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:10.15479/at:ista:18681' apa: '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. https://doi.org/10.15479/at:ista:18681' 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. https://doi.org/10.15479/at:ista:18681.' 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.' ista: 'Tavakoli M. 2024. Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy. Institute of Science and Technology Austria.' mla: 'Tavakoli, Mojtaba. 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, doi:10.15479/at:ista:18681.' 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.' corr_author: '1' das_tickbox: '1' date_created: 2024-12-19T02:30:39Z date_published: 2024-12-20T00:00:00Z date_updated: 2026-07-28T08:33:52Z day: '20' ddc: - '600' - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:18681 doi_confirm: '1' file: - access_level: closed checksum: b61651d417cafddd740a8528f46068c5 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: mtavakol date_created: 2024-12-20T10:23:17Z date_updated: 2024-12-20T10:31:37Z file_id: '18699' file_name: Thesis_Mojtaba Tavakoli_.docx file_size: 118593521 relation: source_file - access_level: closed checksum: c80bcfd1a34c23afc3538052325283e5 content_type: application/pdf creator: mtavakol date_created: 2024-12-20T10:25:12Z date_updated: 2026-07-28T08:33:51Z embargo: 2027-08-01 embargo_to: open_access file_id: '18700' file_name: Thesis_Mojtaba Tavakoli_.pdf file_size: 63885521 relation: main_file file_date_updated: 2026-07-28T08:33:51Z has_accepted_license: '1' language: - iso: eng month: '12' oa_version: Published Version page: '230' 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 publication_identifier: isbn: - 978-3-99078-048-0 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11160' relation: part_of_dissertation status: public - id: '18688' relation: part_of_dissertation status: public - id: '18677' relation: part_of_dissertation status: public - id: '18689' relation: part_of_dissertation status: public status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: 'Developing molecular and structural tools for studying brain architecture with super resolution expansion microscopy. LICONN: Molecularly-informed connectomics reconstruction with light microscopy' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: publisher _id: '18132' abstract: - lang: eng text: "In this thesis, we are dealing with both arithmetic and geometric problems coming from the\r\nstudy of rational points with a particular focus on function fields over finite fields:\r\n(1) Using the circle method we produce upper bounds for the number of rational points of\r\nbounded height on diagonal cubic surfaces and fourfolds over Fq(t). This is based on\r\njoint work with Leonhard Hochfilzer.\r\n(2) We study rational points on smooth complete intersections X defined by cubic and\r\nquadratic hypersurfaces over Fq(t). We refine the Farey dissection of the “unit square”\r\ndeveloped by Vishe [202] and use the circle method with a Kloosterman refinement to\r\nestablish an asymptotic formula for the number of rational points of bounded height on\r\nX when dim(X) ≥ 23. Under the same hypotheses, we also verify weak approximation.\r\n(3) In joint work with Hochfilzer, we obtain upper bounds for the number of rational points of\r\nbounded height on del Pezzo surfaces of low degree over any global field. Our approach\r\nis to take hyperplane sections, which reduces the problem to uniform estimates for the\r\nnumber of rational points on curves.\r\n(4) We develop a version of the circle method capable of counting Fq-points on jet schemes\r\nof moduli spaces of rational curves on hypersurfaces. Combining this with a spreading\r\nout argument and a result of Mustaţă [150], this allows us to show that these moduli\r\nspaces only have canonical singularities under suitable assumptions on the degree and the\r\ndimension.\r\nIn addition, we give an overview of guiding questions and conjectures in the field of rational\r\npoints and explain the basic mechanism underlying the circle method.\r\n" alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Jakob full_name: Glas, Jakob id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb last_name: Glas citation: ama: Glas J. Counting rational points over function fields. 2024. doi:10.15479/at:ista:18132 apa: Glas, J. (2024). Counting rational points over function fields. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18132 chicago: Glas, Jakob. “Counting Rational Points over Function Fields.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18132. ieee: J. Glas, “Counting rational points over function fields,” Institute of Science and Technology Austria, 2024. ista: Glas J. 2024. Counting rational points over function fields. Institute of Science and Technology Austria. mla: Glas, Jakob. Counting Rational Points over Function Fields. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18132. short: J. Glas, Counting Rational Points over Function Fields, Institute of Science and Technology Austria, 2024. corr_author: '1' das_tickbox: '0' date_created: 2024-09-23T18:58:08Z date_published: 2024-09-23T00:00:00Z date_updated: 2026-07-29T10:41:27Z day: '23' ddc: - '512' degree_awarded: PhD department: - _id: GradSch - _id: TiBr doi: 10.15479/at:ista:18132 doi_confirm: '1' file: - access_level: closed checksum: 2f8cf5cefdab108b1979caa8146cae9a content_type: application/x-zip-compressed creator: jglas date_created: 2024-09-23T18:49:22Z date_updated: 2024-09-23T18:49:22Z file_id: '18133' file_name: PhDthesis (3).zip file_size: 5382106 relation: source_file - access_level: open_access checksum: 08bb6f14c42b47ff25882a2ce3ea0d8a content_type: application/pdf creator: jglas date_created: 2024-09-25T14:08:57Z date_updated: 2024-09-25T14:08:57Z file_id: '18140' file_name: example-phd.pdf file_size: 2380127 relation: main_file success: 1 file_date_updated: 2024-09-25T14:08:57Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '195' project: - _id: bd8a4fdc-d553-11ed-ba76-80a0167441a3 grant_number: P36278 name: Rational curves via function field analytic number theory publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '18293' relation: part_of_dissertation status: public - id: '18173' relation: part_of_dissertation status: public - id: '18295' relation: part_of_dissertation status: public - id: '18294' relation: part_of_dissertation status: public researchdata_availability: no status: public supervisor: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 supplementarymaterial: no title: Counting rational points over function fields tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: dissertation user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 year: '2024' ... --- _id: '14687' abstract: - lang: eng 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. 