[{"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"grant_number":"P32896","name":"Causes and consequences of population fragmentation","_id":"c08d3278-5a5b-11eb-8a69-fdb09b55f4b8"},{"grant_number":"26380","name":"Polygenic Adaptation in a Metapopulation","_id":"34c872fe-11ca-11ed-8bc3-8534b82131e6"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:14711","department":[{"_id":"NiBa"},{"_id":"GradSch"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","ec_funded":1,"article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file":[{"date_created":"2024-01-03T18:30:13Z","access_level":"closed","file_id":"14730","date_updated":"2024-01-03T18:30:13Z","checksum":"de179b1c6758f182ff0c70d8b38c1501","file_size":16986244,"relation":"source_file","content_type":"application/zip","creator":"oolusany","file_name":"FinalSubmission_Thesis_OLUSANYA.zip"},{"creator":"oolusany","file_size":6460403,"content_type":"application/pdf","relation":"main_file","file_name":"FinalSubmission2_Thesis_OLUSANYA.pdf","success":1,"access_level":"open_access","date_created":"2024-01-03T18:31:34Z","checksum":"0e331585e3cd4823320aab4e69e64ccf","file_id":"14731","date_updated":"2024-01-03T18:31:34Z"}],"day":"19","author":[{"orcid":"0000-0003-1971-8314","id":"41AD96DC-F248-11E8-B48F-1D18A9856A87","full_name":"Olusanya, Oluwafunmilola O","last_name":"Olusanya","first_name":"Oluwafunmilola O"}],"degree_awarded":"MS","title":"Local adaptation, genetic load and extinction in metapopulations","status":"public","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","id":"10658","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"10787"},{"status":"public","id":"14732","relation":"part_of_dissertation"}]},"has_accepted_license":"1","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"SSU"}],"supervisor":[{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"last_name":"Polechova","first_name":"Jitka","full_name":"Polechova, Jitka"},{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"date_published":"2024-01-19T00:00:00Z","ddc":["576"],"year":"2024","_id":"14711","abstract":[{"lang":"eng","text":"In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies.\r\n\r\nFor species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges\r\nas well as in highly fragmented populations.\r\n\r\nIn this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters.\r\n\r\nChapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate.\r\n\r\nIn chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist.\r\n\r\nThe focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts.\r\n\r\nChapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence.\r\n\r\nOverall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management."}],"date_updated":"2025-05-26T09:05:10Z","oa_version":"Published Version","month":"01","type":"dissertation","page":"183","file_date_updated":"2024-01-03T18:31:34Z","date_created":"2023-12-26T22:49:53Z"},{"alternative_title":["ISTA Thesis"],"status":"public","citation":{"apa":"Chiossi, H. S. C. (2024). <i>Adaptive hierarchical representations in the hippocampus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>","mla":"Chiossi, Heloisa S. C. <i>Adaptive Hierarchical Representations in the Hippocampus</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>.","ista":"Chiossi HSC. 2024. Adaptive hierarchical representations in the hippocampus. Institute of Science and Technology Austria.","ama":"Chiossi HSC. Adaptive hierarchical representations in the hippocampus. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:14821\">10.15479/at:ista:14821</a>","short":"H.S.C. Chiossi, Adaptive Hierarchical Representations in the Hippocampus, Institute of Science and Technology Austria, 2024.","chicago":"Chiossi, Heloisa S. C. “Adaptive Hierarchical Representations in the Hippocampus.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:14821\">https://doi.org/10.15479/at:ista:14821</a>.","ieee":"H. S. C. Chiossi, “Adaptive hierarchical representations in the hippocampus,” Institute of Science and Technology Austria, 2024."},"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_published":"2024-01-19T00:00:00Z","supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"year":"2024","_id":"14821","page":"89","month":"01","oa_version":"Published Version","type":"dissertation","date_updated":"2024-02-01T09:50:29Z","date_created":"2024-01-16T14:25:21Z","file_date_updated":"2024-01-19T11:04:05Z","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:14821","publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"JoCs"}],"article_processing_charge":"No","ec_funded":1,"author":[{"first_name":"Heloisa","last_name":"Chiossi","id":"2BBA502C-F248-11E8-B48F-1D18A9856A87","full_name":"Chiossi, Heloisa"}],"day":"19","file":[{"file_id":"14838","date_updated":"2024-01-19T11:04:05Z","checksum":"d3fa3de1abd5af5204c13e9d55375615","date_created":"2024-01-19T11:04:05Z","access_level":"closed","file_name":"PhD_Thesis_190124.docx","file_size":8656268,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","creator":"hchiossi"},{"file_size":6567275,"relation":"main_file","content_type":"application/pdf","embargo":"2025-01-19","embargo_to":"open_access","creator":"hchiossi","file_name":"PhD_Thesis_190124.pdf","date_created":"2024-01-19T11:03:59Z","access_level":"closed","file_id":"14839","date_updated":"2024-01-19T11:03:59Z","checksum":"13adc8dcfb5b6b18107f89f0a98fa8bd"}],"title":"Adaptive hierarchical representations in the hippocampus","degree_awarded":"PhD"},{"date_updated":"2025-06-30T13:21:09Z","abstract":[{"lang":"eng","text":"This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty.\r\nChapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance?\r\nChapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance.\r\nChapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2.\r\nChapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal."}],"type":"dissertation","oa_version":"Published Version","month":"02","page":"158","date_created":"2024-02-23T14:02:04Z","file_date_updated":"2024-02-23T14:20:16Z","year":"2024","_id":"15020","has_accepted_license":"1","publication_status":"published","oa":1,"acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton","first_name":"Nicholas H"},{"first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["576","519"],"date_published":"2024-02-23T00:00:00Z","status":"public","alternative_title":["ISTA Thesis"],"citation":{"mla":"Hledik, Michal. <i>Genetic Information and Biological Optimization</i>. Institute of Science and Technology Austria, 2024, doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>.","ista":"Hledik M. 2024. Genetic information and biological optimization. Institute of Science and Technology Austria.","apa":"Hledik, M. (2024). <i>Genetic information and biological optimization</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>","ama":"Hledik M. Genetic information and biological optimization. 2024. doi:<a href=\"https://doi.org/10.15479/at:ista:15020\">10.15479/at:ista:15020</a>","short":"M. Hledik, Genetic Information and Biological Optimization, Institute of Science and Technology Austria, 2024.","ieee":"M. Hledik, “Genetic information and biological optimization,” Institute of Science and Technology Austria, 2024.","chicago":"Hledik, Michal. “Genetic Information and Biological Optimization.” Institute of Science and Technology Austria, 2024. <a href=\"https://doi.org/10.15479/at:ista:15020\">https://doi.org/10.15479/at:ista:15020</a>."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"7553","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"7606"},{"relation":"part_of_dissertation","id":"12081","status":"public"}]},"day":"23","file":[{"file_name":"hledik thesis pdfa 2b.pdf","success":1,"creator":"mhledik","file_size":7102089,"content_type":"application/pdf","relation":"main_file","checksum":"b2d3da47c98d481577a4baf68944fe41","file_id":"15021","date_updated":"2024-02-23T13:50:53Z","access_level":"open_access","date_created":"2024-02-23T13:50:53Z"},{"file_name":"hledik thesis source.zip","file_size":14014790,"relation":"source_file","content_type":"application/zip","creator":"mhledik","file_id":"15022","date_updated":"2024-02-23T14:20:16Z","checksum":"eda9b9430da2610fee7ce1c1419a479a","date_created":"2024-02-23T13:50:54Z","access_level":"closed"}],"author":[{"last_name":"Hledik","first_name":"Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","full_name":"Hledik, Michal"}],"title":"Genetic information and biological optimization","department":[{"_id":"GradSch"},{"_id":"NiBa"},{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","ec_funded":1,"article_processing_charge":"No","publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:15020","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"_id":"bd6958e0-d553-11ed-ba76-86eba6a76c00","name":"Understanding the evolution of continuous genomes","grant_number":"101055327"}],"language":[{"iso":"eng"}],"keyword":["Theoretical biology","Optimality","Evolution","Information"]},{"title":"MDPs as distribution transformers: Affine invariant synthesis for safety objectives","day":"17","file":[{"checksum":"f143c8eedf609f20f2aad2eeb496d53f","date_updated":"2023-09-20T08:46:43Z","file_id":"14349","access_level":"open_access","date_created":"2023-09-20T08:46:43Z","success":1,"file_name":"2023_LNCS_Akshay.pdf","creator":"dernst","relation":"main_file","content_type":"application/pdf","file_size":531745}],"author":[{"last_name":"Akshay","first_name":"S.","full_name":"Akshay, S."