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. article_number: e202316476 article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Bhargavi full_name: Pant, Bhargavi id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112 last_name: Pant - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 2024;63(28). doi:10.1002/anie.202316476 apa: Jethwa, R. B., Mondal, S., Pant, B., & Freunberger, S. A. (2024). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202316476 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.” Angewandte Chemie International Edition. Wiley, 2024. https://doi.org/10.1002/anie.202316476. 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,” Angewandte Chemie International Edition, vol. 63, no. 28. Wiley, 2024. 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. mla: Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition, vol. 63, no. 28, e202316476, Wiley, 2024, doi:10.1002/anie.202316476. short: R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition 63 (2024). corr_author: '1' date_created: 2023-12-15T16:10:13Z date_published: 2024-07-08T00:00:00Z date_updated: 2026-07-29T12:57:15Z day: '08' ddc: - '540' department: - _id: StFr - _id: GradSch doi: 10.1002/anie.202316476 ec_funded: 1 external_id: isi: - '001241932700001' pmid: - '38095355' file: - access_level: open_access checksum: fe2c23454279eb9d76ed6ca9970c21c7 content_type: application/pdf creator: dernst date_created: 2024-07-16T11:54:46Z date_updated: 2024-07-16T11:54:46Z file_id: '17261' file_name: 2024_AngChemieInt_Jethwa.pdf file_size: 4766445 relation: main_file success: 1 file_date_updated: 2024-07-16T11:54:46Z has_accepted_license: '1' intvolume: ' 63' isi: 1 issue: '28' keyword: - General Chemistry - Catalysis language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '20607' relation: dissertation_contains status: public scopus_import: '1' status: public title: To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 63 year: '2024' ... --- OA_place: repository OA_type: green _id: '20071' abstract: - lang: eng text: Farkas established that a system of linear inequalities has a solution if and only if we cannot obtain a contradiction by taking a linear combination of the inequalities. We state and formally prove several Farkas-like theorems over linearly ordered fields in Lean 4. Furthermore, we extend duality theory to the case when some coefficients are allowed to take "infinite values". acknowledgement: We would like to thank David Bartl and Jasmin Blanchette for frequent consultations. We would also like to express gratitude to Andrew Yang for the proof of Finset.univ sum of zero when not and to Henrik B¨oving for a help with generalization from extended rationals to extended linearly ordered fields. We would also like to acknowledge Antoine Chambert-Loir, Apurva Nakade, Ya¨el Dillies, Richard Copley, Edward van de Meent, Markus Himmel, Mario Carneiro, and Kevin Buzzard. article_number: '2409.08119' article_processing_charge: No arxiv: 1 author: - first_name: Martin full_name: Dvorak, Martin id: 40ED02A8-C8B4-11E9-A9C0-453BE6697425 last_name: Dvorak orcid: 0000-0001-5293-214X - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov citation: ama: Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally  verified. arXiv. doi:10.48550/arXiv.2409.08119 apa: Dvorak, M., & Kolmogorov, V. (n.d.). Duality theory in linear optimization and its extensions -- formally  verified. arXiv. https://doi.org/10.48550/arXiv.2409.08119 chicago: Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally  Verified.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2409.08119. ieee: M. Dvorak and V. Kolmogorov, “Duality theory in linear optimization and its extensions -- formally  verified,” arXiv. . ista: Dvorak M, Kolmogorov V. Duality theory in linear optimization and its extensions -- formally  verified. arXiv, 2409.08119. mla: Dvorak, Martin, and Vladimir Kolmogorov. “Duality Theory in Linear Optimization and Its Extensions -- Formally  Verified.” ArXiv, 2409.08119, doi:10.48550/arXiv.2409.08119. short: M. Dvorak, V. Kolmogorov, ArXiv (n.d.). corr_author: '1' date_created: 2025-07-23T11:21:52Z date_published: 2024-09-12T00:00:00Z date_updated: 2026-07-29T12:56:51Z day: '12' department: - _id: GradSch - _id: VlKo doi: 10.48550/arXiv.2409.08119 external_id: arxiv: - '2409.08119' keyword: - Farkas lemma - linear programming - extended reals - calculus of inductive constructions language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2409.08119 month: '09' oa: 1 oa_version: Preprint publication: arXiv publication_status: draft related_material: link: - description: full version of all definitions, statement, and proofs relation: software url: https://github.com/madvorak/duality/tree/v3.2 record: - id: '22607' relation: later_version status: public - id: '21393' relation: dissertation_contains status: public status: public title: Duality theory in linear optimization and its extensions -- formally verified type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_type: closed access _id: '18266' abstract: - lang: eng text: Matrix games are the most basic model in game theory, and yet robustness with respect to small perturbations of the matrix entries is not fully understood. In this paper, we introduce value positivity and uniform value positivity, two properties that refine the notion of optimality in the context of polynomially perturbed matrix games. The first concept captures how the value depends on the perturbation parameter, and the second consists of the existence of a fixed strategy that guarantees the value of the unperturbed matrix game for every sufficiently small positive parameter. We provide polynomial-time algorithms to check whether a polynomially perturbed matrix game satisfies these properties. We further provide the functional form for a parameterized optimal strategy and the value function. Finally, we translate our results to linear programming and stochastic games, where value positivity is related to the existence of robust solutions. acknowledgement: This research was supported by Fondation CFM pour la Recherche, the H2020 European Research Council [Grant ERC-CoG-863818 (ForM-SMArt)], the Austrian Science Fund [Grant 10.55776/COE12], ANID Chile [Grant ACT210005], and Agence Nationale de la Recherche [Grant ANR-21-CE40-0020]. article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Miquel full_name: Oliu-Barton, Miquel last_name: Oliu-Barton - first_name: Raimundo J full_name: Saona Urmeneta, Raimundo J id: BD1DF4C4-D767-11E9-B658-BC13E6697425 last_name: Saona Urmeneta orcid: 0000-0001-5103-038X citation: ama: Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. Value-positivity for matrix games. Mathematics of Operations Research. 2024;50(4):2433-3282. doi:10.1287/moor.2022.0332 apa: Chatterjee, K., Oliu-Barton, M., & Saona Urmeneta, R. J. (2024). Value-positivity for matrix games. Mathematics of Operations Research. Institute for Operations Research and the Management Sciences. https://doi.org/10.1287/moor.2022.0332 chicago: Chatterjee, Krishnendu, Miquel Oliu-Barton, and Raimundo J Saona Urmeneta. “Value-Positivity for Matrix Games.” Mathematics of Operations Research. Institute for Operations Research and the Management Sciences, 2024. https://doi.org/10.1287/moor.2022.0332. ieee: K. Chatterjee, M. Oliu-Barton, and R. J. Saona Urmeneta, “Value-positivity for matrix games,” Mathematics of Operations Research, vol. 50, no. 4. Institute for Operations Research and the Management Sciences, pp. 2433–3282, 2024. ista: Chatterjee K, Oliu-Barton M, Saona Urmeneta RJ. 2024. Value-positivity for matrix games. Mathematics of Operations Research. 50(4), 2433–3282. mla: Chatterjee, Krishnendu, et al. “Value-Positivity for Matrix Games.” Mathematics of Operations Research, vol. 50, no. 4, Institute for Operations Research and the Management Sciences, 2024, pp. 2433–3282, doi:10.1287/moor.2022.0332. short: K. Chatterjee, M. Oliu-Barton, R.J. Saona Urmeneta, Mathematics of Operations Research 50 (2024) 2433–3282. corr_author: '1' date_created: 2024-10-09T07:02:20Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-07-29T13:14:36Z day: '01' department: - _id: GradSch - _id: KrCh doi: 10.1287/moor.2022.0332 ec_funded: 1 external_id: isi: - '001328875900001' intvolume: ' 50' isi: 1 issue: '4' language: - iso: eng month: '10' oa_version: None page: 2433-3282 project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' publication: Mathematics of Operations Research publication_identifier: eissn: - 1526-5471 issn: - 0364-765X publication_status: published publisher: Institute for Operations Research and the Management Sciences quality_controlled: '1' related_material: record: - id: '20234' relation: dissertation_contains status: public scopus_import: '1' status: public title: Value-positivity for matrix games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '14542' abstract: - lang: eng text: "It is a remarkable property of BCS theory that the ratio of the energy gap at zero temperature Ξ\r\n and the critical temperature Tc is (approximately) given by a universal constant, independent of the microscopic details of the fermionic interaction. This universality has rigorously been proven quite recently in three spatial dimensions and three different limiting regimes: weak coupling, low density and high density. The goal of this short note is to extend the universal behavior to lower dimensions d=1,2 and give an exemplary proof in the weak coupling limit." acknowledgement: We thank Robert Seiringer for comments on the paper. J. H. gratefully acknowledges partial financial support by the ERC Advanced Grant “RMTBeyond”No. 101020331.This research was funded in part by the Austrian Science Fund (FWF) grantnumber I6427. article_number: '2360005 ' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 - first_name: Barbara full_name: Roos, Barbara id: 5DA90512-D80F-11E9-8994-2E2EE6697425 last_name: Roos orcid: 0000-0002-9071-5880 citation: ama: Henheik SJ, Lauritsen AB, Roos B. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 2024;36(9). doi:10.1142/s0129055x2360005x apa: Henheik, S. J., Lauritsen, A. B., & Roos, B. (2024). Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/s0129055x2360005x chicago: Henheik, Sven Joscha, Asbjørn Bækgaard Lauritsen, and Barbara Roos. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics. World Scientific Publishing, 2024. https://doi.org/10.1142/s0129055x2360005x. ieee: S. J. Henheik, A. B. Lauritsen, and B. Roos, “Universality in low-dimensional BCS theory,” Reviews in Mathematical Physics, vol. 36, no. 9. World Scientific Publishing, 2024. ista: Henheik SJ, Lauritsen AB, Roos B. 2024. Universality in low-dimensional BCS theory. Reviews in Mathematical Physics. 