},{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Meggendorfer","first_name":"Tobias","orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","full_name":"Meggendorfer, Tobias"},{"first_name":"Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"Yes (in subscription journal)","ec_funded":1,"scopus_import":"1","publication":"International Conference on Computer Aided Verification","department":[{"_id":"KrCh"}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","doi":"10.1007/978-3-031-37709-9_5","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031377082"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-07-22","name":"CAV: Computer Aided Verification","location":"Paris, France","start_date":"2023-07-17"},"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"file_date_updated":"2023-09-20T08:46:43Z","date_created":"2023-09-10T22:01:12Z","volume":13966,"type":"conference","month":"07","oa_version":"Published Version","date_updated":"2025-07-14T09:09:56Z","abstract":[{"lang":"eng","text":"Markov decision processes can be viewed as transformers of probability distributions. While this view is useful from a practical standpoint to reason about trajectories of distributions, basic reachability and safety problems are known to be computationally intractable (i.e., Skolem-hard) to solve in such models. Further, we show that even for simple examples of MDPs, strategies for safety objectives over distributions can require infinite memory and randomization.\r\nIn light of this, we present a novel overapproximation approach to synthesize strategies in an MDP, such that a safety objective over the distributions is met. More precisely, we develop a new framework for template-based synthesis of certificates as affine distributional and inductive invariants for safety objectives in MDPs. We provide two algorithms within this framework. One can only synthesize memoryless strategies, but has relative completeness guarantees, while the other can synthesize general strategies. The runtime complexity of both algorithms is in PSPACE. We implement these algorithms and show that they can solve several non-trivial examples."}],"page":"86-112","_id":"14317","year":"2023","acknowledgement":"This work was supported in part by the ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385 as well as DST/CEFIPRA/INRIA project EQuaVE and SERB Matrices grant MTR/2018/00074.","date_published":"2023-07-17T00:00:00Z","ddc":["000"],"has_accepted_license":"1","publication_status":"published","oa":1,"citation":{"chicago":"Akshay, S., Krishnendu Chatterjee, Tobias Meggendorfer, and Dorde Zikelic. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” In <i>International Conference on Computer Aided Verification</i>, 13966:86–112. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>.","ieee":"S. Akshay, K. Chatterjee, T. Meggendorfer, and D. Zikelic, “MDPs as distribution transformers: Affine invariant synthesis for safety objectives,” in <i>International Conference on Computer Aided Verification</i>, Paris, France, 2023, vol. 13966, pp. 86–112.","short":"S. Akshay, K. Chatterjee, T. Meggendorfer, D. Zikelic, in:, International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 86–112.","ama":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In: <i>International Conference on Computer Aided Verification</i>. Vol 13966. Springer Nature; 2023:86-112. doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>","apa":"Akshay, S., Chatterjee, K., Meggendorfer, T., &#38; Zikelic, D. (2023). MDPs as distribution transformers: Affine invariant synthesis for safety objectives. In <i>International Conference on Computer Aided Verification</i> (Vol. 13966, pp. 86–112). Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">https://doi.org/10.1007/978-3-031-37709-9_5</a>","mla":"Akshay, S., et al. “MDPs as Distribution Transformers: Affine Invariant Synthesis for Safety Objectives.” <i>International Conference on Computer Aided Verification</i>, vol. 13966, Springer Nature, 2023, pp. 86–112, doi:<a href=\"https://doi.org/10.1007/978-3-031-37709-9_5\">10.1007/978-3-031-37709-9_5</a>.","ista":"Akshay S, Chatterjee K, Meggendorfer T, Zikelic D. 2023. MDPs as distribution transformers: Affine invariant synthesis for safety objectives. International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 86–112."},"intvolume":"     13966","status":"public","alternative_title":["LNCS"]},{"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/14506","department":[{"_id":"GradSch"},{"_id":"KrPi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","ec_funded":1,"article_processing_charge":"No","file":[{"file_name":"thesis_yeo.zip","file_size":3037720,"relation":"source_file","content_type":"application/x-zip-compressed","creator":"cchlebak","file_id":"14598","date_updated":"2023-11-23T10:29:55Z","checksum":"521c72818d720a52b377207b2ee87b6a","date_created":"2023-11-23T10:29:55Z","access_level":"closed"},{"creator":"cchlebak","relation":"main_file","content_type":"application/pdf","file_size":2717256,"success":1,"file_name":"thesis_yeo.pdf","access_level":"open_access","date_created":"2023-11-23T10:30:08Z","checksum":"0ed5d16899687aecf13d843c9878c9f2","date_updated":"2023-11-23T10:30:08Z","file_id":"14599"}],"day":"10","author":[{"last_name":"Yeo","first_name":"Michelle X","orcid":"0009-0001-3676-4809","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","full_name":"Yeo, Michelle X"}],"degree_awarded":"PhD","title":"Advances in efficiency and privacy in payment channel network analysis","status":"public","alternative_title":["ISTA Thesis"],"citation":{"chicago":"Yeo, Michelle X. “Advances in Efficiency and Privacy in Payment Channel Network Analysis.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>.","ieee":"M. X. Yeo, “Advances in efficiency and privacy in payment channel network analysis,” Institute of Science and Technology Austria, 2023.","short":"M.X. Yeo, Advances in Efficiency and Privacy in Payment Channel Network Analysis, Institute of Science and Technology Austria, 2023.","ama":"Yeo MX. Advances in efficiency and privacy in payment channel network analysis. 2023. doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>","apa":"Yeo, M. X. (2023). <i>Advances in efficiency and privacy in payment channel network analysis</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14506\">https://doi.org/10.15479/14506</a>","mla":"Yeo, Michelle X. <i>Advances in Efficiency and Privacy in Payment Channel Network Analysis</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14506\">10.15479/14506</a>.","ista":"Yeo MX. 2023. Advances in efficiency and privacy in payment channel network analysis. Institute of Science and Technology Austria."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"9969","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"14490"},{"status":"public","id":"13238","relation":"part_of_dissertation"}]},"has_accepted_license":"1","oa":1,"publication_status":"published","ddc":["000"],"date_published":"2023-11-10T00:00:00Z","supervisor":[{"last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z"}],"year":"2023","_id":"14506","type":"dissertation","month":"11","oa_version":"Published Version","date_updated":"2025-07-14T09:09:52Z","abstract":[{"lang":"eng","text":"Payment channel networks are a promising approach to improve the scalability bottleneck\r\nof cryptocurrencies. Two design principles behind payment channel networks are\r\nefficiency and privacy. Payment channel networks improve efficiency by allowing users\r\nto transact in a peer-to-peer fashion along multi-hop routes in the network, avoiding\r\nthe lengthy process of consensus on the blockchain. Transacting over payment channel\r\nnetworks also improves privacy as these transactions are not broadcast to the blockchain.\r\nDespite the influx of recent protocols built on top of payment channel networks and\r\ntheir analysis, a common shortcoming of many of these protocols is that they typically\r\nfocus only on either improving efficiency or privacy, but not both. Another limitation\r\non the efficiency front is that the models used to model actions, costs and utilities of\r\nusers are limited or come with unrealistic assumptions.