36(9), 2360005. mla: Henheik, Sven Joscha, et al. “Universality in Low-Dimensional BCS Theory.” Reviews in Mathematical Physics, vol. 36, no. 9, 2360005, World Scientific Publishing, 2024, doi:10.1142/s0129055x2360005x. short: S.J. Henheik, A.B. Lauritsen, B. Roos, Reviews in Mathematical Physics 36 (2024). corr_author: '1' date_created: 2023-11-15T23:48:14Z date_published: 2024-10-01T00:00:00Z date_updated: 2026-07-29T13:18:16Z day: '01' ddc: - '510' department: - _id: GradSch - _id: LaEr - _id: RoSe doi: 10.1142/s0129055x2360005x ec_funded: 1 external_id: arxiv: - '2301.05621' isi: - '001099640300002' file: - access_level: open_access checksum: 2b053a4223b4db14b90520999ec56054 content_type: application/pdf creator: dernst date_created: 2025-01-09T07:56:28Z date_updated: 2025-01-09T07:56:28Z file_id: '18786' file_name: 2024_ReviewsmathPhysics_Henheik.pdf file_size: 503910 relation: main_file success: 1 file_date_updated: 2025-01-09T07:56:28Z has_accepted_license: '1' intvolume: ' 36' isi: 1 issue: '9' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta - _id: bda63fe5-d553-11ed-ba76-a16e3d2f256b grant_number: I06427 name: Mathematical Challenges in BCS Theory of Superconductivity publication: Reviews in Mathematical Physics publication_identifier: eissn: - 1793-6659 issn: - 0129-055X publication_status: published publisher: World Scientific Publishing quality_controlled: '1' related_material: record: - id: '18135' relation: dissertation_contains status: public - id: '19540' relation: dissertation_contains status: public scopus_import: '1' status: public title: Universality in low-dimensional BCS theory tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2024' ... --- OA_place: publisher _id: '17485' abstract: - lang: eng text: "Large language models (LLMs) have made tremendous progress in the past few years, from being able to generate coherent text to matching or surpassing humans in a wide variety of creative, knowledge or reasoning tasks. Much of this can be attributed to massively increased scale, both in the size of the model as well as the amount of training data, from 100s of millions to 100s of billions, or even trillions. This trend is expected to continue, which, although exciting, also raises major practical concerns. Already today's 100+ billion parameter LLMs require top-of-the-line hardware just to run. Hence, it is clear that sustaining these developments will require significant efficiency advances.\r\n\r\nHistorically, one of the most practical ways of improving model efficiency has been compression, especially in the form of sparsity or quantization. While this has been studied extensively in the past, existing accurate methods are all designed for models around 100 million parameters; scaling them up to ones literally 1000x larger is highly challenging. In this thesis, we introduce a new unified sparsification and quantization approach OBC, which through additional algorithmic enhancements leads to GPTQ and SparseGPT, the first techniques fast and accurate enough to compress 100+ billion parameter models to 4- or even 3-bit precision and 50% weight-sparsity, respectively. Additionally, we show how weight-only quantizion does not just bring space savings but also up to 4.5x faster generation speed, via custom GPU kernels.\r\n\r\nIn fact, we show for the first time that it is possible to develop an FP16 times INT4 mixed-precision matrix multiplication kernel, called Marlin, which comes close to simultaneously maximizing both memory and compute utilization, making weight-only quantization highly practical even for multi-user serving. Further, we demonstrate that GPTQ can be scaled to widely overparametrized trillion-parameter models, where extreme sub-1-bit compression rates can be achieved without any inference slow-down, by co-designing a bespoke entropy coding scheme together with an efficient kernel.\r\n\r\nFinally, we also study compression from the perspective of someone with access to massive amounts of compute resources for training large models completely from scratch. Here the key questions evolve around the joint scaling behavior between compression, model size, and amount of training data used. Based on extensive experimental results for both vision and text models, we introduce the first scaling law which accurately captures the relationship between weight-sparsity, number of non-zero weights and data. This further allows us to characterize the optimal sparsity, which we find to increase the longer a fixed cost model is being trained.\r\n\r\nOverall, this thesis presents contributions to three different angles of large model efficiency: affordable but accurate algorithms, highly efficient systems implementations, and fundamental scaling laws for compressed training." acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Elias full_name: Frantar, Elias id: 09a8f98d-ec99-11ea-ae11-c063a7b7fe5f last_name: Frantar citation: ama: 'Frantar E. Compressing large neural networks: Algorithms, systems and scaling laws. 2024. doi:10.15479/at:ista:17485' apa: 'Frantar, E. (2024). Compressing large neural networks: Algorithms, systems and scaling laws. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17485' chicago: 'Frantar, Elias. “Compressing Large Neural Networks: Algorithms, Systems and Scaling Laws.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17485.' ieee: 'E. Frantar, “Compressing large neural networks: Algorithms, systems and scaling laws,” Institute of Science and Technology Austria, 2024.' ista: 'Frantar E. 2024. Compressing large neural networks: Algorithms, systems and scaling laws. Institute of Science and Technology Austria.' mla: 'Frantar, Elias. Compressing Large Neural Networks: Algorithms, Systems and Scaling Laws. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17485.' short: 'E. Frantar, Compressing Large Neural Networks: Algorithms, Systems and Scaling Laws, Institute of Science and Technology Austria, 2024.' corr_author: '1' date_created: 2024-09-02T11:01:48Z date_published: 2024-09-05T00:00:00Z date_updated: 2026-07-29T13:48:40Z day: '05' ddc: - '000' degree_awarded: PhD department: - _id: GradSch - _id: DaAl doi: 10.15479/at:ista:17485 doi_confirm: '1' ec_funded: 1 file: - access_level: closed checksum: 5d785645805a78c5b4ce7cc3df557b09 content_type: application/zip creator: efrantar date_created: 2024-09-05T12:04:11Z date_updated: 2024-09-05T12:04:11Z file_id: '17570' file_name: thesis-final.zip file_size: 1615167 relation: source_file - access_level: open_access checksum: a9dd1c2d23734986924eb44ebb55fd8f content_type: application/pdf creator: efrantar date_created: 2024-09-06T16:24:59Z date_updated: 2024-09-06T16:24:59Z file_id: '17880' file_name: frantar_thesis_final.pdf file_size: 2376611 relation: main_file success: 1 file_date_updated: 2024-09-06T16:24:59Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '129' project: - _id: 268A44D6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '805223' name: Elastic Coordination for Scalable Machine Learning publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '17378' relation: part_of_dissertation status: public - id: '17087' relation: part_of_dissertation status: public - id: '14458' relation: part_of_dissertation status: public - id: '18062' relation: part_of_dissertation status: public - id: '18061' relation: part_of_dissertation status: public status: public supervisor: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: 'Compressing large neural networks: Algorithms, systems and scaling laws' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: repository _id: '17465' abstract: - lang: eng 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" acknowledged_ssus: - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Aleksandr full_name: Shevchenko, Aleksandr id: F2B06EC2-C99E-11E9-89F0-752EE6697425 last_name: Shevchenko citation: ama: Shevchenko A. High-dimensional limits in artificial neural networks. 2024. doi:10.15479/at:ista:17465 apa: Shevchenko, A. (2024). High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17465 chicago: Shevchenko, Alexander. “High-Dimensional Limits in Artificial Neural Networks.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17465. ieee: A. Shevchenko, “High-dimensional limits in artificial neural networks,” Institute of Science and Technology Austria, 2024. ista: Shevchenko A. 2024. High-dimensional limits in artificial neural networks. Institute of Science and Technology Austria. mla: Shevchenko, Alexander. High-Dimensional Limits in Artificial Neural Networks. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17465. short: A. Shevchenko, High-Dimensional Limits in Artificial Neural Networks, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-08-28T15:14:25Z date_published: 2024-08-29T00:00:00Z date_updated: 2026-06-18T17:55:53Z day: '29' ddc: - '519' degree_awarded: PhD department: - _id: GradSch - _id: DaAl - _id: MaMo doi: 10.15479/at:ista:17465 file: - access_level: open_access checksum: da6dd3166078934577f6af93d27000e2 content_type: application/pdf creator: ashevche date_created: 2024-09-02T09:23:32Z date_updated: 2024-10-05T22:30:05Z embargo: 2024-10-04 file_id: '17482' file_name: thesis_a2b.pdf file_size: 4468610 relation: main_file - access_level: closed checksum: 76a39ef252239560923cdda4ce0a31a4 content_type: application/zip creator: ashevche date_created: 2024-09-02T09:23:46Z date_updated: 2024-10-05T22:30:05Z embargo_to: open_access file_id: '17483' file_name: Thesis Alex - ISTA.zip file_size: 15930999 relation: source_file file_date_updated: 2024-10-05T22:30:05Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '232' project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli - _id: 9B9290DE-BA93-11EA-9121-9846C619BF3A grant_number: W1260-N35 name: Vienna Graduate School on Computational Optimization publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '11420' relation: part_of_dissertation status: public - id: '14459' relation: part_of_dissertation status: public - id: '9198' relation: part_of_dissertation status: public - id: '17469' relation: part_of_dissertation status: public status: public supervisor: - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X title: High-dimensional limits in artificial neural networks type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2024' ... --- OA_place: publisher _id: '17881' 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." acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 citation: ama: Mukhopadhyay S. Thermal effects in one dimensional Josephson chains. 2024. doi:10.15479/at:ista:17881 apa: Mukhopadhyay, S. (2024). Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17881 chicago: Mukhopadhyay, Soham. “Thermal Effects in One Dimensional Josephson Chains.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:17881. ieee: S. Mukhopadhyay, “Thermal effects in one dimensional Josephson chains,” Institute of Science and Technology Austria, 2024. ista: Mukhopadhyay S. 2024. Thermal effects in one dimensional Josephson chains. Institute of Science and Technology Austria. mla: Mukhopadhyay, Soham. Thermal Effects in One Dimensional Josephson Chains. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17881. short: S. Mukhopadhyay, Thermal Effects in One Dimensional Josephson Chains, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-09-08T10:23:25Z date_published: 2024-09-10T00:00:00Z date_updated: 2026-06-03T07:16:04Z day: '10' ddc: - '539' degree_awarded: PhD department: - _id: GradSch - _id: AnHi doi: 10.15479/at:ista:17881 file: - access_level: open_access checksum: ed7763c3bbd59e1d7e1b664de3a26f3c content_type: application/pdf creator: smukhopa date_created: 2024-09-12T10:46:04Z date_updated: 2025-03-13T23:30:04Z embargo: 2025-03-13 file_id: '18059' file_name: PhD_Thesis_Soham_Mukhopadhyay.pdf file_size: 10297052 relation: main_file - access_level: closed checksum: e352667482701dd18a9a0e7418aef465 content_type: application/zip creator: smukhopa date_created: 2024-09-12T10:50:58Z date_updated: 2025-03-13T23:30:04Z embargo_to: open_access file_id: '18060' file_name: PhD_Thesis_Soham_Mukhopadhyay_source.zip file_size: 29178634 relation: source_file file_date_updated: 2025-03-13T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '82' project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition publication_identifier: isbn: - 978-3-99078-043-5 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14032' relation: part_of_dissertation status: public - id: '18057' relation: part_of_dissertation status: public status: public supervisor: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 title: Thermal effects in one dimensional Josephson chains type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: repository _id: '18057' abstract: - lang: eng 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." acknowledged_ssus: - _id: NanoFab - _id: M-Shop 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" article_number: '2408.07829' article_processing_charge: No arxiv: 1 author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay orcid: 0000-0001-5263-5559 - first_name: Diego A full_name: Lancheros Naranjo, Diego A id: 6c55e976-15b2-11ec-abd3-d790e8937fde last_name: Lancheros Naranjo - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv. doi:10.48550/arXiv.2408.07829 apa: Mukhopadhyay, S., Lancheros Naranjo, D. A., Senior, J. L., & Higginbotham, A. P. (n.d.). Dual relaxation oscillations in a Josephson junction array. arXiv. https://doi.org/10.48550/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.