\r\nThis thesis aims to address some of the shortcomings of recent protocols and algorithms\r\non payment channel networks, particularly in their privacy and efficiency aspects. We\r\nfirst present a payment route discovery protocol based on hub labelling and private\r\ninformation retrieval that hides the route query and is also efficient. We then present\r\na rebalancing protocol that formulates the rebalancing problem as a linear program\r\nand solves the linear program using multiparty computation so as to hide the channel\r\nbalances. The rebalancing solution as output by our protocol is also globally optimal.\r\nWe go on to develop more realistic models of the action space, costs, and utilities of\r\nboth existing and new users that want to join the network. In each of these settings,\r\nwe also develop algorithms to optimise the utility of these users with good guarantees\r\non the approximation and competitive ratios."}],"page":"162","date_created":"2023-11-10T08:10:43Z","file_date_updated":"2023-11-23T10:30:08Z"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"JiFr"},{"_id":"MaLo"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_processing_charge":"No","ec_funded":1,"author":[{"last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2198-0509","full_name":"Gnyliukh, Nataliia"}],"day":"10","file":[{"file_name":"Thesis_Gnyliukh_final_08_11_23.docx","creator":"ngnyliuk","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":20824903,"checksum":"3d5e680bfc61f98e308c434f45cc9bd6","date_updated":"2023-11-20T09:18:51Z","file_id":"14567","access_level":"closed","date_created":"2023-11-20T09:18:51Z"},{"checksum":"bfc96d47fc4e7e857dd71656097214a4","file_id":"14568","date_updated":"2023-11-23T13:10:55Z","access_level":"closed","date_created":"2023-11-20T09:23:11Z","file_name":"Thesis_Gnyliukh_final_20_11_23.pdf","embargo_to":"open_access","creator":"ngnyliuk","file_size":24871844,"content_type":"application/pdf","relation":"main_file","embargo":"2024-11-23"}],"title":"Mechanism of clathrin-coated vesicle  formation during endocytosis in plants","degree_awarded":"PhD","project":[{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"keyword":["Clathrin-Mediated Endocytosis","vesicle scission","Dynamin-Related Protein 2","SH3P2","TPLATE complex","Total internal reflection fluorescence microscopy","Arabidopsis thaliana"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-037-4"]},"doi":"10.15479/at:ista:14510","year":"2023","_id":"14510","page":"180","oa_version":"Published Version","type":"dissertation","month":"11","date_updated":"2024-03-25T23:30:25Z","file_date_updated":"2023-11-23T13:10:55Z","date_created":"2023-11-10T09:10:06Z","alternative_title":["ISTA Thesis"],"status":"public","related_material":{"record":[{"status":"public","id":"14591","relation":"part_of_dissertation"},{"id":"9887","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"8139","status":"public"}]},"citation":{"short":"N. Gnyliukh, Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants, Institute of Science and Technology Austria, 2023.","chicago":"Gnyliukh, Nataliia. “Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>.","ieee":"N. Gnyliukh, “Mechanism of clathrin-coated vesicle  formation during endocytosis in plants,” Institute of Science and Technology Austria, 2023.","apa":"Gnyliukh, N. (2023). <i>Mechanism of clathrin-coated vesicle  formation during endocytosis in plants</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14510\">https://doi.org/10.15479/at:ista:14510</a>","ista":"Gnyliukh N. 2023. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. Institute of Science and Technology Austria.","mla":"Gnyliukh, Nataliia. <i>Mechanism of Clathrin-Coated Vesicle  Formation during Endocytosis in Plants</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>.","ama":"Gnyliukh N. Mechanism of clathrin-coated vesicle  formation during endocytosis in plants. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14510\">10.15479/at:ista:14510</a>"},"publication_status":"published","has_accepted_license":"1","ddc":["570"],"date_published":"2023-11-10T00:00:00Z","supervisor":[{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"},{"first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"LifeSc"}]},{"doi":"10.3233/FAIA230264","quality_controlled":"1","publication_identifier":{"isbn":["9781643684369"],"issn":["0922-6389"]},"conference":{"start_date":"2023-09-30","location":"Krakow, Poland","name":"ECAI: European Conference on Artificial Intelligence","end_date":"2023-10-04"},"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"}],"arxiv":1,"title":"Reachability poorman discrete-bidding games","author":[{"last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","orcid":"0000-0002-1712-2165","full_name":"Meggendorfer, Tobias","last_name":"Meggendorfer","first_name":"Tobias"},{"first_name":"Suman","last_name":"Sadhukhan","full_name":"Sadhukhan, Suman"},{"full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","last_name":"Tkadlec","first_name":"Josef"},{"last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde"}],"license":"https://creativecommons.org/licenses/by-nc/4.0/","file":[{"access_level":"open_access","date_created":"2023-11-13T10:16:10Z","checksum":"1390ca38480fa4cf286b0f1a42e8c12f","file_id":"14529","date_updated":"2023-11-13T10:16:10Z","creator":"dernst","file_size":501011,"content_type":"application/pdf","relation":"main_file","file_name":"2023_FAIA_Avni.pdf","success":1}],"day":"28","publication":"Frontiers in Artificial Intelligence and Applications","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"ec_funded":1,"scopus_import":"1","article_processing_charge":"No","publisher":"IOS Press","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["000"],"date_published":"2023-09-28T00:00:00Z","oa":1,"publication_status":"published","has_accepted_license":"1","intvolume":"       372","citation":{"chicago":"Avni, Guy, Tobias Meggendorfer, Suman Sadhukhan, Josef Tkadlec, and Dorde Zikelic. “Reachability Poorman Discrete-Bidding Games.” In <i>Frontiers in Artificial Intelligence and Applications</i>, 372:141–48. IOS Press, 2023. <a href=\"https://doi.org/10.3233/FAIA230264\">https://doi.org/10.3233/FAIA230264</a>.","ieee":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, and D. Zikelic, “Reachability poorman discrete-bidding games,” in <i>Frontiers in Artificial Intelligence and Applications</i>, Krakow, Poland, 2023, vol. 372, pp. 141–148.","short":"G. Avni, T. Meggendorfer, S. Sadhukhan, J. Tkadlec, D. Zikelic, in:, Frontiers in Artificial Intelligence and Applications, IOS Press, 2023, pp. 141–148.","ama":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. Reachability poorman discrete-bidding games. In: <i>Frontiers in Artificial Intelligence and Applications</i>. Vol 372. IOS Press; 2023:141-148. doi:<a href=\"https://doi.org/10.3233/FAIA230264\">10.3233/FAIA230264</a>","apa":"Avni, G., Meggendorfer, T., Sadhukhan, S., Tkadlec, J., &#38; Zikelic, D. (2023). Reachability poorman discrete-bidding games. In <i>Frontiers in Artificial Intelligence and Applications</i> (Vol. 372, pp. 141–148). Krakow, Poland: IOS Press. <a href=\"https://doi.org/10.3233/FAIA230264\">https://doi.org/10.3233/FAIA230264</a>","ista":"Avni G, Meggendorfer T, Sadhukhan S, Tkadlec J, Zikelic D. 2023. Reachability poorman discrete-bidding games. Frontiers in Artificial Intelligence and Applications. ECAI: European Conference on Artificial Intelligence vol. 372, 141–148.","mla":"Avni, Guy, et al. “Reachability Poorman Discrete-Bidding Games.” <i>Frontiers in Artificial Intelligence and Applications</i>, vol. 372, IOS Press, 2023, pp. 141–48, doi:<a href=\"https://doi.org/10.3233/FAIA230264\">10.3233/FAIA230264</a>."},"external_id":{"arxiv":["2307.15218"]},"status":"public","volume":372,"date_created":"2023-11-12T23:00:56Z","file_date_updated":"2023-11-13T10:16:10Z","page":"141-148","type":"conference","oa_version":"Published Version","month":"09","abstract":[{"text":"We consider bidding games, a class of two-player zero-sum graph games. The game proceeds as follows. Both players have bounded budgets. A token is placed on a vertex of a graph, in each turn the players simultaneously submit bids, and the higher bidder moves the token, where we break bidding ties in favor of Player 1. Player 1 wins the game iff the token visits a designated target vertex. We consider, for the first time, poorman discrete-bidding in which the granularity of the bids is restricted and the higher bid is paid to the bank. Previous work either did not impose granularity restrictions or considered Richman bidding (bids are paid to the opponent). While the latter mechanisms are technically more accessible, the former is more appealing from a practical standpoint. Our study focuses on threshold budgets, which is the necessary and sufficient initial budget required for Player 1 to ensure winning against a given Player 2 budget. We first show existence of thresholds. In DAGs, we show that threshold budgets can be approximated with error bounds by thresholds under continuous-bidding and that they exhibit a periodic behavior. We identify closed-form solutions in special cases. We implement and experiment with an algorithm to find threshold budgets.","lang":"eng"}],"date_updated":"2025-07-14T09:09:57Z","_id":"14518","acknowledgement":"This research was supported in part by ISF grant no. 1679/21, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie SkłodowskaCurie Grant Agreement No. 665385.","year":"2023"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)"},"article_processing_charge":"No","ec_funded":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"title":"Automated verification and control of infinite state stochastic systems","degree_awarded":"PhD","author":[{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","last_name":"Zikelic","first_name":"Dorde"}],"day":"15","file":[{"access_level":"open_access","date_created":"2023-11-15T13:43:28Z","checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_id":"14540","date_updated":"2023-11-15T13:43:28Z","creator":"cchlebak","file_size":2116426,"content_type":"application/pdf","relation":"main_file","file_name":"main.pdf","success":1},{"date_updated":"2023-11-15T13:44:24Z","file_id":"14541","checksum":"80ca37618a3c7b59866875f8be9b15ed","date_created":"2023-11-15T13:44:24Z","access_level":"closed","file_name":"thesis_source.zip","relation":"source_file","content_type":"application/x-zip-compressed","file_size":35884057,"creator":"cchlebak"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"doi":"10.15479/14539","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-036-7"]},"_id":"14539","year":"2023","date_created":"2023-11-15T13:39:10Z","file_date_updated":"2023-11-15T13:44:24Z","page":"256","oa_version":"Published Version","month":"11","type":"dissertation","date_updated":"2025-07-14T09:10:10Z","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1194","status":"public"},{"status":"public","id":"12000","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"12511","status":"public"},{"id":"14600","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14601"},{"relation":"part_of_dissertation","status":"public","id":"9644"},{"relation":"part_of_dissertation","status":"public","id":"10414"}]},"citation":{"apa":"Zikelic, D. (2023). <i>Automated verification and control of infinite state stochastic systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>","ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","mla":"Zikelic, Dorde. <i>Automated Verification and Control of Infinite State Stochastic Systems</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:<a href=\"https://doi.org/10.15479/14539\">10.15479/14539</a>","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/14539\">https://doi.org/10.15479/14539</a>.","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023."},"alternative_title":["ISTA Thesis"],"status":"public","date_published":"2023-11-15T00:00:00Z","ddc":["000"],"supervisor":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"}],"publication_status":"published","oa":1},{"day":"22","author":[{"first_name":"Matin","last_name":"Ansaripour","full_name":"Ansaripour, Matin"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"},{"last_name":"Lechner","first_name":"Mathias","full_name":"Lechner, Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","last_name":"Zikelic"}],"title":"Learning provably stabilizing neural controllers for discrete-time stochastic systems","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","ec_funded":1,"publication":"21st International Symposium on Automated Technology for Verification and Analysis","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031453281"],"issn":["0302-9743"]},"quality_controlled":"1","doi":"10.1007/978-3-031-45329-8_17","project":[{"name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","grant_number":"101020093"},{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"}],"language":[{"iso":"eng"}],"conference":{"end_date":"2023-10-27","location":"Singapore, Singapore","name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2023-10-24"},"abstract":[{"lang":"eng","text":"We consider the problem of learning control policies in discrete-time stochastic systems which guarantee that the system stabilizes within some specified stabilization region with probability 1. Our approach is based on the novel notion of stabilizing ranking supermartingales (sRSMs) that we introduce in this work. Our sRSMs overcome the limitation of methods proposed in previous works whose applicability is restricted to systems in which the stabilizing region cannot be left once entered under any control policy. We present a learning procedure that learns a control policy together with an sRSM that formally certifies probability 1 stability, both learned as neural networks. We show that this procedure can also be adapted to formally verifying that, under a given Lipschitz continuous control policy, the stochastic system stabilizes within some stabilizing region with probability 1. Our experimental evaluation shows that our learning procedure can successfully learn provably stabilizing policies in practice."}],"date_updated":"2025-07-14T09:09:59Z","month":"10","oa_version":"None","type":"conference","page":"357-379","date_created":"2023-11-19T23:00:56Z","volume":14215,"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","_id":"14559","publication_status":"published","date_published":"2023-10-22T00:00:00Z","status":"public","alternative_title":["LNCS"],"citation":{"chicago":"Ansaripour, Matin, Krishnendu Chatterjee, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” In <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, 14215:357–79. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">https://doi.org/10.1007/978-3-031-45329-8_17</a>.","ieee":"M. Ansaripour, K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “Learning provably stabilizing neural controllers for discrete-time stochastic systems,” in <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, Singapore, Singapore, 2023, vol. 14215, pp. 357–379.","short":"M. Ansaripour, K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, 21st International Symposium on Automated Technology for Verification and Analysis, Springer Nature, 2023, pp. 357–379.","ama":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. Learning provably stabilizing neural controllers for discrete-time stochastic systems. In: <i>21st International Symposium on Automated Technology for Verification and Analysis</i>. Vol 14215. Springer Nature; 2023:357-379. doi:<a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">10.1007/978-3-031-45329-8_17</a>","apa":"Ansaripour, M., Chatterjee, K., Henzinger, T. A., Lechner, M., &#38; Zikelic, D. (2023). Learning provably stabilizing neural controllers for discrete-time stochastic systems. In <i>21st International Symposium on Automated Technology for Verification and Analysis</i> (Vol. 14215, pp. 357–379). Singapore, Singapore: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">https://doi.org/10.1007/978-3-031-45329-8_17</a>","ista":"Ansaripour M, Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. Learning provably stabilizing neural controllers for discrete-time stochastic systems. 21st International Symposium on Automated Technology for Verification and Analysis. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 14215, 357–379.","mla":"Ansaripour, Matin, et al. “Learning Provably Stabilizing Neural Controllers for Discrete-Time Stochastic Systems.” <i>21st International Symposium on Automated Technology for Verification and Analysis</i>, vol. 14215, Springer Nature, 2023, pp. 357–79, doi:<a href=\"https://doi.org/10.1007/978-3-031-45329-8_17\">10.1007/978-3-031-45329-8_17</a>."},"intvolume":"     14215"},{"doi":"10.1101/2023.10.09.561523","date_published":"2023-10-10T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2023.10.09.561523v2"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa":1,"publication_status":"submitted","related_material":{"record":[{"status":"public","id":"14510","relation":"dissertation_contains"}]},"citation":{"chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>.","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. .","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>","apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, <a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>."},"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"status":"public","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","date_created":"2023-11-22T10:17:49Z","author":[{"last_name":"Gnyliukh","first_name":"Nataliia","orcid":"0000-0002-2198-0509","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia"},{"last_name":"Johnson","first_name":"Alexander J","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"full_name":"Nagel, Marie-Kristin","last_name":"Nagel","first_name":"Marie-Kristin"},{"id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline","first_name":"Aline","last_name":"Monzer"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria","last_name":"Hlavata","first_name":"Annamaria"},{"full_name":"Isono, Erika","last_name":"Isono","first_name":"Erika"},{"first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7309-9724","full_name":"Loose, Martin"},{"last_name":"Friml","first_name":"Jiří","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"date_updated":"2023-12-01T13:51:06Z","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"day":"10","month":"10","type":"preprint","oa_version":"Preprint","publication":"bioRxiv","_id":"14591","ec_funded":1,"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2023","department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}]},{"page":"104","date_updated":"2023-12-07T14:12:25Z","type":"dissertation","oa_version":"Published Version","month":"11","file_date_updated":"2023-12-06T13:14:15Z","date_created":"2023-12-04T13:17:37Z","year":"2023","_id":"14641","publication_status":"published","has_accepted_license":"1","supervisor":[{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","last_name":"Hof"}],"ddc":["570"],"date_published":"2023-11-30T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"CampIT"}],"alternative_title":["ISTA Thesis"],"status":"public","citation":{"apa":"Hennessey-Wesen, M. (2023). <i>Adaptive mutation in E. coli modulated by luxS</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>","ista":"Hennessey-Wesen M. 2023. Adaptive mutation in E. coli modulated by luxS. Institute of Science and Technology Austria.","mla":"Hennessey-Wesen, Mike. <i>Adaptive Mutation in E. Coli Modulated by LuxS</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>.","ama":"Hennessey-Wesen M. Adaptive mutation in E. coli modulated by luxS. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14641\">10.15479/at:ista:14641</a>","short":"M. Hennessey-Wesen, Adaptive Mutation in E. Coli Modulated by LuxS, Institute of Science and Technology Austria, 2023.","chicago":"Hennessey-Wesen, Mike. “Adaptive Mutation in E. Coli Modulated by LuxS.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14641\">https://doi.org/10.15479/at:ista:14641</a>.","ieee":"M. Hennessey-Wesen, “Adaptive mutation in E. coli modulated by luxS,” Institute of Science and Technology Austria, 2023."},"author":[{"first_name":"Mike","last_name":"Hennessey-Wesen","id":"3F338C72-F248-11E8-B48F-1D18A9856A87","full_name":"Hennessey-Wesen, Mike"}],"file":[{"file_name":"mike_thesis_v06-12-2023.odt","file_size":46405919,"relation":"source_file","content_type":"application/vnd.oasis.opendocument.text","creator":"mhenness","file_id":"14648","date_updated":"2023-12-06T13:13:26Z","checksum":"4127c285b34f4bf7fb31ef24f9d14c25","date_created":"2023-12-06T13:13:26Z","access_level":"closed"},{"access_level":"closed","date_created":"2023-12-06T13:14:15Z","checksum":"f5203a61eddaf35235bbc51904d73982","date_updated":"2023-12-06T13:14:15Z","file_id":"14649","embargo_to":"open_access","creator":"mhenness","relation":"main_file","embargo":"2024-11-30","content_type":"application/pdf","file_size":21282155,"file_name":"mike_thesis_v06-12-2023.pdf"}],"day":"30","title":"Adaptive mutation in E. coli modulated by luxS","degree_awarded":"PhD","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"BjHo"}],"article_processing_charge":"No","ec_funded":1,"publication_identifier":{"issn":["2663 - 337X"]},"doi":"10.15479/at:ista:14641","project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"keyword":["microfluidics","miceobiology","mutations","quorum sensing"],"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"project":[{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"doi":"10.15479/at:ista:14651","publication_identifier":{"issn":["2663 - 337X"]},"article_processing_charge":"No","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","degree_awarded":"PhD","title":"Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus","day":"12","file":[{"file_name":"Phd_Thesis_LA.pdf","success":1,"file_size":34101468,"content_type":"application/pdf","relation":"main_file","creator":"larathoo","file_id":"14684","date_updated":"2023-12-13T15:37:55Z","checksum":"520bdb61e95e66070e02824947d2c5fa","date_created":"2023-12-13T15:37:55Z","access_level":"open_access"},{"checksum":"d8e59afd0817c98fba2564a264508e5c","date_updated":"2023-12-14T08:58:18Z","file_id":"14685","access_level":"closed","date_created":"2023-12-13T15:42:23Z","file_name":"Phd_Thesis_LA.zip","creator":"larathoo","content_type":"application/zip","relation":"source_file","file_size":31052872},{"date_created":"2023-12-11T19:24:59Z","access_level":"closed","date_updated":"2023-12-14T08:58:18Z","file_id":"14681","checksum":"9a778c949932286f4519e1f1fca2820d","content_type":"application/zip","relation":"supplementary_material","file_size":10713896,"creator":"larathoo","file_name":"Supplementary_Materials.zip"}],"author":[{"full_name":"Arathoon, Louise S","orcid":"0000-0003-1771-714X","id":"2CFCFF98-F248-11E8-B48F-1D18A9856A87","first_name":"Louise S","last_name":"Arathoon"}],"citation":{"short":"L.S. Arathoon, Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus, Institute of Science and Technology Austria, 2023.","chicago":"Arathoon, Louise S. “Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>.","ieee":"L. S. Arathoon, “Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus,” Institute of Science and Technology Austria, 2023.","apa":"Arathoon, L. S. (2023). <i>Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14651\">https://doi.org/10.15479/at:ista:14651</a>","mla":"Arathoon, Louise S. <i>Investigating Inbreeding Depression and the Self-Incompatibility Locus of Antirrhinum Majus</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>.","ista":"Arathoon LS. 2023. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. Institute of Science and Technology Austria.","ama":"Arathoon LS. Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14651\">10.15479/at:ista:14651</a>"},"related_material":{"record":[{"id":"11411","status":"public","relation":"part_of_dissertation"}]},"status":"public","alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"date_published":"2023-12-12T00:00:00Z","has_accepted_license":"1","oa":1,"publication_status":"published","_id":"14651","year":"2023","file_date_updated":"2023-12-14T08:58:18Z","date_created":"2023-12-11T19:30:37Z","abstract":[{"lang":"eng","text":"For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism."}],"date_updated":"2023-12-22T11:04:45Z","type":"dissertation","month":"12","oa_version":"Published Version","page":"96"},{"external_id":{"pmid":["37758476"]},"status":"public","intvolume":"        43","citation":{"apa":"Nardin, M., Csicsvari, J. L., Tkačik, G., &#38; Savin, C. (2023). The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. Society of Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>","ista":"Nardin M, Csicsvari JL, Tkačik G, Savin C. 2023. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. The Journal of Neuroscience. 43(48), 8140–8156.","mla":"Nardin, Michele, et al. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>, vol. 43, no. 48, Society of Neuroscience, 2023, pp. 8140–56, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>.","ama":"Nardin M, Csicsvari JL, Tkačik G, Savin C. The structure of hippocampal CA1 interactions optimizes spatial coding across experience. <i>The Journal of Neuroscience</i>. 2023;43(48):8140-8156. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">10.1523/JNEUROSCI.0194-23.2023</a>","short":"M. Nardin, J.L. Csicsvari, G. Tkačik, C. Savin, The Journal of Neuroscience 43 (2023) 8140–8156.","chicago":"Nardin, Michele, Jozsef L Csicsvari, Gašper Tkačik, and Cristina Savin. “The Structure of Hippocampal CA1 Interactions Optimizes Spatial Coding across Experience.” <i>The Journal of Neuroscience</i>. Society of Neuroscience, 2023. <a href=\"https://doi.org/10.1523/JNEUROSCI.0194-23.2023\">https://doi.org/10.1523/JNEUROSCI.0194-23.2023</a>.","ieee":"M. Nardin, J. L. Csicsvari, G. Tkačik, and C. Savin, “The structure of hippocampal CA1 interactions optimizes spatial coding across experience,” <i>The Journal of Neuroscience</i>, vol. 43, no. 48. Society of Neuroscience, pp. 8140–8156, 2023."},"publication_status":"published","oa":1,"has_accepted_license":"1","ddc":["570"],"date_published":"2023-11-29T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1523/JNEUROSCI.0194-23.2023","open_access":"1"}],"acknowledgement":"M.N. was supported by the European Union Horizon 2020 Grant 665385. J.C. was supported by the European Research Council Consolidator Grant 281511. G.T. was supported by the Austrian Science Fund (FWF) Grant P34015. C.S. was supported by an Institute of Science and Technology fellow award and by the National Science Foundation (NSF) Award No. 1922658. We thank Peter Baracskay, Karola Kaefer, and Hugo Malagon-Vina for the acquisition of the data. We also thank Federico Stella, Wiktor Młynarski, Dori Derdikman, Colin Bredenberg, Roman Huszar, Heloisa Chiossi, Lorenzo Posani, and Mohamady El-Gaby for comments on an earlier version of the manuscript.","year":"2023","_id":"14656","page":"8140-8156","date_updated":"2023-12-11T11:37:20Z","abstract":[{"text":"Although much is known about how single neurons in the hippocampus represent an animal's position, how circuit interactions contribute to spatial coding is less well understood. Using a novel statistical estimator and theoretical modeling, both developed in the framework of maximum entropy models, we reveal highly structured CA1 cell-cell interactions in male rats during open field exploration. The statistics of these interactions depend on whether the animal is in a familiar or novel environment. In both conditions the circuit interactions optimize the encoding of spatial information, but for regimes that differ in the informativeness of their spatial inputs. This structure facilitates linear decodability, making the information easy to read out by downstream circuits. Overall, our findings suggest that the efficient coding hypothesis is not only applicable to individual neuron properties in the sensory periphery, but also to neural interactions in the central brain.","lang":"eng"}],"month":"11","oa_version":"Published Version","type":"journal_article","volume":43,"file_date_updated":"2023-12-11T11:30:37Z","date_created":"2023-12-10T23:00:58Z","project":[{"grant_number":"281511","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","call_identifier":"FP7","_id":"257A4776-B435-11E9-9278-68D0E5697425"},{"name":"Efficient coding with biophysical realism","_id":"626c45b5-2b32-11ec-9570-e509828c1ba6","grant_number":"P34015"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"language":[{"iso":"eng"}],"issue":"48","publication_identifier":{"eissn":["1529-2401"]},"doi":"10.1523/JNEUROSCI.0194-23.2023","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Society of Neuroscience","pmid":1,"department":[{"_id":"JoCs"},{"_id":"GaTk"}],"publication":"The Journal of Neuroscience","scopus_import":"1","ec_funded":1,"article_processing_charge":"Yes (in subscription journal)","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","author":[{"id":"30BD0376-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8849-6570","full_name":"Nardin, Michele","first_name":"Michele","last_name":"Nardin"},{"last_name":"Csicsvari","first_name":"Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"},{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin"}],"file":[{"creator":"dernst","embargo_to":"open_access","embargo":"2024-06-01","content_type":"application/pdf","relation":"main_file","file_size":2280632,"file_name":"2023_JourNeuroscience_Nardin.pdf","access_level":"closed","date_created":"2023-12-11T11:30:37Z","checksum":"e2503c8f84be1050e28f64320f1d5bd2","date_updated":"2023-12-11T11:30:37Z","file_id":"14674"}],"day":"29","title":"The structure of hippocampal CA1 interactions optimizes spatial coding across experience"},{"supervisor":[{"full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K"}],"ddc":["570"],"date_published":"2023-12-20T00:00:00Z","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"publication_status":"published","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6328"},{"id":"7885","status":"public","relation":"part_of_dissertation"},{"id":"12272","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14274"},{"relation":"part_of_dissertation","status":"public","id":"14360"}]},"citation":{"ieee":"J. A. Stopp, “Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function,” Institute of Science and Technology Austria, 2023.","chicago":"Stopp, Julian A. “Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>.","short":"J.A. Stopp, Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function, Institute of Science and Technology Austria, 2023.","ama":"Stopp JA. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>","mla":"Stopp, Julian A. <i>Neutrophils on the Hunt: Migratory Strategies Employed by Neutrophils to Fulfill Their Effector Function</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:14697\">10.15479/at:ista:14697</a>.","ista":"Stopp JA. 2023. Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function. Institute of Science and Technology Austria.","apa":"Stopp, J. A. (2023). <i>Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:14697\">https://doi.org/10.15479/at:ista:14697</a>"},"alternative_title":["ISTA Thesis"],"status":"public","file_date_updated":"2023-12-20T10:41:42Z","date_created":"2023-12-18T19:14:28Z","page":"226","date_updated":"2023-12-21T14:30:02Z","oa_version":"Published Version","type":"dissertation","month":"12","_id":"14697","year":"2023","doi":"10.15479/at:ista:14697","publication_identifier":{"issn":["2663 - 337X"],"isbn":["978-3-99078-038-1"]},"language":[{"iso":"eng"}],"project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"title":"Neutrophils on the hunt: Migratory strategies employed by neutrophils to fulfill their effector function","degree_awarded":"PhD","author":[{"full_name":"Stopp, Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","last_name":"Stopp"}],"day":"20","file":[{"date_updated":"2023-12-20T09:35:34Z","file_id":"14699","checksum":"457927165d5d556305d3086f6b83e5c7","date_created":"2023-12-20T09:35:34Z","access_level":"closed","file_name":"Thesis.pdf","content_type":"application/pdf","embargo":"2024-12-20","relation":"main_file","file_size":51585778,"embargo_to":"open_access","creator":"jstopp"},{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_size":69625950,"creator":"jstopp","file_name":"Thesis.docx","date_created":"2023-12-20T09:35:35Z","access_level":"closed","date_updated":"2023-12-20T10:41:42Z","file_id":"14700","checksum":"e8d26449ac461f5e8478a62c9507506f"}],"article_processing_charge":"No","ec_funded":1,"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"GradSch"},{"_id":"MiSi"}]},{"publication":"Formal Aspects of Computing","ec_funded":1,"article_processing_charge":"Yes (via OA deal)","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"title":"On lexicographic proof rules for probabilistic termination","arxiv":1,"article_number":"11","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Kafshdar Goharshady, Ehsan","first_name":"Ehsan","last_name":"Kafshdar Goharshady"},{"last_name":"Novotný","first_name":"Petr","full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zárevúcky, Jiří","last_name":"Zárevúcky","first_name":"Jiří"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde"}],"file":[{"checksum":"3bb133eeb27ec01649a9a36445d952d9","file_id":"14804","date_updated":"2024-01-16T08:11:24Z","access_level":"open_access","date_created":"2024-01-16T08:11:24Z","file_name":"2023_FormalAspectsComputing_Chatterjee.pdf","success":1,"creator":"dernst","file_size":502522,"relation":"main_file","content_type":"application/pdf"}],"day":"23","keyword":["Theoretical Computer Science","Software"],"language":[{"iso":"eng"}],"issue":"2","project":[{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"}],"doi":"10.1145/3585391","quality_controlled":"1","publication_identifier":{"issn":["0934-5043"],"eissn":["1433-299X"]},"_id":"14778","acknowledgement":"This research was partially supported by the ERC CoG (grant no. 863818; ForM-SMArt), the Czech Science Foundation (grant no. GA21-24711S), and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","year":"2023","volume":35,"date_created":"2024-01-10T09:27:43Z","file_date_updated":"2024-01-16T08:11:24Z","abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"date_updated":"2025-07-14T09:10:10Z","type":"journal_article","month":"06","oa_version":"Published Version","related_material":{"record":[{"relation":"earlier_version","id":"10414","status":"public"}]},"intvolume":"        35","citation":{"apa":"Chatterjee, K., Kafshdar Goharshady, E., Novotný, P., Zárevúcky, J., &#38; Zikelic, D. (2023). On lexicographic proof rules for probabilistic termination. <i>Formal Aspects of Computing</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3585391\">https://doi.org/10.1145/3585391</a>","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>Formal Aspects of Computing</i>, vol. 35, no. 2, 11, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3585391\">10.1145/3585391</a>.","ista":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2023. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 35(2), 11.","ama":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. <i>Formal Aspects of Computing</i>. 2023;35(2). doi:<a href=\"https://doi.org/10.1145/3585391\">10.1145/3585391</a>","short":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, Formal Aspects of Computing 35 (2023).","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>Formal Aspects of Computing</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3585391\">https://doi.org/10.1145/3585391</a>.","ieee":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” <i>Formal Aspects of Computing</i>, vol. 35, no. 2. Association for Computing Machinery, 2023."},"external_id":{"arxiv":["2108.02188"]},"status":"public","ddc":["000"],"date_published":"2023-06-23T00:00:00Z","publication_status":"published","oa":1,"has_accepted_license":"1"},{"citation":{"short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, in:, Proceedings of the 37th AAAI Conference on Artificial Intelligence, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–11935.","ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” in <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, Washington, DC, United States, 2023, vol. 37, no. 10, pp. 11926–11935.","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, 37:11926–35. Association for the Advancement of Artificial Intelligence, 2023. <a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">https://doi.org/10.1609/aaai.v37i10.26407</a>.","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. 2023. Learning control policies for stochastic systems with reach-avoid guarantees. Proceedings of the 37th AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence vol. 37, 11926–11935.","mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>, vol. 37, no. 10, Association for the Advancement of Artificial Intelligence, 2023, pp. 11926–35, doi:<a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">10.1609/aaai.v37i10.26407</a>.","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., &#38; Chatterjee, K. (2023). Learning control policies for stochastic systems with reach-avoid guarantees. In <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i> (Vol. 37, pp. 11926–11935). Washington, DC, United States: Association for the Advancement of Artificial Intelligence. <a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">https://doi.org/10.1609/aaai.v37i10.26407</a>","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. In: <i>Proceedings of the 37th AAAI Conference on Artificial Intelligence</i>. Vol 37. Association for the Advancement of Artificial Intelligence; 2023:11926-11935. doi:<a href=\"https://doi.org/10.1609/aaai.v37i10.26407\">10.1609/aaai.v37i10.26407</a>"},"intvolume":"        37","related_material":{"record":[{"relation":"earlier_version","status":"public","id":"14600"}]},"status":"public","external_id":{"arxiv":["2210.05308"]},"date_published":"2023-06-26T00:00:00Z","publication_status":"published","_id":"14830","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","date_created":"2024-01-18T07:44:31Z","volume":37,"abstract":[{"lang":"eng","text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold p in [0,1] over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on 3 stochastic non-linear reinforcement learning tasks."}],"date_updated":"2025-07-14T09:10:02Z","oa_version":"Preprint","month":"06","type":"conference","page":"11926-11935","language":[{"iso":"eng"}],"issue":"10","keyword":["General Medicine"],"conference":{"end_date":"2023-02-14","start_date":"2023-02-07","name":"AAAI: Conference on Artificial Intelligence","location":"Washington, DC, United States"},"project":[{"grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"},{"grant_number":"863818","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"quality_controlled":"1","doi":"10.1609/aaai.v37i10.26407","publication_identifier":{"eissn":["2374-3468"],"issn":["2159-5399"]},"ec_funded":1,"article_processing_charge":"No","publication":"Proceedings of the 37th AAAI Conference on Artificial Intelligence","department":[{"_id":"ToHe"},{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for the Advancement of Artificial Intelligence","title":"Learning control policies for stochastic systems with reach-avoid guarantees","arxiv":1,"day":"26","author":[{"last_name":"Zikelic","first_name":"Dorde","full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"full_name":"Henzinger, Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","first_name":"Thomas A"},{"first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"}]},{"file_date_updated":"2023-05-24T16:12:59Z","date_created":"2023-05-23T17:07:53Z","abstract":[{"text":"Deep learning has become an integral part of a large number of important applications, and many of the recent breakthroughs have been enabled by the ability to train very large models, capable to capture complex patterns and relationships from the data. At the same time, the massive sizes of modern deep learning models have made their deployment to smaller devices more challenging; this is particularly important, as in many applications the users rely on accurate deep learning predictions, but they only have access to devices with limited memory and compute power. One solution to this problem is to prune neural networks, by setting as many of their parameters as possible to zero, to obtain accurate sparse models with lower memory footprint. Despite the great research progress in obtaining sparse models that preserve accuracy, while satisfying memory and computational constraints, there are still many challenges associated with efficiently training sparse models, as well as understanding their generalization properties.\r\n\r\nThe focus of this thesis is to investigate how the training process of sparse models can be made more efficient, and to understand the differences between sparse and dense models in terms of how well they can generalize to changes in the data distribution. We first study a method for co-training sparse and dense models, at a lower cost compared to regular training. With our method we can obtain very accurate sparse networks, and dense models that can recover the baseline accuracy. Furthermore, we are able to more easily analyze the differences, at prediction level, between the sparse-dense model pairs. Next, we investigate the generalization properties of sparse neural networks in more detail, by studying how well different sparse models trained on a larger task can adapt to smaller, more specialized tasks, in a transfer learning scenario. Our analysis across multiple pruning methods and sparsity levels reveals that sparse models provide features that can transfer similarly to or better than the dense baseline. However, the choice of the pruning method plays an important role, and can influence the results when the features are fixed (linear finetuning), or when they are allowed to adapt to the new task (full finetuning). Using sparse models with fixed masks for finetuning on new tasks has an important practical advantage, as it enables training neural networks on smaller devices. However, one drawback of current pruning methods is that the entire training cycle has to be repeated to obtain the initial sparse model, for every sparsity target; in consequence, the entire training process is costly and also multiple models need to be stored. In the last part of the thesis we propose a method that can train accurate dense models that are compressible in a single step, to multiple sparsity levels, without additional finetuning. Our method results in sparse models that can be competitive with existing pruning methods, and which can also successfully generalize to new tasks.","lang":"eng"}],"date_updated":"2023-08-04T10:33:27Z","month":"05","oa_version":"Published Version","type":"dissertation","page":"147","_id":"13074","year":"2023","acknowledged_ssus":[{"_id":"ScienComp"}],"supervisor":[{"first_name":"Christoph","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"date_published":"2023-05-23T00:00:00Z","ddc":["000"],"has_accepted_license":"1","oa":1,"publication_status":"published","citation":{"chicago":"Peste, Elena-Alexandra. “Efficiency and Generalization of Sparse Neural Networks.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>.","ieee":"E.-A. Peste, “Efficiency and generalization of sparse neural networks,” Institute of Science and Technology Austria, 2023.","short":"E.-A. Peste, Efficiency and Generalization of Sparse Neural Networks, Institute of Science and Technology Austria, 2023.","ama":"Peste E-A. Efficiency and generalization of sparse neural networks. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>","apa":"Peste, E.-A. (2023). <i>Efficiency and generalization of sparse neural networks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13074\">https://doi.org/10.15479/at:ista:13074</a>","mla":"Peste, Elena-Alexandra. <i>Efficiency and Generalization of Sparse Neural Networks</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13074\">10.15479/at:ista:13074</a>.","ista":"Peste E-A. 2023. Efficiency and generalization of sparse neural networks. Institute of Science and Technology Austria."},"related_material":{"record":[{"id":"11458","status":"public","relation":"part_of_dissertation"},{"id":"13053","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12299"}]},"status":"public","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","title":"Efficiency and generalization of sparse neural networks","file":[{"creator":"epeste","relation":"main_file","content_type":"application/pdf","file_size":2152072,"success":1,"file_name":"PhD_Thesis_Alexandra_Peste_final.pdf","access_level":"open_access","date_created":"2023-05-24T16:11:16Z","checksum":"6b3354968403cb9d48cc5a83611fb571","date_updated":"2023-05-24T16:11:16Z","file_id":"13087"},{"creator":"epeste","relation":"source_file","content_type":"application/zip","file_size":1658293,"file_name":"PhD_Thesis_APeste.zip","access_level":"closed","date_created":"2023-05-24T16:12:59Z","checksum":"8d0df94bbcf4db72c991f22503b3fd60","date_updated":"2023-05-24T16:12:59Z","file_id":"13088"}],"day":"23","author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","first_name":"Elena-Alexandra","last_name":"Peste"}],"article_processing_charge":"No","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"publisher":"Institute of Science and Technology Austria","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.15479/at:ista:13074","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223"}]},{"_id":"13126","acknowledgement":"We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","year":"2023","date_created":"2023-06-07T07:15:12Z","file_date_updated":"2023-08-04T13:19:47Z","date_updated":"2024-02-21T12:18:19Z","abstract":[{"text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease.","lang":"eng"}],"type":"research_data","month":"08","oa_version":"Published Version","related_material":{"record":[{"id":"14257","status":"public","relation":"used_in_publication"}],"link":[{"relation":"research_data","url":"https://pub.ista.ac.at/group_danzl/data/CATS/","description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. "}]},"citation":{"apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>","short":"J.G. Danzl, (2023).","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>.","ieee":"J. G. 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Paris, France: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">https://doi.org/10.1007/978-3-031-30823-9_1</a>","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, vol. 13993, Springer Nature, 2023, pp. 3–25, doi:<a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">10.1007/978-3-031-30823-9_1</a>.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, 13993:3–25. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-30823-9_1\">https://doi.org/10.1007/978-3-031-30823-9_1</a>.","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in <i>Tools and Algorithms for the Construction and Analysis of Systems </i>, Paris, France, 2023, vol. 13993, pp. 3–25.","short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25."},"intvolume":"     13993","status":"public","alternative_title":["LNCS"],"file_date_updated":"2023-06-19T08:29:30Z","date_created":"2023-06-18T22:00:47Z","volume":13993,"oa_version":"Published Version","type":"conference","month":"04","date_updated":"2025-07-14T09:09:52Z","abstract":[{"lang":"eng","text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions."}],"page":"3-25","_id":"13142","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","quality_controlled":"1","doi":"10.1007/978-3-031-30823-9_1","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308222"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-04-27","location":"Paris, France","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","start_date":"2023-04-22"},"project":[{"call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","day":"22","file":[{"file_name":"2023_LNCS_Chatterjee.pdf","success":1,"creator":"dernst","file_size":528455,"relation":"main_file","content_type":"application/pdf","checksum":"3d8a8bb24d211bc83360dfc2fd744307","file_id":"13150","date_updated":"2023-06-19T08:29:30Z","access_level":"open_access","date_created":"2023-06-19T08:29:30Z"}],"author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"id":"3DC22916-F248-11E8-B48F-1D18A9856A87","full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","first_name":"Dorde","last_name":"Zikelic"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"scopus_import":"1","ec_funded":1,"article_processing_charge":"No","publication":"Tools and Algorithms for the Construction and Analysis of Systems ","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature"},{"intvolume":"        20","related_material":{"link":[{"relation":"software","url":"https://github.com/danzllab/LIONESS"}],"record":[{"relation":"research_data","status":"public","id":"12817"},{"status":"public","id":"14770","relation":"shorter_version"}]},"citation":{"short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","ieee":"P. Velicky <i>et al.</i>, “Dense 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20. Springer Nature, pp. 1256–1265, 2023.","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>.","mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265.","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01936-6\">https://doi.org/10.1038/s41592-023-01936-6</a>","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20:1256-1265. doi:<a href=\"https://doi.org/10.1038/s41592-023-01936-6\">10.1038/s41592-023-01936-6</a>"},"status":"public","external_id":{"isi":["001025621500001"],"pmid":["37429995"]},"date_published":"2023-08-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1038/s41592-023-01936-6","open_access":"1"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"publication_status":"published","oa":1,"_id":"13267","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","year":"2023","volume":20,"date_created":"2023-07-23T22:01:13Z","page":"1256-1265","abstract":[{"lang":"eng","text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"date_updated":"2024-01-10T08:37:48Z","oa_version":"Published Version","type":"journal_article","month":"08","isi":1,"language":[{"iso":"eng"}],"project":[{"grant_number":"I03600","call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","name":"Optical control of synaptic function via adhesion molecules"},{"grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"2548AE96-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"_id":"23889792-32DE-11EA-91FC-C7463DDC885E","name":"High content imaging to decode human immune cell interactions in health and allergic disease"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program","grant_number":"665385"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"},{"grant_number":"715508","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Biophysics and circuit function of a giant cortical glumatergic synapse"},{"_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9","call_identifier":"H2020","name":"Synaptic computations of the hippocampal CA3 circuitry","grant_number":"101026635"},{"name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","_id":"2668BFA0-B435-11E9-9278-68D0E5697425","grant_number":"LT00057"}],"doi":"10.1038/s41592-023-01936-6","quality_controlled":"1","publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"publication":"Nature Methods","scopus_import":"1","article_processing_charge":"Yes","ec_funded":1,"article_type":"original","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"title":"Dense 4D nanoscale reconstruction of living brain tissue","author":[{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","first_name":"Philipp","last_name":"Velicky"},{"full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba","first_name":"Eder"},{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","first_name":"Julia M","last_name":"Michalska"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia"},{"full_name":"Wei, Donglai","first_name":"Donglai","last_name":"Wei"},{"full_name":"Lin, Zudi","last_name":"Lin","first_name":"Zudi"},{"full_name":"Watson, Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake"},{"full_name":"Troidl, Jakob","last_name":"Troidl","first_name":"Jakob"},{"first_name":"Johanna","last_name":"Beyer","full_name":"Beyer, Johanna"},{"full_name":"Ben Simon, Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"},{"full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","first_name":"Christoph M","last_name":"Sommer"},{"last_name":"Jahr","first_name":"Wiebke","full_name":"Jahr, Wiebke","id":"425C1CE8-F248-11E8-B48F-1D18A9856A87"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","full_name":"Cenameri, Alban","last_name":"Cenameri","first_name":"Alban"},{"full_name":"Broichhagen, Johannes","last_name":"Broichhagen","first_name":"Johannes"},{"full_name":"Grant, Seth G.N.","first_name":"Seth G.N.","last_name":"Grant"},{"full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"},{"last_name":"Novarino","first_name":"Gaia","full_name":"Novarino, Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","first_name":"Johann G","last_name":"Danzl"}],"day":"01"}]