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2408.07829. ieee: S. Mukhopadhyay, D. A. Lancheros Naranjo, J. L. Senior, and A. P. Higginbotham, “Dual relaxation oscillations in a Josephson junction array,” arXiv. . ista: Mukhopadhyay S, Lancheros Naranjo DA, Senior JL, Higginbotham AP. Dual relaxation oscillations in a Josephson junction array. arXiv, 2408.07829. mla: Mukhopadhyay, Soham, et al. “Dual Relaxation Oscillations in a Josephson Junction Array.” ArXiv, 2408.07829, doi:10.48550/arXiv.2408.07829. short: S. Mukhopadhyay, D.A. Lancheros Naranjo, J.L. Senior, A.P. Higginbotham, ArXiv (n.d.). corr_author: '1' date_created: 2024-09-11T09:25:22Z date_published: 2024-08-14T00:00:00Z date_updated: 2026-07-29T22:30:18Z day: '14' department: - _id: AnHi - _id: GradSch doi: 10.48550/arXiv.2408.07829 ec_funded: 1 external_id: arxiv: - '2408.07829' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2408.07829 month: '08' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter publication: arXiv publication_status: draft related_material: record: - id: '20324' relation: later_version status: public - id: '17881' relation: dissertation_contains status: public status: public title: Dual relaxation oscillations in a Josephson junction array type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher _id: '17119' 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 citation: ama: Kelemen RK. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. 2024. doi:10.15479/at:ista:17119 apa: Kelemen, R. K. (2024). Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:17119 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. https://doi.org/10.15479/at:ista:17119. 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. ista: Kelemen RK. 2024. Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver. Institute of Science and Technology Austria. mla: Kelemen, Réka K. Characterizing the Sequence and Expression Evolution of the T-Haplotype, a Model Meiotic Driver. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:17119. 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. corr_author: '1' date_created: 2024-06-07T16:14:13Z date_published: 2024-06-20T00:00:00Z date_updated: 2026-04-07T13:21:37Z day: '20' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: BeVi doi: 10.15479/at:ista:17119 ec_funded: 1 file: - access_level: closed checksum: fab59146e3b3dc2e5d214576984a2a63 content_type: application/zip creator: rkelemen date_created: 2024-06-07T16:09:17Z date_updated: 2025-01-10T23:30:10Z embargo_to: open_access file_id: '17121' file_name: thesis.zip file_size: 180557931 relation: source_file - access_level: open_access checksum: 91cc4c25a792239e8a7688e8aec7c62a content_type: application/pdf creator: rkelemen date_created: 2024-07-10T08:00:20Z date_updated: 2025-01-10T23:30:10Z embargo: 2025-01-10 file_id: '17213' file_name: thesis_to_archive.pdf file_size: 19405484 relation: main_file file_date_updated: 2025-01-10T23:30:10Z has_accepted_license: '1' keyword: - meiotic driver - neofunctionalization - single nucleus sequencing language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: '105' project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publication_identifier: isbn: - 978-3-99078-039-8 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '542' relation: part_of_dissertation status: public - id: '10767' relation: part_of_dissertation status: public status: public supervisor: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 title: Characterizing the sequence and expression evolution of the t-haplotype, a model meiotic driver tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18477' 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." acknowledged_ssus: - _id: EM-Fac - _id: LifeSc alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Beata M full_name: Kaczmarek, Beata M id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarek citation: ama: Kaczmarek BM. Biochemical and structural insights into ADAR1 RNA editing. 2024. doi:10.15479/at:ista:18477 apa: Kaczmarek, B. M. (2024). Biochemical and structural insights into ADAR1 RNA editing. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18477 chicago: Kaczmarek, Beata M. “Biochemical and Structural Insights into ADAR1 RNA Editing.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18477. ieee: 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. mla: Kaczmarek, Beata M. Biochemical and Structural Insights into ADAR1 RNA Editing. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18477. short: B.M. Kaczmarek, Biochemical and Structural Insights into ADAR1 RNA Editing, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-27T07:35:13Z date_published: 2024-10-29T00:00:00Z date_updated: 2026-04-07T13:23:59Z day: '29' ddc: - '572' degree_awarded: PhD department: - _id: GradSch - _id: CaBe doi: 10.15479/at:ista:18477 file: - access_level: closed checksum: 2053294ea4d770c495e4cc501e2a218b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: bkaczmar date_created: 2024-10-29T11:56:36Z date_updated: 2025-10-29T23:30:02Z embargo_to: open_access file_id: '18485' file_name: 20241029_PhD_thesis_BKaczmarek.docx file_size: 23136626 relation: source_file - access_level: open_access checksum: 8ce857a4cd44b776791eaf180ac9dbb3 content_type: application/pdf creator: bkaczmar date_created: 2024-10-29T11:56:44Z date_updated: 2025-10-29T23:30:02Z embargo: 2025-10-29 file_id: '18486' file_name: 20241029_PhD_thesis_BKaczmarek.pdf file_size: 11707360 relation: main_file file_date_updated: 2025-10-29T23:30:02Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '124' publication_identifier: isbn: - 978-3-99078-045-9 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 title: Biochemical and structural insights into ADAR1 RNA editing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '15352' 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. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl alternative_title: - ISTA Master's Thesis article_processing_charge: No author: - first_name: Julie Stefanie full_name: Murmann, Julie Stefanie id: 1d390868-f128-11eb-9611-a0ca5f7833b5 last_name: Murmann citation: ama: 'Murmann JS. Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. 2024. doi:10.15479/at:ista:15352' apa: 'Murmann, J. S. (2024). Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15352' 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. https://doi.org/10.15479/at:ista:15352.' 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.' 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.' mla: '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, doi:10.15479/at:ista:15352.' 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.' corr_author: '1' date_created: 2024-05-02T08:31:38Z date_published: 2024-05-02T00:00:00Z date_updated: 2026-04-07T13:05:00Z day: '02' ddc: - '570' degree_awarded: MS department: - _id: SaSi - _id: GradSch doi: 10.15479/at:ista:15352 file: - access_level: open_access checksum: 095817a6c944954ac3f277e547031a33 content_type: application/pdf creator: cchlebak date_created: 2024-05-02T12:26:13Z date_updated: 2025-05-02T22:30:04Z embargo: 2025-05-02 file_id: '15354' file_name: Murmann_Thesis_final_2024_2.pdf file_size: 5936142 relation: main_file - access_level: closed checksum: 43b632255372973a437ac87739cfd4db content_type: application/x-zip-compressed creator: cchlebak date_created: 2024-05-02T12:37:56Z date_updated: 2025-05-02T22:30:04Z embargo_to: open_access file_id: '15355' file_name: Murmann_Thesis_final_2024.zip file_size: 20645510 relation: source_file file_date_updated: 2025-05-02T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '54' publication_identifier: issn: - 2791-4585 publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 title: 'Investigating acute microglia response to seizure activity in vivo: Combining 2-Photon imaging and EEG recording' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '14821' abstract: - lang: eng 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Heloisa full_name: Chiossi, Heloisa id: 2BBA502C-F248-11E8-B48F-1D18A9856A87 last_name: Chiossi orcid: 0009-0004-2973-278X citation: ama: Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:10.15479/at:ista:14821 apa: Chiossi, H. S. C. (2024). Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:14821 chicago: Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:14821. ieee: H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024. ista: Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria. mla: Chiossi, Heloisa S. C. Adaptive Hierarchical Representations in the Hippocampus. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:14821. short: H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-01-16T14:25:21Z date_published: 2024-01-19T00:00:00Z date_updated: 2026-04-07T13:21:56Z day: '19' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoCs doi: 10.15479/at:ista:14821 ec_funded: 1 file: - access_level: closed checksum: d3fa3de1abd5af5204c13e9d55375615 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: hchiossi date_created: 2024-01-19T11:04:05Z date_updated: 2025-01-19T23:30:04Z embargo_to: open_access file_id: '14838' file_name: PhD_Thesis_190124.docx file_size: 8656268 relation: source_file - access_level: open_access checksum: 13adc8dcfb5b6b18107f89f0a98fa8bd content_type: application/pdf creator: hchiossi date_created: 2024-01-19T11:03:59Z date_updated: 2025-01-19T23:30:04Z embargo: 2025-01-19 file_id: '14839' file_name: PhD_Thesis_190124.pdf file_size: 6567275 relation: main_file file_date_updated: 2025-01-19T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: '89' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: Adaptive hierarchical representations in the hippocampus type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '15101' 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." acknowledged_ssus: - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: JingJing full_name: Chen, JingJing id: 2C4E65C8-F248-11E8-B48F-1D18A9856A87 last_name: Chen citation: ama: Chen J. Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse. 2024. doi:10.15479/at:ista:15101 apa: 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. https://doi.org/10.15479/at:ista:15101 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. https://doi.org/10.15479/at:ista:15101. 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. 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. mla: 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, doi:10.15479/at:ista:15101. 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. corr_author: '1' date_created: 2024-03-11T10:09:54Z date_published: 2024-03-11T00:00:00Z date_updated: 2026-04-07T13:24:22Z day: '11' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: PeJo doi: 10.15479/at:ista:15101 ec_funded: 1 file: - access_level: closed checksum: db4947474ffa271e66c254b6fe876a55 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jchen date_created: 2024-03-11T14:10:58Z date_updated: 2024-04-02T22:30:03Z embargo_to: open_access file_id: '15104' file_name: Thesis_Jingjing CHEN.docx file_size: 11271363 relation: source_file - access_level: open_access checksum: a5eeae8b5702cd540f5d03469bc33dde content_type: application/pdf creator: jchen date_created: 2024-03-11T14:11:06Z date_updated: 2024-04-02T22:30:03Z embargo: 2024-04-01 file_id: '15105' file_name: Thesis_Jingjing CHEN_merged.pdf file_size: 16627311 relation: main_file file_date_updated: 2024-04-02T22:30:03Z has_accepted_license: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: '84' project: - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glutamatergic synapse - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: Synaptic communication in neuronal microcircuits - _id: bd88be38-d553-11ed-ba76-81d5a70a6ef5 grant_number: P36232 name: Mechanisms of GABA release in hippocampal circuits - _id: 26B66A3E-B435-11E9-9278-68D0E5697425 grant_number: '25383' name: Development of nanodomain coupling between Ca2+ channels and release sensors at a central inhibitory synapse publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '14843' relation: part_of_dissertation status: public status: public supervisor: - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 title: Developmental transformation of nanodomain coupling between Ca2+ channels and release sensors at a central GABAergic synapse tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_place: publisher _id: '18471' abstract: - lang: eng 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. " acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: PreCl - _id: M-Shop - _id: ScienComp alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Nathalie full_name: Agudelo Duenas, Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas citation: ama: Agudelo Duenas N. Visualizing the neuronal transcriptional landscape with tissue context. 2024. doi:10.15479/at:ista:18471 apa: Agudelo Duenas, N. (2024). Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18471 chicago: Agudelo Duenas, Nathalie. “Visualizing the Neuronal Transcriptional Landscape with Tissue Context.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18471. ieee: N. Agudelo Duenas, “Visualizing the neuronal transcriptional landscape with tissue context,” Institute of Science and Technology Austria, 2024. ista: Agudelo Duenas N. 2024. Visualizing the neuronal transcriptional landscape with tissue context. Institute of Science and Technology Austria. mla: Agudelo Duenas, Nathalie. Visualizing the Neuronal Transcriptional Landscape with Tissue Context. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18471. short: N. Agudelo Duenas, Visualizing the Neuronal Transcriptional Landscape with Tissue Context, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-10-26T20:02:42Z date_published: 2024-10-28T00:00:00Z date_updated: 2026-04-14T08:34:37Z day: '28' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: JoDa doi: 10.15479/at:ista:18471 ec_funded: 1 file: - access_level: closed checksum: 6d7c7725d040d8debc070dcb35ac965d content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: nagudelo date_created: 2024-10-26T22:29:06Z date_updated: 2025-05-05T22:30:04Z embargo_to: open_access file_id: '18475' file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.docx file_size: 183077763 relation: source_file - access_level: open_access checksum: 52f9c0bf2bdafa3baf827b73814a53ff content_type: application/pdf creator: nagudelo date_created: 2024-10-26T23:13:33Z date_updated: 2025-05-05T22:30:04Z embargo: 2025-05-05 file_id: '18476' file_name: PhD_thesis_Nathalie_Agudelo_Duenas_ISTA_final.pdf file_size: 47027710 relation: main_file file_date_updated: 2025-05-05T22:30:04Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '97' project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232 name: Molecular Drug Targets publication_identifier: isbn: - 978-3-99078-044-2 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 title: Visualizing the neuronal transcriptional landscape with tissue context tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- OA_embargo: '12' OA_place: publisher _id: '18574' abstract: - lang: eng 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" acknowledged_ssus: - _id: Bio - _id: ScienComp - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib 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." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Divyansh full_name: Gupta, Divyansh id: 2A485EBE-F248-11E8-B48F-1D18A9856A87 last_name: Gupta orcid: 0000-0001-7400-6665 citation: ama: Gupta D. Visual adaptations to natural statistics. 2024. doi:10.15479/at:ista:18574 apa: Gupta, D. (2024). Visual adaptations to natural statistics. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18574 chicago: Gupta, Divyansh. “Visual Adaptations to Natural Statistics.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18574. ieee: 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. mla: Gupta, Divyansh. Visual Adaptations to Natural Statistics. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18574. short: D. Gupta, Visual Adaptations to Natural Statistics, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-20T21:30:44Z date_published: 2024-11-22T00:00:00Z date_updated: 2026-04-07T13:24:48Z day: '22' ddc: - '573' degree_awarded: PhD department: - _id: GradSch - _id: MaJö doi: 10.15479/at:ista:18574 ec_funded: 1 file: - access_level: closed checksum: ebb000d361c36b22ed6e639a931c6b7c content_type: application/zip creator: dgupta date_created: 2024-11-25T14:44:03Z date_updated: 2025-11-11T23:30:02Z embargo_to: open_access file_id: '18589' file_name: PhD Thesis - Divyansh Gupta.zip file_size: 75512262 relation: source_file - access_level: open_access checksum: 1282401eb71598bc311058b0fcefc6a1 content_type: application/pdf creator: dgupta date_created: 2024-11-26T11:43:19Z date_updated: 2025-11-11T23:30:02Z embargo: 2025-11-11 file_id: '18591' file_name: PDFA_PhD_Thesis___Divyansh_Gupta-26_11_24.pdf file_size: 6412619 relation: main_file file_date_updated: 2025-11-11T23:30:02Z has_accepted_license: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: '86' project: - _id: bdaf81a8-d553-11ed-ba76-c95961984540 grant_number: '101086580' name: 'Action Selection in the Midbrain: Neuromodulation of Visuomotor Senses' - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention publication_identifier: isbn: - 978-3-99078-050-3 issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12349' relation: part_of_dissertation status: public - id: '12370' relation: research_data status: public status: public supervisor: - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 title: Visual adaptations to natural statistics tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ...